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Compositions and methods relating to Lyme disease

09816992 ยท 2017-11-14

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Inventors

Cpc classification

International classification

Abstract

Compositions and methods of the present invention relating to B. burgdorferi HtrA sensu lato (BbHtrA) protease activity, its substrates, cleavage products, biological effects and use in detection, diagnosis and/or treatment of Lyme disease are provided.

Claims

1. A method of aiding in the diagnosis of Lyme disease, comprising: assaying a first sample obtained from a subject having, or suspected of having, Lyme disease for one or more peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on host protein substrate at a cleavage site selected from the group consisting of SEQ ID NOs: 114, 119, 122, 74, 159, 132, 149, 80, 158, 72, 98, 102, 162, 125, and 107 produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on at least one host protein substrate, to produce an assay result wherein detection of the one or more peptides is indicative of an active Borrelia burgdorferi sensu lato infection in the subject.

2. The method of claim 1, further comprising: assaying a second sample obtained from the subject having, or suspected of having, Lyme disease to detect at least one inflammatory cytokine or chemokine selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL2, CCL5, MIF and Serpin E, wherein detection of the one or more peptides in combination with an increase in CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL2, CCL5, and/or substantially no increase in MIF and/or Serpin E compared to a standard is indicative of an active Borrelia burgdorferi sensu lato infection in the subject.

3. The method of claim 1, further comprising: assaying a further sample obtained from a subject having, or suspected of having, Lyme disease for one or more of the peptides.

4. The method of claim 1, wherein the first sample is selected from: whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, wherein the biopsy sample is skin or joint tissue.

5. The method of claim 2, wherein the second sample is selected from: whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, wherein the biopsy sample is skin or joint tissue.

6. The method of claim 1, wherein detecting the one or more peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on at least one host protein substrate comprises an immunoassay and/or mass spectrometry.

7. The method of claim 3, wherein the further sample is selected from: whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, wherein the biopsy sample is skin or joint tissue.

8. A method of aiding in the diagnosis, assessment and/or treatment of Lyme disease, comprising: assaying a sample obtained from a subject having, or suspected of having, Lyme disease for proteolytic activity of Borrelia burgdorferi sensu lato HtrA to detect the presence of Borrelia burgdorferi sensu lato HtrA, wherein presence of Borrelia burgdorferi sensu lato HtrA is indicative of Borrelia burgdorferi sensu lato active infection of the subject.

9. The method of claim 8, wherein the assaying comprises contacting the sample with a substrate for Borrelia burgdorferi sensu lato HtrA and determining whether the substrate is cleaved by proteolytic activity of Borrelia burgdorferi sensu lato HtrA.

10. The method of claim 9 wherein the substrate is selected from the group consisting of: casein, aggrecan, decorin, biglycan, brevican, neurocan, versican, fibronectin, fibromodulin, cartilage oligomeric matrix protein and E-cadherin.

11. The method of claim 9 wherein the substrate comprises a detectable label.

12. The method of claim 9 wherein the substrate is a chromogenic or fluorogenic substrate.

13. A commercial package for aiding in the diagnosis of Lyme disease in a subject comprising: a reagent selected from the group consisting of: one or more peptides selected from the group consisting of: one or more peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host substrate at a cleavage site selected from the group consisting of SEQ ID NOs: 114, 119, 122, 74, 159, 132, 149, 80, 158, 72, 98, 102, 162, 125, and 107; a binding agent characterized by substantially specific binding to a Borrelia burgdorferi sensu lato HtrA protease; a binding agent characterized by substantially specific binding to a neoepitope of a Borrelia burgdorferi sensu lato HtrA cleavage product; and one or more substrates for Borrelia burgdorferi sensu lato HtrA protease.

14. The commercial package of claim 13, wherein the one or more substrates is selected from the group consisting of: one or more substrates for Borrelia burgdorferi sensu lato HtrA selected from the group consisting of aggrecan, fibronectin, biglycan, decorin, brevican, neurocan, versican, cartilage oligomeric matrix protein (COMP), fibromodulin, and E-cadherin.

15. The commercial package of claim 13 wherein the one or more peptides are arrayed on a support.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1A is an image showing BbHtrA (3 g) as visualized by Coomassie stain (left panel) and as visualized by anti-His tag Western blot (right panel);

(2) FIG. 1B shows BbHtrA.sup.S226A (2 g) as visualized by Coomassie stain (left panel) and as visualized by anti-His tag Western blot (right panel);

(3) FIG. 2A is an image showing equivalent protein loading for gel electrophoresis;

(4) FIG. 2B is an image of results of a Western blot of the proteins shown in FIG. 2B showing loss of surface protein signal (OspA), retention of internal protein signal (FlaB) and diminished BbHtrA signal;

(5) FIG. 3A is an image showing results of Western blot analysis to detect anti-BbHtrA antibodies in serum samples from human subjects having early or late Lyme disease and from healthy human control subjects;

(6) FIG. 3B is an image showing results of Western blot analysis to detect anti-BbHtrA IgG+ antibodies in serum samples from human subjects having Lyme disease and from healthy human control subjects;

(7) FIG. 4A is an image showing results of SDS-PAGE analysis showing that BbHtrA cleaves recombinant human aggrecan (G1-IGD-G2 domains) within the IGD;

(8) FIG. 4B is an image showing results of SDS-PAGE analysis showing that BbHtrA cleaves native, fully glycosylated aggrecan;

(9) FIG. 4C is an image showing results of SDS-PAGE analysis showing a temperature and dose dependent increase in BbHtrA activity against recombinant aggrecan;

(10) FIG. 5 is an image of SDS-PAGE analysis showing that BbHtrA specifically degrades aggrecan, e-cadherin, brevican, neurocan, versican, biglycan and decorin;

(11) FIG. 6A is an image showing Western blot analysis of BbHtrA-generated aggrecan fragments recognized by monoclonal antibody BC-3;

(12) FIG. 6B is a schematic showing the proteolytic sites within the IGD and the epitopes for the antibodies raised against the neoepitopes;

(13) FIG. 7A shows major and minor peptides identified by Edman degradation of the BbHtrA-generated aggrecan fragments;

(14) FIG. 7B is a schematic diagram of the pathologic proteolytic cleavage sites within the aggrecan IGD showing possible location of BbHtrA-generated minor signals;

(15) FIG. 8A is an image showing SDS-PAGE analysis of BbHtrA degradation of fibronectin;

(16) FIG. 8B is a table showing results of tandem LC MS/MS analysis of BbHtrA degradation of fibronectin;

(17) FIG. 9A is an image of a dot immunoblot analysis of cytokines induced in chondrocytes upon stimulation with BbHtrA, heat-denatured BbHtrA, lipopolysaccharide, or medium alone;

(18) FIG. 9B is a key to show the identity of cytokines identified in the cytokine analyses shown in FIG. 9A and in FIG. 10;

(19) FIG. 10 is an image of a dot immunoblot analysis of cytokines induced in chondrocytes upon stimulation with BbHtrA, BbHtrA.sup.S226A, lipopolysaccharide or medium alone;

(20) FIG. 11A is an image of a silver stain of an SDS-PAGE gel of BbHtrA self-digestion products showing the location of amino terminal signals obtained by Edman degradation;

(21) FIG. 11B shows a ClustalW alignment of BbHtrA and E. coli DegQ showing conserved paired phenylalanines at the site of BbHtrA self digestion;

(22) FIG. 12A is an image of a -casein zymogram of the indicated lysates and recombinant proteins;

(23) FIG. 12B is an image of a Western blot of the same lysates and recombinant proteins used in the image of FIG. 12A immunostained with polyclonal anti-BbHtrA;

(24) FIG. 12C is an image of a control for the Western blot of FIG. 12B immunostained with monoclonal anti-FlaB;

(25) FIG. 12D is an image of a Coomassie stained gel of lysates and recombinant proteins used in FIGS. 12A-C;

(26) FIG. 13 shows alignment of amino acid sequences of bovine and human decorin;

(27) FIG. 14 shows alignment of amino acid sequences of bovine and human biglycan;

(28) FIG. 15 shows alignment of amino acid sequences of bovine and human fibromodulin;

(29) FIG. 16 shows alignment of amino acid sequences of bovine and human cartilage oligomeric matrix protein (COMP); and

(30) FIG. 17 shows alignment of amino acid sequences of bovine and human aggrecan.

DETAILED DESCRIPTION OF THE INVENTION

(31) Compositions and methods for aiding in the detection and diagnosis of Lyme disease in a subject are provided according to the present invention. Compositions and methods for treatment and/or prevention of Lyme disease in a subject in need thereof are provided according to the present invention.

(32) Scientific and technical terms used herein are intended to have the meanings commonly understood by those of ordinary skill in the art. Such terms are found defined and used in context in various standard references illustratively including J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; 3rd Ed., 2001; F. M. Ausubel, Ed., Short Protocols in Molecular Biology, Current Protocols; 5th Ed., 2002; B. Alberts et al., Molecular Biology of the Cell, 4th Ed., Garland, 2002; D. L. Nelson and M. M. Cox, Lehninger Principles of Biochemistry, 4th Ed., W.H. Freeman & Company, 2004; Engelke, D. R., RNA Interference (RNAi): Nuts and Bolts of RNAi Technology, DNA Press LLC, Eagleville, Pa., 2003; Herdewijn, P. (Ed.), Oligonucleotide Synthesis: Methods and Applications, Methods in Molecular Biology, Humana Press, 2004; A. Nagy, M. Gertsenstein, K. Vintersten, R. Behringer, Manipulating the Mouse Embryo: A Laboratory Manual, 3rd edition, Cold Spring Harbor Laboratory Press; Dec. 15, 2002, ISBN-10: 0879695919; Kursad Turksen (Ed.), Embryonic stem cells: methods and protocols in Methods Mol Biol. 2002; 185, Humana Press; Current Protocols in Stem Cell Biology, ISBN: 9780470151808.

(33) The singular terms a, an, and the are not intended to be limiting and include plural referents unless explicitly state or the context clearly indicates otherwise.

(34) It has been reported that that Borrelia burgdorferi do not produce proteases capable of damaging host proteins, Radolf, J. D., et al., Nature Reviews Microbiol. online 9 Jan. 2012; Smith, B. G., et al., J Am Acad. Orthop. Surg., 2011, 19(2): 91-100; Guyard, C., et al., Molec. Microbiol. 2006, 60 (3), 710-722; Klempner, M. S., et al., J. Infect. Dis., 1995, 171(5):1258-1265; Coleman, J. L. et al., Infect. Immun., 63(7):2478-2484, 1995. Unexpectedly, a protease activity capable of cleaving host proteins has been identified and characterized as B. burgdorferi HtrA sensu lato (BbHtrA), a member of the high temperature requirement factor A protease/chaperone family, by the present inventors as described herein. B. burgdorferi sensu lato HtrA is found by the present inventors to degrade extracellular matrix proteins, such as, but not limited to, aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, cartilage oligomeric matrix protein (COMP) and e-cadherin. BbHtrA stimulates the release of numerous cytokines and chemokines in the infected host. BbHtrA protease activity may contribute to the various pathologies associated with Lyme disease, particularly Lyme arthritis.

(35) Methods of Aiding in the Diagnosis of Lyme Disease

(36) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention.

(37) Lyme disease, also known as Lyme borreliosis, is caused by bacteria transmitted to mammals through the bite of infected Ixodes ticks.

(38) Borrelia burgdorferi, Borrelia garinii and Borrelia afzelii cause Lyme disease in Eurasia and Borrelia burgdorferi causes Lyme disease in the United States and Canada. B. garinii has been found in pelagic bird colonies off the coast of North America, so there may be potential for infection by this agent in North America. The three Lyme disease agents Borrelia burgdorferi, Borrelia garinii and Borrelia afzelii are referred to as Borrelia burgdorferi sensu lato, that is, in the broad sense. The North American genospecies Borrelia burgdorferi is called Borrelia burgdorferi sensu stricto, in the strict sense.

(39) Lyme disease is characterized by three stages: 1) early localized Lyme disease; 2) early disseminated Lyme disease; and 3) late disseminated Lyme disease.

(40) A subject may be suspected of having Lyme disease where symptoms are consistent with those of Lyme disease and where an Ixodes tick bite is known or may have occurred. A characteristic rash called erythema migrans occurs in 70-80% of Lyme disease patients at the site of an infected tick bite.

(41) Early localized Lyme disease is characterized by erythema migrans. Early disseminated Lyme disease typically occurs days to weeks after the initial bite by an infected tick and possible signs include secondary erythema migrans, early neuroborreliosis (cranial nerve palsy, meningitis, or radiculoneuropathy) or, uncommonly, Lyme carditis (atrioventricular node conduction block). Non-specific symptoms such as malaise, fever, headache, and muscle and joint pains may be present. Late disseminated Lyme disease occurs months to years after the initial bite by an infected tick. The most common manifestation of late disseminated Lyme disease in North America is Lyme arthritis, which is characterized by intermittent attacks in large joints, particularly the knees. Rarely, late neuroborreliosis develops, with manifestations including encephalopathy, encephalomyelitis, and/or peripheral neuropathy. Wormser, G. P., et al. Clin Infect Dis 2006; 43:1089-1134.

(42) Lyme arthritis is a late manifestation of Lyme disease affecting up to 60% of untreated patients in the United States. Ten percent of patients treated with antibiotics continue to suffer from recurrent bouts of Lyme arthritis, Steere, A. C. and L. Glickstein, Nat Rev Immunol, 2004. 4(2): p. 143-52. Cartilage loss and subsequent bone destruction which are features of osteoarthritis and rheumatoid arthritis also occur in advanced cases of Lyme arthritis, Lawson, J. P. et al., Radiology, 1985, 154(1):37-43. Lyme arthritis develops when the bacteria invade joint tissue, most commonly the knee, and trigger inflammation as part of a strong host immune response. Despite this vigorous immune response, Borrelia are able to persist in joints which are thought to be a protective niche for the bacteria due to limited perfusion, Liang, F. T., et al., Am J Pathol, 2004, 165(3):977-85.

(43) In the early localized stage of Lyme disease, direct detection of Borrelia burgdorferi can sometimes be achieved by bacterial culture or PCR from a skin sample obtained at the site of the erythema migrans rash. In early disseminated infection, direct detection of Borrelia burgdorferi can sometimes be achieved by bacterial culture or PCR of blood can be successful. However, in later stages of Lyme disease the bacteria are difficult to detect.

(44) Borrelia burgdorferi sensu lato, which cause Lyme disease, are found by the present inventors to have a serine protease activity, termed herein Borrelia burgdorferi sensu lato HtrA protease activity. Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting one or more peptides produced by Borrelia burgdorferi sensu lato HtrA protease activity on at least one host protein substrate in a sample obtained from a subject having or suspected of having Lyme disease.

(45) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting one or more peptides produced by Borrelia burgdorferi sensu lato HtrA protease activity on a host extracellular matrix protein. As disclosed herein aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and e-cadherin are substrates for Borrelia burgdorferi sensu lato HtrA. According to aspects of methods of the present invention, one or more peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host extracellular matrix protein such as, but not limited to, aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and e-cadherin may be assayed in a sample obtained from a subject having or suspected of having Lyme disease according to methods of the invention.

(46) The term subject is used herein to refer to a human subject and can also refer to a mammalian subject capable of infection by Borrelia burgdorferi sensu lato, including, but not limited to, non-human primates rodents and dogs.

(47) A sample which is assayed for one or more peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on at least one host protein substrate is any sample type containing the peptide or peptides to be assayed, such as, but not limited to whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, such as a skin biopsy or an arthroscopic biopsy sample of joint tissue.

(48) Detection of peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on at least one host protein substrate can be accomplished by qualitative and/or quantitative assays including, but not limited to, immunoassay and mass spectrometry.

(49) Assays according to the present invention optionally and preferably compare the assay result to a standard.

(50) Standards are well-known in the art and the standard used can be any appropriate standard. In one example, a standard for use in assay of one or more Borrelia burgdorferi sensu lato HtrA cleavage products is an amount of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention present in a comparable control sample from a control subject. In a further example, a standard for use in assay of one or more inflammatory cytokines and chemokines is an amount of one or more inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL2, and CCL5 and one or more inflammatory cytokines and chemokines selected from selected from: C5a, CD40 ligand, G-CSF, GM-CSF, IFN-g, IL-1a, IL-1b, IL-ra, IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-13, IL-16, IL-17, IL-17E, IL-23, IL-27, IL-32a, CXCL10, CXCL11, MIF, CCL3, CCL4 and Serpin E1, present in a comparable control sample from a control subject. Control samples may be obtained from one or more subjects who do not have a Borrelia burgdorferi sensu lato infection, for example. A preferred control sample is a comparable control sample obtained from one or more subjects residing in an area where Borrelia burgdorferi sensu lato is not endemic. Travel histories may be obtained from potential control subjects living in areas where Borrelia burgdorferi sensu lato is not endemic to identify potential control subjects who have visited areas where Borrelia burgdorferi sensu lato is endemic and such persons are eliminated as control subjects. The types of subjects with other diseases commonly confused with Lyme disease where no Borrelia burgdorferi sensu lato infection is present and which would be suitable for a comparator population has been defined by the Clinical Laboratory Standards Institute as described in Barbour A G et al., Western Blot Assay for Antibodies to Borrelia burgdorferi: Approved Guideline M34-A, 2000, Clinical Laboratory Standards, Institute, Wayne Pa. A standard in an assay of Borrelia burgdorferi sensu lato HtrA cleavage products may be a reference level of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention determined in a sample of an individual control subject or in a population of control subjects. A standard in an assay of indicated cytokines and/or chemokines may be a reference level of the indicated cytokines and/or chemokines determined in a sample of an individual control subject or in a population of control subjects. A standard may be such a reference level stored in a print or electronic medium for recall and comparison to an assay result.

(51) A standard in an assay of Borrelia burgdorferi sensu lato HtrA cleavage products can be an amount of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention present in a comparable sample obtained from the same subject at a different time. For example, a standard can be an amount of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention present in a comparable sample obtained from the same subject at an earlier time. A first sample can be obtained from an individual subject at a first time to obtain a subject-specific baseline level of the one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention in the first sample. A second sample can be obtained from the individual subject at a second time and assayed for one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention to monitor differences in the levels of the one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention compared to the first sample, thereby monitoring Lyme disease in the subject. Additional samples can be obtained from the subject at additional time points and assayed for one or more Borrelia burgdorferi sensu lato HtrA cleavage products to monitor differences in the levels of the corresponding Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention compared to the first sample, second sample or other samples, thereby monitoring Lyme disease in the subject.

(52) A standard can be an average level of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention present in comparable samples of one or more populations. The average level is determined by assay of the one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention in comparable samples obtained from each member of the population. The term comparable sample is used to indicate that the samples are of the same type. For example, each of the comparable samples is a serum sample. In a further example, each of the comparable samples is a biopsy sample. In a further example, each of the comparable samples is a synovial fluid sample. In a further example, each of the comparable samples is a whole blood, plasma, serum, urine, cerebrospinal fluid, joint tissue or skin sample.

(53) A difference detected in levels of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention compared to a standard can be an increase or decrease in level of the one or more Borrelia burgdorferi sensu lato HtrA cleavage products. A difference detected in levels of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention compared to a standard can be a detectable level of the one or more Borrelia burgdorferi sensu lato HtrA cleavage products where the Borrelia burgdorferi sensu lato HtrA cleavage products are undetectable in the standard. A difference detected in levels of one or more Borrelia burgdorferi sensu lato HtrA cleavage products of the present invention compared to a standard can be an undetectable level of the one or more Borrelia burgdorferi sensu lato HtrA cleavage products where the Borrelia burgdorferi sensu lato HtrA cleavage products are detectable in the standard.

(54) A standard in an assay of cytokines and/or chemokines can be an amount of the indicated cytokines and/or chemokines in a comparable sample obtained from the same subject at a different time. For example, a standard can be an amount of one or more cytokines and/or chemokines present in a comparable sample obtained from the same subject at an earlier time. A first sample can be obtained from an individual subject at a first time to obtain a subject-specific baseline level of the one or more cytokines and/or chemokines in the first sample. A second sample can be obtained from the individual subject at a second time and assayed for one or more cytokines and/or chemokines to monitor differences in the levels of the one or more cytokines and/or chemokines compared to the first sample, thereby monitoring Lyme disease in the subject. Additional samples can be obtained from the subject at additional time points and assayed for one or more cytokines and/or chemokines to monitor differences in the levels of the corresponding cytokines and/or chemokines compared to the first sample, second sample or other samples, thereby monitoring Lyme disease in the subject.

(55) A standard can be an average level of one or more cytokines and/or chemokines present in comparable samples of one or more populations. The average level is determined by assay of the one or more cytokines and/or chemokines in comparable samples obtained from each member of the population. The term comparable sample is used to indicate that the samples are of the same type. For example, each of the comparable samples is a serum sample. In a further example, each of the comparable samples is a biopsy sample. In a further example, each of the comparable samples is a synovial fluid sample. In a further example, each of the comparable samples is a whole blood, plasma, serum, urine, cerebrospinal fluid, joint tissue or skin sample.

(56) A difference detected in levels of one or more cytokines and/or chemokines compared to a standard can be an increase or decrease in level of the one or more cytokines and/or chemokines. A difference detected in levels of one or more cytokines and/or chemokines compared to a standard can be a detectable level of the one or more cytokines and/or chemokines where the cytokines and/or chemokines are undetectable in the standard. A difference detected in levels of one or more cytokines and/or chemokines compared to a standard can be an undetectable level of the one or more cytokines and/or chemokines where the cytokines and/or chemokines are detectable in the standard.

(57) Assay results can be analyzed using statistical analysis by any of various methods, exemplified by parametric or non-parametric tests, analysis of variance, analysis of covariance, logistic regression for multivariate analysis, Fisher's exact test, the chi-square test, Student's T-test, the Mann-Whitney test, Wilcoxon signed ranks test, McNemar test, Friedman test and Page's L trend test. These and other statistical tests are well-known in the art as detailed in Hicks, C M, Research Methods for Clinical Therapists: Applied Project Design and Analysis, Churchill Livingstone; 5th Ed., 2009; and Freund, R J et al., Statistical Methods, Academic Press; 3rd Ed., 2010.

(58) Immunoassays are well-known in the art and include, but are not limited to, enzyme-linked immunosorbent assay (ELISA), antigen capture, flow cytometry, immunoblot, immunoprecipitation, immunodiffusion, immunocytochemistry, radioimmunoassay, and combinations of any of these. Immunoassays for both qualitative and quantitative assay of a sample are described in detail in standard references, illustratively including Wild, D., The Immunoassay Handbook, 3rd Ed., Elsevier Science, 2005; Gosling, J. P., Imunoassays: A Practical Approach, Practical Approach Series, Oxford University Press, 2005; E. Harlow and D. Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988; F. Breitling and S. Dbel, Recombinant Antibodies, John Wiley & Sons, New York, 1999; H. Zola, Monoclonal Antibodies: Preparation and Use of Monoclonal Antibodies and Engineered Antibody Derivatives, Basics: From Background to Bench, BIOS Scientific Publishers, 2000; B. K. C. Lo, Antibody Engineering: Methods and Protocols, Methods in Molecular Biology, Humana Press, 2003; F. M. Ausubel et al., Eds., Short Protocols in Molecular Biology, Current Protocols, Wiley, 2002; Ormerod, M. G., Flow Cytometry: a practical approach, Oxford University Press, 2000; and Givan, A. L., Flow Cytometry: first principles, Wiley, New York, 2001.

(59) In particular embodiments, an assay for one or more peptides includes use of a mass spectrometry technique. For example, a peptide can be ionized using an ionization method such as electrospray ionization (ESI), matrix-assisted laser desorption/ionization (MALDI) or surface enhanced laser desorption/ionization (SELDI). Mass analysis is conducted using, for example, time-of-flight (TOF) mass spectrometry or Fourier transform ion cyclotron resonance mass spectrometry. Mass spectrometry techniques are known in the art and exemplary detailed descriptions of methods for protein and/or peptide assay are found in Li J., et al., Clin Chem., 48(8):1296-304, 2002; Hortin, G. L., Clinical Chemistry 52: 1223-1237, 2006; Hortin, G. L., Clinical Chemistry 52: 1223-1237, 2006; A. L. Burlingame, et al. (Eds.), Mass Spectrometry in Biology and Medicine, Humana Press, 2000; and D. M. Desiderio, Mass Spectrometry of Peptides, CRC Press, 1990.

(60) A peptide contained in a sample from a subject is optionally purified for assay according to a method of the present invention.

(61) The term purified in the context of a sample refers to separation of a desired material in the sample from at least one other component present in the sample.

(62) In particular embodiments, a peptide or peptides is optionally substantially purified from the sample to produce a substantially purified sample for use in an inventive assay. The term substantially purified refers to a desired material separated from other substances naturally present in a sample obtained from the subject so that the desired material makes up at least about 1-100% of the mass, by weight, such as about 1%, 5%, 10%, 25%, 50% 75% or greater than about 75% of the mass, by weight, of the substantially purified sample.

(63) Sample purification is achieved by techniques illustratively including electrophoretic methods such as gel electrophoresis and 2-D gel electrophoresis; chromatography methods such as HPLC, ion exchange chromatography, affinity chromatography, size exclusion chromatography, thin layer and paper chromatography. It is appreciated that electrophoresis and chromatographic methods can also be used to separate a peptide or peptides from other components in a sample in the course of performing an assay, as in, for example separation of proteins in immunoblot assays. Enrichment (initial purification) may be achieved by centrifugation and/or differential extraction using polar or non-polar solvents.

(64) Peptides which may be detected in a sample obtained from a subject having or suspected of having Lyme disease according to methods of the present invention are specific products of cleavage by Borrelia burgdorferi sensu lato HtrA protease activity, i.e. Borrelia burgdorferi sensu lato HtrA cleavage products.

(65) The term Borrelia burgdorferi sensu lato HtrA cleavage product encompasses, but is not limited to, Borrelia burgdorferi sensu lato HtrA cleavage products identified herein as SEQ ID NO:33-69 and 70-414.

(66) Borrelia burgdorferi sensu lato HtrA cleavage products of decorin include those identified herein as SEQ ID NO:33-37; SEQ ID NO:52-55 and SEQ ID NO:315-364.

(67) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of decorin including one or more of: the peptide of SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(68) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of decorin including one or more of: the peptide of SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(69) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of decorin including one or more of: the peptide of SEQ ID NO:315-364, wherein each of the peptides of SEQ ID NO: 315-364 has 5 amino acids closest to the amino terminus and has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional amino acids; a homologue or variant thereof having at least 95% identity to the reference peptide; a fragment of the one or more peptides of SEQ ID NO: 315-364, the fragment having at least the 5 amino acids closest to the amino terminus; a fragment of the one or more peptides of SEQ ID NO: 315-364, the fragment having at least the 5 amino acids closest to the amino terminus and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional of the amino acids; or a combination of any two or more thereof.

(70) Borrelia burgdorferi sensu lato HtrA cleavage products of biglycan include those identified herein as SEQ ID NO:38-40; SEQ ID NO:56-58 and SEQ ID NO:214-263.

(71) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of biglycan including one or more of: the peptide of SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(72) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of biglycan including one or more of: the peptide of SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(73) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of biglycan including one or more of: the peptide of SEQ ID NO:214-263, wherein each of the peptides of SEQ ID NO:214-263 has 5 amino acids closest to the amino terminus and has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional amino acids; a homologue or variant thereof having at least 95% identity to the reference peptide; a fragment of the one or more peptides of SEQ ID NO: 214-263, the fragment having at least the 5 amino acids closest to the amino terminus; a fragment of the one or more peptides of SEQ ID NO: 214-263, the fragment having at least the 5 amino acids closest to the amino terminus and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional of the amino acids; or a combination of any two or more thereof.

(74) Borrelia burgdorferi sensu lato HtrA cleavage products of aggrecan include those identified herein as SEQ ID NO:41-43; SEQ ID NO:59-61 and SEQ ID NO:163-213.

(75) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of aggrecan including one or more of: the peptide of SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(76) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of aggrecan including one or more of: the peptide of SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(77) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of aggrecan including one or more of: the peptide of SEQ ID NO:163-213, wherein each of the peptides of SEQ ID NO: 163-213 has 5 amino acids closest to the amino terminus and has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional amino acids; a homologue or variant thereof having at least 95% identity to the reference peptide; a fragment of the one or more peptides of SEQ ID NO:163-213, the fragment having at least the 5 amino acids closest to the amino terminus; a fragment of the one or more peptides of SEQ ID NO:163-213, the fragment having at least the 5 amino acids closest to the amino terminus and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional of the amino acids; or a combination of any two or more thereof.

(78) Borrelia burgdorferi sensu lato HtrA cleavage products of fibromodulin include those identified herein as SEQ ID NO:44-46; SEQ ID NO:62-64 and SEQ ID NO:365-414.

(79) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of fibromodulin including one or more of: the peptide of SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(80) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of fibromodulin including one or more of: the peptide of SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(81) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of fibromodulin including one or more of: the peptide of SEQ ID NO:365-414, wherein each of the peptides of SEQ ID NO:365-414 has 5 amino acids closest to the amino terminus and has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional amino acids; a homologue or variant thereof having at least 95% identity to the reference peptide; a fragment of the one or more peptides of SEQ ID NO:365-414, the fragment having at least the 5 amino acids closest to the amino terminus; a fragment of the one or more peptides of SEQ ID NO:365-414, the fragment having at least the 5 amino acids closest to the amino terminus and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional of the amino acids; or a combination of any two or more thereof

(82) Borrelia burgdorferi sensu lato HtrA cleavage products of COMP include those identified herein as SEQ ID NO:47-51; SEQ ID NO:65-69 and SEQ ID NO:264-314.

(83) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of COMP including one or more of: the peptide of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(84) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of COMP including one or more of: the peptide of SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, a homologue or variant thereof having at least 95% identity to the reference peptide, or a combination of any two or more thereof.

(85) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of COMP including one or more of: the peptide of SEQ ID NO:264-314, wherein each of the peptides of SEQ ID NO: 264-314 has 5 amino acids closest to the amino terminus and has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional amino acids; a homologue or variant thereof having at least 95% identity to the reference peptide; a fragment of the one or more peptides of SEQ ID NO:264-314, the fragment having at least the 5 amino acids closest to the amino terminus; a fragment of the one or more peptides of SEQ ID NO:264-314, the fragment having at least the 5 amino acids closest to the amino terminus and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or 28 additional of the amino acids; or a combination of any two or more thereof

(86) Methods according to aspects of the present invention include assay for Borrelia burgdorferi sensu lato HtrA cleavage products of a protein or peptide substrate having one or more cleavage sites having SEQ ID NO:70-162, a homologue or variant thereof, cleaved by Borrelia burgdorferi sensu lato HtrA.

(87) Methods and compositions of the present invention are not limited to particular Borrelia burgdorferi sensu lato HtrA cleavage products identified by SEQ ID NO herein and homologues and variants of a reference nucleic acid or protein may be assayed and used according to aspects of the present invention.

(88) Homologues and variants of a Borrelia burgdorferi sensu lato HtrA cleavage product described herein include, for example, naturally occurring mutants and Borrelia burgdorferi sensu lato HtrA cleavage products derived from orthologues.

(89) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting a Borrelia burgdorferi sensu lato HtrA protease, or a fragment thereof, and/or a nucleic acid encoding Borrelia burgdorferi sensu lato HtrA protease, or a fragment thereof, in a sample obtained from a subject having, or suspected of having, Lyme disease.

(90) According to aspects of the present invention, detecting a Borrelia burgdorferi sensu lato HtrA protease in a sample obtained from a subject includes qualitative and/or quantitative assays including, but not limited to, immunoassay and mass spectrometry. According to aspects of the present invention, detecting a Borrelia burgdorferi sensu lato HtrA protease in a sample obtained from a subject includes qualitative and/or quantitative assays including, but not limited to, antigen capture. Binding agent compositions which bind substantially specifically to Borrelia burgdorferi sensu lato HtrA protease are provided according to the present invention along with methods for use of the binding agents to detect Borrelia burgdorferi sensu lato HtrA protease in a sample obtained from a subject having, or suspected of having, Lyme disease.

(91) According to aspects of the present invention, detecting a nucleic acid encoding Borrelia burgdorferi sensu lato HtrA protease in a sample obtained from a subject includes, but is not limited to, amplification techniques such as, but not limited to, PCR, RT-PCR ligation-mediated PCR and phi-29 PCR; nucleic acid hybridization techniques such as, but not limited to, Northern blot, Southern blot, RNase protection assay, dot blot and in situ hybridization. Nucleic acid assays for both qualitative and quantitative assay of a nucleic acid in a sample are described in detail in standard references, illustratively including J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; 3rd Ed., 2001; F. M. Ausubel et al., Eds., Short Protocols in Molecular Biology, Current Protocols, Wiley, 2002; C. W. Dieffenbach et al., PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 2003; and V. Demidov et al., DNA Amplification: Current Technologies and Applications, Taylor & Francis, 2004.

(92) A sample which is assayed to detect a Borrelia burgdorferi sensu lato HtrA protease, or a fragment thereof, and/or a nucleic acid encoding Borrelia burgdorferi sensu lato HtrA protease, or a fragment thereof, is any sample type containing or suspected of containing the Borrelia burgdorferi sensu lato HtrA protease to be assayed, such as, but not limited to whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, such as skin or an arthroscopic biopsy sample of joint tissue.

(93) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an antibody which specifically binds to Borrelia burgdorferi sensu lato HtrA protease in a sample obtained from a subject having, or suspected of having, Lyme disease. Detecting an antibody which specifically binds to Borrelia burgdorferi sensu lato HtrA protease in a sample obtained from a subject having, or suspected of having, Lyme disease includes qualitative and/or quantitative assays including, but not limited to, immunoassay and mass spectrometry.

(94) A sample which is assayed to detect an antibody which specifically binds to Borrelia burgdorferi sensu lato HtrA protease is any sample type containing or suspected of containing the antibody or antibodies to be assayed, such as, but not limited to whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, such as skin or an arthroscopic biopsy sample of joint tissue.

(95) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in inflammatory cytokines and chemokines in a sample obtained from a subject having, or suspected of having, Lyme disease compared to a control.

(96) It is understood by the ordinarily skilled artisan that detecting an increase in inflammatory cytokines and chemokines refers to detecting an increase in inflammatory cytokines and chemokines as determinable by use of appropriate controls.

(97) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in one or more of: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, in a sample obtained from a subject having, or suspected of having, Lyme disease.

(98) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in at least 2, 3, 4, 5 or 6 inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, in a sample obtained from a subject having, or suspected of having, Lyme disease.

(99) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in at least 2, 3, 4, 5 or 6 inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, in a sample obtained from a subject having, or suspected of having, Lyme disease and further includes detecting substantially no increase in at least 1 inflammatory cytokine or chemokine selected from: C5a, CD40 ligand, G-CSF, GM-CSF, IFN-g, IL-1a, IL-1b, IL-ra, IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-13, IL-16, IL-17, IL-17E, IL-23, IL-27, IL-32a, CXCL10, CXCL11, MIF, CCL3, CCL4 and Serpin E1.

(100) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in at least 2, 3, 4, 5 or 6 inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, in a sample obtained from a subject having, or suspected of having, Lyme disease and further includes detecting substantially no increase in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 inflammatory cytokines and chemokines selected from: C5a, CD40 ligand, G-CSF, GM-CSF, IFN-g, IL-1a, IL-1b, IL-ra, IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-13, IL-16, IL-17, IL-17E, IL-23, IL-27, IL-32a, CXCL10, CXCL11, MIF, CCL3, CCL4 and Serpin E1.

(101) Inflammatory cytokines and/or chemokines are assayed by qualitative and/or quantitative assays including, but not limited to, immunoassay and mass spectrometry.

(102) Binding agents, such as antibodies, substantially specific for a specified cytokine or chemokine are generated according to well-known methodology or may be obtained commercially.

(103) A sample which is assayed to detect an increase in inflammatory cytokines and chemokines is any sample type containing the inflammatory cytokines and chemokines to be assayed, such as, but not limited to whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, such as skin or an arthroscopic biopsy sample of joint tissue.

(104) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in inflammatory cytokines and chemokines in a sample obtained from a subject having, or suspected of having, Lyme disease compared to a control; and detecting one or more Borrelia burgdorferi sensu lato HtrA cleavage products.

(105) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in one or more of: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, and detecting one or more Borrelia burgdorferi sensu lato HtrA cleavage products identified herein as SEQ ID NO:33-414, a homologue or variant thereof having at least 95% identity to the reference peptide, a fragment thereof having at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33 or 34 amino acids, or a combination of any two or more thereof in a sample obtained from a subject having, or suspected of having, Lyme disease.

(106) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in at least 2, 3, 4, 5 or 6 inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, and detecting one or more Borrelia burgdorferi sensu lato HtrA cleavage products identified herein as SEQ ID NO:33-414, a homologue or variant thereof having at least 95% identity to the reference peptide, a fragment thereof having at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33 or 34 amino acids, or a combination of any two or more thereof, in a sample obtained from a subject having, or suspected of having, Lyme disease.

(107) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in at least 2, 3, 4, 5 or 6 inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, detecting substantially no increase in at least 1 inflammatory cytokine or chemokine selected from: C5a, CD40 ligand, G-CSF, GM-CSF, IFN-g, IL-1a, IL-1b, IL-ra, IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-13, IL-16, IL-17, IL-17E, IL-23, IL-27, IL-32a, CXCL10, CXCL11, MIF, CCL3, CCL4 and Serpin E1, and detecting one or more Borrelia burgdorferi sensu lato HtrA cleavage products identified herein as SEQ ID NO:33-414, a homologue or variant thereof having at least 95% identity to the reference peptide, a fragment thereof having at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33 or 34 amino acids, or a combination of any two or more thereof, in a sample obtained from a subject having, or suspected of having, Lyme disease in a sample obtained from a subject having, or suspected of having, Lyme disease.

(108) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting an increase in at least 2, 3, 4, 5 or 6 inflammatory cytokines and chemokines selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL5 and CCL2, detecting substantially no increase in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 inflammatory cytokines and chemokines selected from: C5a, CD40 ligand, G-CSF, GM-CSF, IFN-g, IL-1a, IL-1b, IL-ra, IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-13, 11-16, IL-17, IL-17E, IL-23, IL-27, IL-32a, CXCL10, CXCL11, MIF, CCL3, CCL4 and Serpin E1, and detecting one or more Borrelia burgdorferi sensu lato HtrA cleavage products identified herein as SEQ ID NO:33-414, a homologue or variant thereof having at least 95% identity to the reference peptide, a fragment thereof having at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33 or 34 amino acids, or a combination of any two or more thereof, in a sample obtained from a subject having, or suspected of having, Lyme disease.

(109) Binding Agents

(110) The term binding agent as used herein refers to an agent characterized by substantially specific binding to a specified substance. The phrase substantially specific and grammatical equivalents as used herein in reference to binding of a binding agent to a specified substance refers to binding of the binding agent to the specified substance without substantial binding to other substances present in a sample to be assayed for presence of the specified substance. It is understood by the ordinarily skilled artisan that substantially specific binding refers to substantially specific binding as determinable by use of appropriate controls to distinguish it from nonspecific binding.

(111) The term binding refers to a physical or chemical interaction between a binding agent and the target. Binding includes, but is not limited to, ionic bonding, non-ionic bonding, covalent bonding, hydrogen bonding, hydrophobic interaction, hydrophilic interaction, and Van der Waals interaction.

(112) Compositions and methods are provided according to the present invention wherein a binding agent is an antibody in particular embodiments. The term antibody is used herein in its broadest sense and includes single antibodies and mixtures of antibodies characterized by substantially specific binding to an antigen. An antibody provided according to compositions and methods is illustratively a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a humanized antibody, and/or an antigen binding antibody fragment, for example. The term antibody refers to a standard intact immunoglobulin having four polypeptide chains including two heavy chains (H) and two light chains (L) linked by disulfide bonds in particular embodiments. Antigen binding antibody fragments illustratively include an Fab fragment, an Fab fragment, an F(ab)2 fragment, an Fd fragment, an Fv fragment, an scFv fragment and a domain antibody (dAb), for example. In addition, the term antibody refers to antibodies of various classes including IgG, IgM, IgA, IgD and IgE, as well as subclasses, illustratively including for example human subclasses IgG1, IgG2, IgG3 and IgG4 and murine subclasses IgG1, IgG2, IgG2a. IgG2b, IgG3 and IgGM, for example.

(113) In particular embodiments, an antibody which is characterized by substantially specific binding has a dissociation constant, Kd, less than about 10.sup.7M, such as less than about 10.sup.8M, less than about 10.sup.9M or less than about 10.sup.10M, or less depending on the specific composition. Binding affinity of an antibody can be determined by Scatchard analysis such as described in P. J. Munson and D. Rodbard, Anal. Biochem., 107:220-239, 1980 or by other methods such as Biomolecular Interaction Analysis using plasmon resonance.

(114) An immunogenic fragment is a peptide or protein having about 4-500 amino acids, and in particular embodiments, at least 5 amino acids, or in further embodiments, at least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 50, 100, 200, 300, or 400 amino acids.

(115) Peptides and/or proteins used as immunogens may be conjugated to a carrier, such as keyhole limpet hemocyanin or bovine serum albumin. Broadly, an immunogen is administered to an animal in particular methods, such as a rabbit, goat, mouse, rat, sheep or chicken and immunoglobulins produced in the animal are obtained from the animal, and optionally, purified for screening and use.

(116) Antibodies and methods for preparation of antibodies are well-known in the art. Details of methods of antibody generation and screening of generated antibodies for substantially specific binding to an antigen are described in standard references such as E. Harlow and D. Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988; F. Breitling and S. Dibel, Recombinant Antibodies, John Wiley & Sons, New York, 1999; H. Zola, Monoclonal Antibodies: Preparation and Use of Monoclonal Antibodies and Engineered Antibody Derivatives, Basics: From Background to Bench, BIOS Scientific Publishers, 2000; and B. K. C. Lo, Antibody Engineering: Methods and Protocols, Methods in Molecular Biology, Humana Press, 2003.

(117) In particular embodiments, monoclonal antibodies and methods including use of monoclonal antibodies are provided by the present invention. Monoclonal antibodies are prepared using techniques known in the art such as described in E. Harlow and D. Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988; F. Breitling and S. Dibel, Recombinant Antibodies, John Wiley & Sons, New York, 1999; H. Zola, Monoclonal Antibodies: Preparation and Use of Monoclonal Antibodies and Engineered Antibody Derivatives, Basics: From Background to Bench, BIOS Scientific Publishers, 2000; and B. K. C. Lo, Antibody Engineering: Methods and Protocols, Methods in Molecular Biology, Humana Press, 2003, for example. Monoclonal antibodies according to the present invention and/or used in methods according to the present invention are produced by techniques illustratively including, but not limited to, hybridoma techniques, recombinant nucleic acid methodology and/or isolation from a phage library, for example as described in the above cited references. Monoclonal antibodies are advantageously used in particular embodiments due to the specificity of the binding of monoclonal antibodies which recognize a single epitope.

(118) Particular methods of monoclonal antibody preparation include obtaining spleen cells from an animal immunized with an immunogen and fusing the antibody-secreting lymphocytes with myeloma or transformed cells to obtain a hybridoma cell capable of replicating indefinitely in culture.

(119) Hybridoma cells producing antibodies substantially specific for a biomarker of Lyme disease are provided according to the present invention.

(120) Antibodies obtained are tested for substantially specific binding to the immunogen by methods illustratively including ELISA, Western blot and immunocytochemistry.

(121) A binding agent can be a nucleic acid binding agent. A nucleic acid binding agent, such as, but not limited to, a nucleic acid probe or primer able to hybridize to a target Borrelia burgdorferi sensu lato HtrA mRNA or cDNA can be used for detecting and/or quantifying mRNA or cDNA encoding a Borrelia burgdorferi sensu lato HtrA protein or a fragment thereof. A nucleic acid probe can be an oligonucleotide of at least 10, 15, 30, 50 or 100 nucleotides in length and sufficient to specifically hybridize under stringent conditions to Borrelia burgdorferi sensu lato HtrA nucleic acid such as mRNA or cDNA or complementary sequence thereof. A nucleic acid primer can be an oligonucleotide of at least 10, 15 or 20 nucleotides in length and sufficient to specifically hybridize under stringent conditions to the mRNA or cDNA, or complementary sequence thereof.

(122) A binding agent can be an isolated non-immunoglobulin protein, peptide or nucleic acid which binds to a molecule of interest with substantial specificity. For example, a binding agent is illustratively an aptamer which substantially specifically binds to a Borrelia burgdorferi sensu lato HtrA cleavage product. The term aptamer refers to a peptide and/or nucleic acid that substantially specifically binds to a specified substance. In the case of a nucleic acid aptamer, the aptamer is characterized by binding interaction with a target other than Watson/Crick base pairing or triple helix binding with a second and/or third nucleic acid. Such binding interaction may include Van der Waals interaction, hydrophobic interaction, hydrogen bonding and/or electrostatic interactions, for example. Similarly, peptide-based aptamers are characterized by specific binding to a target wherein the aptamer is not a naturally occurring ligand for the target. Techniques for identification and generation of peptide and nucleic acid aptamers is known in the art as described, for example, in F. M. Ausubel et al., Eds., Short Protocols in Molecular Biology, Current Protocols, Wiley, 2002; S. Klussman, Ed., The Aptamer Handbook: Functional Oligonucleotides and Their Applications, Wiley, 2006; and J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 3.sup.rd Ed., 2001.

(123) Binding Agents Specific for Products of Borrelia burgdorferi Sensu Lato HtrA Cleavage of a Substrate

(124) Binding agent compositions characterized by substantially specific binding to one or more products of Borrelia burgdorferi sensu lato HtrA cleavage of a substrate are provided according to the present invention along with methods for use of the binding agents.

(125) Isolated antibodies characterized by substantially specific binding to a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a substrate are provided according to the present invention.

(126) In particular aspects, antibodies characterized by substantially specific binding to one or more peptides produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on at least one host protein substrate are used in methods described herein.

(127) A Borrelia burgdorferi sensu lato HtrA cleavage product and/or a fragment thereof is used as an immunogen to produce an antibody characterized by substantially specific binding to the Borrelia burgdorferi sensu lato HtrA cleavage product. Alternatively, or in combination, full-length Borrelia burgdorferi sensu lato HtrA substrate may be used as an immunogen to produce antibodies.

(128) A Borrelia burgdorferi sensu lato HtrA cleavage product and/or fragment thereof for use as an immunogen may be obtained by techniques illustratively including isolation from a sample obtained from a subject containing the product or fragment of the product, produced by recombinant techniques or chemically synthesized, for example as described in Harrington, M. G., Methods Enzymol. 182:488-495, 1990; J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 3.sup.rd Ed., 2001; and Merrifield, JACS, 85:2149-2154, 1963.

(129) According to one embodiment, a Borrelia burgdorferi sensu lato HtrA cleavage product used as an immunogen is a Borrelia burgdorferi sensu lato HtrA cleavage product of aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin.

(130) A binding agent provided according to embodiments of the present invention is characterized by substantially specific binding to a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin. In further embodiments, a monoclonal antibody provided according to the present invention binds substantially specifically to a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin and does not bind substantially specifically to uncleaved aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin, or cleavage fragments of these proteins other than produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA.

(131) For example, a particular monoclonal antibody according to the present invention recognizes a neoepitope at or near the cleavage site of a Borrelia burgdorferi sensu lato HtrA cleavage product, wherein the neoepitope is not present and/or not antigenic in the uncleaved protein and cleavage fragments other than a Borrelia burgdorferi sensu lato HtrA cleavage product or fragment thereof. A Borrelia burgdorferi sensu lato HtrA cleavage product or fragment thereof is indicative of Lyme disease according to particular embodiments of the present invention.

(132) Isolated antibodies which specifically bind to a neoepitope of a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a human host protein are provided according to the present invention.

(133) Isolated antibodies which specifically bind to a neoepitope of a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin are provided according to the present invention.

(134) The term neoepitope refers to the amino terminal 5-10 amino acid residues of a substrate of Borrelia burgdorferi sensu lato HtrA which are exposed subsequent to proteolytic activity.

(135) Commercial packages for aiding in the diagnosis of Lyme disease in a subject are provided according to embodiments of the present invention which include a binding agent characterized by substantially specific binding to a Borrelia burgdorferi sensu lato HtrA cleavage product. One or more auxiliary components are optionally included in commercial packages of the present invention, such as, but not limited to, a control reagent, buffer, diluent or a reconstituting agent.

(136) Binding Agents Specific for Borrelia burgdorferi Sensu Lato HtrA

(137) Binding agent compositions which bind substantially specifically to Borrelia burgdorferi sensu lato HtrA, or a fragment thereof, are provided according to the present invention along with methods for use of the binding agents.

(138) Isolated antibodies which bind substantially specifically to Borrelia burgdorferi sensu lato HtrA protease are provided according to the present invention.

(139) In particular aspects, antibodies which bind substantially specifically to Borrelia burgdorferi sensu lato HtrA protease are used in methods described herein.

(140) A Borrelia burgdorferi sensu lato HtrA protease and/or a fragment thereof is used as an immunogen to produce an antibody specific to the Borrelia burgdorferi sensu lato HtrA protease.

(141) A Borrelia burgdorferi sensu lato HtrA protease and/or fragment thereof for use as an immunogen may be obtained by techniques illustratively including isolation from a sample obtained from a subject containing the protease or fragment of the protease, produced by recombinant techniques or chemically synthesized.

(142) Commercial packages for aiding in the diagnosis of Lyme disease in a subject are provided according to aspects of the present invention which include a binding agent for substantially specific binding to a Borrelia burgdorferi sensu lato HtrA protease. One or more auxiliary components are optionally included in commercial packages of the present invention, such as, but not limited to, a control reagent, buffer, diluent or a reconstituting agent.

(143) According to aspects of the present invention, commercial packages for aiding in the diagnosis, assessment and/or treatment of Lyme disease in a subject are provided according to aspects of the present invention which include: a binding agent, such as an antibody, characterized by substantially specific binding to a Borrelia burgdorferi sensu lato HtrA protease; and one or more substrates for Borrelia burgdorferi sensu lato HtrA protease.

(144) According to aspects of the present invention, commercial packages for aiding in the diagnosis of Lyme disease in a subject are provided according to aspects of the present invention which include: a binding agent, such as an antibody, for substantially characterized by binding to a Borrelia burgdorferi sensu lato HtrA protease; and one or more substrates for Borrelia burgdorferi sensu lato HtrA protease including a Borrelia burgdorferi sensu lato HtrA protease cleavage sites selected from SEQ ID NO:70-162, such as aggrecan, fibronectin, biglycan, decorin, brevican, neurocan, versican, cartilage oligomeric matrix protein (COMP), fibromodulin, E-cadherin, a fragment or homologue thereof containing one or more Borrelia burgdorferi sensu lato HtrA protease cleavage sites selected from SEQ ID NO:70-162.

(145) According to aspects of the present invention, commercial packages for aiding in the diagnosis, assessment and/or treatment of Lyme disease in a subject are provided according to aspects of the present invention which include a binding agent characterized by substantially specific binding to a neoepitope of a Borrelia burgdorferi sensu lato HtrA cleavage product.

(146) According to aspects of the present invention, commercial packages for aiding in the diagnosis, assessment and/or treatment of Lyme disease in a subject are provided according to aspects of the present invention which include at least one antibody characterized by substantially specific binding to a neoepitope of a Borrelia burgdorferi sensu lato HtrA cleavage product.

(147) According to aspects of the present invention, commercial packages for aiding in the diagnosis, assessment and/or treatment of Lyme disease in a subject are provided according to aspects of the present invention which include two or more antibodies wherein each antibody is characterized by substantially specific binding to a neoepitope of a different Borrelia burgdorferi sensu lato HtrA cleavage product. Multiple anti-Borrelia burgdorferi sensu lato HtrA cleavage product antibodies are provided according to aspects of inventive commercial packages of the present invention. Such antibodies are optionally arrayed on a support for multiplex analysis of Borrelia burgdorferi sensu lato HtrA cleavage products in a sample obtained from a subject having or suspected of having Lyme disease.

(148) According to further aspects, commercial kits of the present invention include at least one, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, antibodies characterized by substantially specific binding to a neoepitope of a Borrelia burgdorferi sensu lato HtrA cleavage product and one or more antibodies characterized by substantially specific binding to at least one cytokine or chemokine selected from: CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL2, and CCL5. Commercial kits of the present invention optionally further include at least one cytokine or chemokine selected from: C5a, CD40 ligand, G-CSF, GM-CSF, IFN-g, IL-1a, IL-1b, IL-ra, IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-13, IL-16, IL-17, IL-17E, IL-23, IL-27, IL-32a, CXCL10, CXCL11, MIF, CCL3, CCL4 and Serpin E1. Such antibodies are optionally arrayed on a support for multiplex analysis of Borrelia burgdorferi sensu lato HtrA cleavage products and chemokines/cytokines in a sample obtained from a subject having or suspected of having Lyme disease.

(149) Amino Acid and Nucleic Acid Sequences

(150) The term Borrelia burgdorferi sensu lato HtrA encompasses Borrelia burgdorferi HtrA identified herein as SEQ ID NO: 1, encoded by nucleic acid sequence SEQ ID NO:2; Borrelia garinii HtrA identified herein as SEQ ID NO:5, encoded by nucleic acid sequence SEQ ID NO:6; Borrelia afzelii HtrA identified herein as SEQ ID NO:7, encoded by nucleic acid sequence SEQ ID NO:8; Borrelia burgdorferi HtrA identified herein as SEQ ID NO:9, encoded by nucleic acid sequence SEQ ID NO:10; Borrelia garinii HtrA identified herein as SEQ ID NO:13, encoded by nucleic acid sequence SEQ ID NO:14; Borrelia afzelii HtrA identified herein as SEQ ID NO:15, encoded by nucleic acid sequence SEQ ID NO: 16; Borrelia burgdorferi HtrA identified herein as SEQ ID NO:17, encoded by nucleic acid sequence SEQ ID NO:18; Borrelia garinii HtrA identified herein as SEQ ID NO:21, encoded by nucleic acid sequence SEQ ID NO:22; and Borrelia afzelii HtrA identified herein as SEQ ID NO:23, encoded by nucleic acid sequence SEQ ID NO:24.

(151) Methods and compositions of the present invention are not limited to particular amino acid and nucleic sequences identified by SEQ ID NO herein and homologues and variants of a reference nucleic acid or protein may be used.

(152) Homologues and variants of a nucleic acid or protein described herein are characterized by conserved functional properties compared to the corresponding nucleic acid or protein.

(153) Borrelia burgdorferi HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:1, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:2 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:1.

(154) Borrelia garinii HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:5, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:6 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:5.

(155) Borrelia afzelii HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:7, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:8 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:7.

(156) Borrelia burgdorferi HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:9, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:10 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:9.

(157) Borrelia garinii HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:13, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO: 14 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:13.

(158) Borrelia afzelii HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:15, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:16 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:15.

(159) Borrelia burgdorferi HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO: 17, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:18 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO: 17.

(160) Borrelia garinii HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:21, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:22 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:21.

(161) Borrelia afzelii HtrA and Borrelia burgdorferi sensu lato HtrA encompasses proteins having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the protein having the amino acid sequence set forth in SEQ ID NO:23, or a protein encoded by a nucleic acid sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:24 or a complement thereof so long as the protein is characterized by protease function of the protein of SEQ ID NO:23.

(162) A catalytic triad is at amino acid positions corresponding to 119H, 149D and 226S in the full-length protein, and at amino acid positions 82H, 112D and 189S in the mature protein, lacking a signal peptide. Mutations may be made such that the catalytic triad is 226Ser/119His/149Glu, 226Ser/119His/149His, 226Ser/119Glu/149Asp, 226Ser/119His, 226Ser/149Lys, or 226Ser alone at the indicated corresponding positions or analogous positions in variants or homologs of proteins disclosed herein.

(163) The term fragment of Borrelia burgdorferi sensu lato HtrA refers to any fragment of a Borrelia burgdorferi sensu lato HtrA that is operable in the described method utilizing the fragment, as understood by the ordinarily skilled artisan. A fragment of Borrelia burgdorferi sensu lato HtrA is operative in any of the inventive methods described herein utilizing a Borrelia burgdorferi sensu lato HtrA.

(164) Borrelia burgdorferi sensu lato HtrA nucleic acid as used herein refers to an isolated nucleic acid having a sequence that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the nucleic acid sequence set forth in SEQ ID NO:2, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:22, SEQ ID NO:24, or an isolated nucleic acid molecule having a sequence that hybridizes under high stringency hybridization conditions to the nucleic acid set forth in SEQ ID NO:2 SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:22, SEQ ID NO:24; or a complement thereof, so long as the nucleic acid effects the function described in the particular inventive method comprising use of the nucleic acid. A fragment of Borrelia burgdorferi sensu lato HtrA nucleic acid is any fragment of a Borrelia burgdorferi sensu lato HtrA DNA that is operable in the described method utilizing the fragment, as understood by the ordinarily skilled artisan. A fragment of Borrelia burgdorferi sensu lato HtrA DNA is operative in any of the inventive methods described herein utilizing a Borrelia burgdorferi sensu lato HtrA nucleic acid.

(165) The terms complement and complementary refers to Watson-Crick base pairing between nucleotides and specifically refers to nucleotides hydrogen bonded to one another with thymine or uracil residues linked to adenine residues by two hydrogen bonds and cytosine and guanine residues linked by three hydrogen bonds. In general, a nucleic acid includes a nucleotide sequence described as having a percent complementarity to a specified second nucleotide sequence. For example, a nucleotide sequence may have 80%, 90%, or 100% complementarity to a specified second nucleotide sequence, indicating that 8 of 10, 9 of 10 or 10 of 10 nucleotides of a sequence are complementary to the specified second nucleotide sequence. For instance, the nucleotide sequence 3-TCGA-5 is 100% complementary to the nucleotide sequence 5-AGCT-3. Further, the nucleotide sequence 3-TCGA- is 100% complementary to a region of the nucleotide sequence 5-TTAGCTGG-3.

(166) The terms hybridization and hybridizes refer to pairing and binding of complementary nucleic acids. Hybridization occurs to varying extents between two nucleic acids depending on factors such as the degree of complementarity of the nucleic acids, the melting temperature, Tm, of the nucleic acids and the stringency of hybridization conditions, as is well known in the art. The term stringency of hybridization conditions refers to conditions of temperature, ionic strength, and composition of a hybridization medium with respect to particular common additives such as formamide and Denhardt's solution. Determination of particular hybridization conditions relating to a specified nucleic acid is routine and is well known in the art, for instance, as described in J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; 3rd Ed., 2001; and F. M. Ausubel, Ed., Short Protocols in Molecular Biology, Current Protocols; 5th Ed., 2002. High stringency hybridization conditions are those which only allow hybridization of substantially complementary nucleic acids. Typically, nucleic acids having about 85-100% complementarity are considered highly complementary and hybridize under high stringency conditions. Intermediate stringency conditions are exemplified by conditions under which nucleic acids having intermediate complementarity, about 50-84% complementarity, as well as those having a high degree of complementarity, hybridize. In contrast, low stringency hybridization conditions are those in which nucleic acids having a low degree of complementarity hybridize.

(167) The terms specific hybridization and specifically hybridizes refer to hybridization of a particular nucleic acid to a target nucleic acid without substantial hybridization to nucleic acids other than the target nucleic acid in a sample.

(168) Stringency of hybridization and washing conditions depends on several factors, including the Tm of the probe and target and ionic strength of the hybridization and wash conditions, as is well-known to the skilled artisan. Hybridization and conditions to achieve a desired hybridization stringency are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 2001; and Ausubel, F. et al., (Eds.), Short Protocols in Molecular Biology, Wiley, 2002.

(169) High stringency hybridization conditions are known to the ordinarily skilled artisan. An example of high stringency hybridization conditions is hybridization of nucleic acids over about 100 nucleotides in length in a solution containing 6SSC, 5Denhardt's solution, 30% formamide, and 100 micrograms/ml denatured salmon sperm at 37 C. overnight followed by washing in a solution of 0.1SSC and 0.1% SDS at 60 C. for 15 minutes. SSC is 0.15M NaCl/0.015M Na citrate. Denhardt's solution is 0.02% bovine serum albumin/0.02% FICOLL/0.02% polyvinylpyrrolidone. Under highly stringent conditions, SEQ ID No. 2, SEQ ID NO:6 and SEQ ID NO:8 will hybridize to the complement of substantially identical targets and not to unrelated sequences.

(170) Percent identity is determined by comparison of amino acid or nucleic acid sequences, including a reference amino acid or nucleic acid sequence and a putative homologue amino acid or nucleic acid sequence. To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=number of identical overlapping positions/total number of positions100%). The two sequences compared are generally the same length or nearly the same length.

(171) The determination of percent identity between two sequences can also be accomplished using a mathematical algorithm. Algorithms used for determination of percent identity illustratively include the algorithms of S. Karlin and S. Altshul, PNAS, 90:5873-5877, 1993; T. Smith and M. Waterman, Adv. Appl. Math. 2:482-489, 1981, S. Needleman and C. Wunsch, J. Mol. Biol., 48:443-453, 1970, W. Pearson and D. Lipman, PNAS, 85:2444-2448, 1988 and others incorporated into computerized implementations such as, but not limited to, GAP, BESTFIT, FASTA, TFASTA, and BLAST, for example incorporated in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Drive, Madison, Wis.) and publicly available from the National Center for Biotechnology Information.

(172) A non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, PNAS 87:2264-2268, modified as in Karlin and Altschul, 1993, PNAS. 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990, J. Mol. Biol. 215:403. BLAST nucleotide searches are performed with the NBLAST nucleotide program parameters set, e.g., for score=100, word length=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the present invention. BLAST protein searches are performed with the XBLAST program parameters set, e.g., to score 50, word length=3 to obtain amino acid sequences homologous to a protein molecule of the present invention. To obtain gapped alignments for comparison purposes, Gapped BLAST are utilized as described in Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402. Alternatively, PSI BLAST is used to perform an iterated search which detects distant relationships between molecules. When utilizing BLAST, Gapped BLAST, and PSI Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) are used. Another preferred, non limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4:11-17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 is used.

(173) The percent identity between two sequences is determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.

(174) One of skill in the art will recognize that one or more nucleic acid or amino acid mutations can be introduced without altering the functional properties of a given nucleic acid or protein, respectively. Mutations can be introduced using standard molecular biology techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis, to produce variants. For example, one or more amino acid substitutions, additions, or deletions can be made without altering the functional properties of a reference protein. Similarly, one or more nucleic acid substitutions, additions, or deletions can be made without altering the functional properties of a reference nucleic acid sequence.

(175) When comparing a reference protein to a putative homologue, amino acid similarity may be considered in addition to identity of amino acids at corresponding positions in an amino acid sequence. Amino acid similarity refers to amino acid identity and conservative amino acid substitutions in a putative homologue compared to the corresponding amino acid positions in a reference protein.

(176) Conservative amino acid substitutions can be made in reference proteins to produce variants.

(177) Conservative amino acid substitutions are art recognized substitutions of one amino acid for another amino acid having similar characteristics. For example, each amino acid may be described as having one or more of the following characteristics: electropositive, electronegative, aliphatic, aromatic, polar, hydrophobic and hydrophilic. A conservative substitution is a substitution of one amino acid having a specified structural or functional characteristic for another amino acid having the same characteristic. Acidic amino acids include aspartate, glutamate; basic amino acids include histidine, lysine, arginine; aliphatic amino acids include isoleucine, leucine and valine; aromatic amino acids include phenylalanine, glycine, tyrosine and tryptophan; polar amino acids include aspartate, glutamate, histidine, lysine, asparagine, glutamine, arginine, serine, threonine and tyrosine; and hydrophobic amino acids include alanine, cysteine, phenylalanine, glycine, isoleucine, leucine, methionine, proline, valine and tryptophan; and conservative substitutions include substitution among amino acids within each group. Amino acids may also be described in terms of relative size; alanine, cysteine, aspartate, glycine, asparagine, proline, threonine, serine, valine are all typically considered to be small.

(178) A variant can include synthetic amino acid analogs, amino acid derivatives and/or non-standard amino acids, illustratively including, without limitation, alpha-aminobutyric acid, citrulline, canavanine, cyanoalanine, diaminobutyric acid, diaminopimelic acid, dihydroxy-phenylalanine, djenkolic acid, homoarginine, hydroxyproline, norleucine, norvaline, 3-phosphoserine, homoserine, 5-hydroxytryptophan, 1-methylhistidine, 3-methylhistidine, and ornithine.

(179) With regard to nucleic acids, it will be appreciated by those of skill in the art that due to the degenerate nature of the genetic code, multiple nucleic acid sequences can encode a particular protein, and that such alternate nucleic acids may be used in compositions and methods of the present invention.

(180) An assay of the present invention can incorporate a support for attachment of a specific binding agent, such as, but not limited to an antibody or probe. A support with attached specific binding agent can be solid or semi-solid and can be any of various materials such as glass, silicon, paper, a synthetic or naturally occurring polymer, such as polystyrene, polycarbonate, polypropylene, PVDF, nylon, cellulose, agarose, dextran, and polyacrylamide or any other material to which a specific binding agent can be stably attached for use in a binding assay. Multiple specific binding agents can be arrayed on such supports for multiplex assays, such as microarrays for example.

(181) Such supports can be in any of a variety of forms and shapes including, but not limited to, microtiter plates, microtiter wells, pins, fibers, beads, magnetic beads, coded beads, slides, silicon chips and membranes such as a nitrocellulose or PVDF membrane. Such supports can further be used to purify a desired target.

(182) A support used can include functional groups for binding to a specific binding agent such as an antibody or neoepitope-containing peptide, including, but not limited to carboxyl, amine, amino, carboxylate, halide, ester, alcohol, carbamide, aldehyde, chloromethyl, sulfur oxide, nitrogen oxide, epoxy and/or tosyl functional groups. Attachment of a specific binding agent to a support is achieved by any of various methods, illustratively including adsorption and chemical bonding. In one example, 1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride, EDC or EDAC chemistry, can be used to attach a specific binding agent to a support. The specific binding agent can be bonded directly or indirectly to the material of the support, for example, via bonding to a coating or linker disposed on the support. Functional groups, modification thereof and attachment of a binding partner to a support are known in the art, for example as described in Fitch, R. M., Polymer Colloids: A Comprehensive Introduction, Academic Press, 1997.

(183) Methods of aiding in the diagnosis, assessment and/or treatment of Lyme disease are provided according to the present invention which include assaying a sample obtained from a subject having, or suspected of having, Lyme disease for proteolytic activity of Borrelia burgdorferi sensu lato HtrA to detect the presence of Borrelia burgdorferi sensu lato HtrA, wherein presence of Borrelia burgdorferi sensu lato HtrA is indicative of Borrelia burgdorferi sensu lato active infection of the subject.

(184) Methods of aiding in the diagnosis, assessment and/or treatment of Lyme disease are provided according to the present invention which include assaying a sample obtained from a subject having, or suspected of having, Lyme disease for proteolytic activity of Borrelia burgdorferi sensu lato HtrA to detect the presence of Borrelia burgdorferi sensu lato HtrA, wherein the assaying comprises contacting the sample with a substrate for Borrelia burgdorferi sensu lato HtrA and determining whether the substrate is cleaved by proteolytic activity of Borrelia burgdorferi sensu lato HtrA and wherein presence of Borrelia burgdorferi sensu lato HtrA is indicative of Borrelia burgdorferi sensu lato active infection of the subject.

(185) Methods of aiding in the diagnosis, assessment and/or treatment of Lyme disease are provided according to the present invention which include assaying a sample obtained from a subject having, or suspected of having, Lyme disease for proteolytic activity of Borrelia burgdorferi sensu lato HtrA to detect the presence of Borrelia burgdorferi sensu lato HtrA, wherein the assaying comprises contacting the sample with a substrate for Borrelia burgdorferi sensu lato HtrA wherein the substrate is selected from the group consisting of: casein, aggrecan, decorin, biglycan, brevican, neurocan, versican, fibronectin, fibromodulin, cartilage oligomeric matrix protein and E-cadherin and determining whether the substrate is cleaved by proteolytic activity of Borrelia burgdorferi sensu lato HtrA and wherein presence of Borrelia burgdorferi sensu lato HtrA is indicative of Borrelia burgdorferi sensu lato active infection of the subject.

(186) Methods of aiding in the diagnosis, assessment and/or treatment of Lyme disease are provided according to the present invention which include assaying a sample obtained from a subject having, or suspected of having, Lyme disease for proteolytic activity of Borrelia burgdorferi sensu lato HtrA to detect the presence of Borrelia burgdorferi sensu lato HtrA, wherein the assaying comprises contacting the sample with a substrate for Borrelia burgdorferi sensu lato HtrA, wherein the substrate comprises a Borrelia burgdorferi sensu lato HtrA cleavage site selected from SEQ ID NO:70-162, a homologue or variant thereof, and determining whether the substrate is cleaved by proteolytic activity of Borrelia burgdorferi sensu lato HtrA and wherein presence of Borrelia burgdorferi sensu lato HtrA is indicative of Borrelia burgdorferi sensu lato active infection of the subject.

(187) A sample is optionally purified to enrich for Borrelia burgdorferi sensu lato HtrA.

(188) For example, an antibody of other binding partner substantially specific for Borrelia burgdorferi sensu lato HtrA is attached to a solid support to capture Borrelia burgdorferi sensu lato HtrA.

(189) According to aspects of the present invention, the substrate includes a detectable label.

(190) The term detectable label refers to a substance that can be measured and/or observed, visually or by any appropriate method illustratively including spectroscopic, optical, photochemical, biochemical, enzymatic, electrical and/or immunochemical methods of detection, to indicate presence of the label. Non-limiting examples of detectable labels that can be used in conjunction with methods described herein illustratively include a fluorescent moiety, a chemiluminescent moiety, a bioluminescent moiety, a magnetic particle, an enzyme, a substrate, a radioisotope and a chromophore. For example, a detectable label can be a dye, such as a fluorophore, a chromophore, a radioactive moiety or a member of a specific binding pair such as biotin. The term member of a specific binding pair refers to a substance that specifically recognizes and interacts with a second substance exemplified by specific binding pairs such as biotin-avidin, biotin-streptavidin, antibody-antigen, and target-aptamer. Non-limiting examples of detectable labels that can be used include fluorescent dyes such as fluorescein and its derivatives, rhodamine and its derivatives, Texas Red, BODIPY dyes including but not limited to BODIPY-FL, BODIPY-TR, BODIPY-TMR, BODIPY-630/650, BODIPY-650/670; 5carboxy-fluorescein (FMA), 6-carboxy-4,5-dichloro-2,7-dimethoxyfluorescein, succinimidyl ester (JOE), 6-carboxytetramethylrhodamine (TAMRA), 6Ncarboxy-X-rhodamine (ROX), HEX, TET, IRD40, IRD41, cyanine dyes such as Cyanine 3 and Cyanine 5, and ALEXA dyes, including but not limited to ALEXA-488, ALEXA-532, ALEXA-546, ALEXA-568, and ALEXA-594; chromophores such as horseradish peroxidase, alkaline phosphatase and digoxigenin; and radioactive moieties such as .sup.32P, .sup.35S, .sup.3H, .sup.125I or .sup.14C; and binding partners such as biotin and biotin derivatives. Detection of a detectable label is achieved by any of various well-known methods such as, but not limited to, spectrophotometric and radiometric methods

(191) According to aspects of the present invention, the substrate is a chromogenic or flurogenic substrate. A chromogenic or fluorogenic substrate is characterized by attachment of a chemical group attached to the substrate which gives rise to color or fluorescence following cleavage by the protease. The generation of color or fluorescence can be detected spectrophotometrically and is proportional to cleavage of the substrate. Chromogenic moieties are known in the art and include, without limitation, pNA.

(192) Methods of aiding in the diagnosis of Lyme disease are provided according to the present invention which include detecting a host antibody specific for a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host protein substrate or on Borrelia burgdorferi sensu lato HtrA itself in a sample obtained from a subject suspected of having Lyme disease.

(193) Detecting a host antibody specific for a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA in a sample obtained from a subject having, or suspected of having, Lyme disease includes qualitative and/or quantitative assays including, but not limited to, immunoassay and mass spectrometry.

(194) A sample which is assayed to detect a host antibody specific for a peptide produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA is any sample type containing or suspected of containing the antibody or antibodies to be assayed, such as, but not limited to whole blood, plasma, serum, urine, cerebrospinal fluid, synovial fluid and/or a biopsy sample, such as skin or an arthroscopic biopsy sample of joint tissue.

(195) One or more peptides containing a neoepitope produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host substrate may be included in an assay to detect host antibodies which specifically bind to the neoepitope. One or more aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin peptides containing a neoepitope produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host substrate may be included in an assay to detect host antibodies which specifically bind to the neoepitope according to aspects of the present invention. The term neoepitope refers to the amino terminal 5-10 amino acid residues of a substrate of Borrelia burgdorferi sensu lato HtrA which are exposed subsequent to proteolytic activity. One or more aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin peptides of SEQ ID NO:33-69 and 162-414 each of which contains a neoepitope produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host substrate may be included in an assay to detect host antibodies which specifically bind to the neoepitope according to aspects of the present invention. Such peptides are optionally arrayed on a support for multiplex analysis to detect host antibodies in a sample obtained from a subject having or suspected of having Lyme disease.

(196) Peptides and proteins described herein may be prepared by any of various methods such as isolation from natural sources, isolation from an in-vitro cleavage reaction, recombinant production or chemical synthetic techniques.

(197) According to aspects of the present invention, commercial packages for aiding in the diagnosis, assessment and/or treatment of Lyme disease in a subject are provided according to aspects of the present invention which include one or more peptides containing a neoepitope produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host substrate may be included in an commercial package for use to detect host antibodies which specifically bind to the neoepitope. The host may be a subject having or suspected of having Lyme disease. Alternatively, the host may be an immunized subject. Multiple peptides containing a neoepitope produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA on a host substrate are provided according to aspects of inventive commercial packages of the present invention. Such peptides are optionally arrayed on a support for multiplex analysis of host antibodies substantially specific for one or more of the peptides. According to further aspects, commercial kits of the present invention include at least one, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, peptides of aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin which are Borrelia burgdorferi sensu lato HtrA cleavage products containing a neoepitope. According to further aspects, commercial kits of the present invention include at least one, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, peptides of aggrecan, biglycan, decorin, fibronectin, brevican, neurocan, versican, fibromodulin, COMP and/or E-cadherin peptides of SEQ ID NO:33-69 and 162-414 each of which contains a neoepitope produced by proteolytic activity of Borrelia burgdorferi sensu lato HtrA. Peptides included in commercial packages according to aspects of the present invention are optionally arrayed on a support. One or more auxiliary components are optionally included in commercial packages of the present invention, such as, but not limited to, a control reagent, buffer, diluent or a reconstituting agent.

(198) Protease Inhibitors

(199) Methods of screening for an inhibitor of Borrelia burgdorferi sensu lato protease activity are provided according to the present invention.

(200) Methods of screening for an inhibitor of Borrelia burgdorferi sensu lato protease activity are provided according to the present invention which include contacting a Borrelia burgdorferi sensu lato HtrA protein with a test agent under conditions that promote protease activity of the Borrelia burgdorferi sensu lato HtrA protein and detecting an effect of the test agent to decrease protease activity of the Borrelia burgdorferi sensu lato HtrA protein, thereby identifying the test agent as an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity.

(201) The term test agent encompasses compounds; small molecules; biochemicals; and biological agents such as proteins, peptides, cytokines, antibodies, and fragments thereof.

(202) Conditions that promote protease activity as described in any of the inventive methods provided herein are well known in the art, including such conditions described in the references provided herein, and otherwise described or illustrated herein.

(203) An assay used in methods of identifying an inhibitor herein may have any of various formats, including, but not limited to, cell-based and array assays. An array assay refers to an ordered array of one or more materials, such as an arrangement of addressable regions including putative inhibitors, for example.

(204) The Borrelia burgdorferi sensu lato HtrA protein is optionally expressed by recombinant methodology for use in methods for screening for an inhibitor of Borrelia burgdorferi sensu lato HtrA. The expressed protein may be produced in a cell or in a cell-free expression system. For example, the nucleic acid sequence of SEQ ID NO:2 is expressed to produce recombinant Borrelia burgdorferi sensu lato HtrA for use in methods for screening for an inhibitor of Borrelia burgdorferi sensu lato HtrA The expressed recombinant Borrelia burgdorferi sensu lato HtrA is contacted with a test agent under conditions that promote protease activity and the effects of the test agent on protease activity are detected and compared to appropriate controls. Detection of a specific decrease in protease activity due to the test agent identifies an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity. The expressed protein is optionally isolated from cells in which it is expressed. Alternatively, the assay may include cells expressing the Borrelia burgdorferi sensu lato HtrA.

(205) Exemplary putative inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity include, but are not limited to, those described in Table I.

(206) TABLE-US-00001 TABLEI Inhibitorcommonor chemicalname Systematicname Elaspol,Sivelestat, N-{2-[({4-[(2,2- ONO5046 dimethylpropanoyl)oxy]phenyl}sulfonyl)amino]benzoyl}glycine Midesteine,MR-889 N-[(Tetrahydro-2-oxothiophen)-3-yl]-2-[[(thiophen-2- yl)carbonyl]thio]propionamide AE-3763 1-[N-[2-[3-(Carboxymethyl)-2-oxoimidazolidin-1-yl]acetyl]-L-valyl-L- prolinamideN-[3,3,3-trifluoro-1(S)-isopropyl-2-oxopropyl]amide ONO-6818 2-(5-amino-6-oxo-2-phenyl-1,6-dihydropyrimidin-1-yl)-N-[(1R,2R)-1-(5- tert-butyl-1,3,4-oxadiazol-2-yl)-1-hydroxy-3-methylbutan-2-yl]acetamide Nafamostat 4-[(Aminoiminomethyl)amino]-benzoicacid6-(aminoiminomethyl)-2- naphthalenylesterdimethanesulfonateesterdimethanesulfonate Camostatmesilate 4-Guanidinobenzoicacid4- [[[(dimethylcarbamoyl)methoxy]carbonyl]methyl]phenyl-methanesulfonicacid AK-968/40385474, [3-[(E)-[[2-[(6-ethoxy-1, MolPort-019-779-730, 3-benzothiazol-2-yl)sulfanyl]acetyl]hydrazinylidene]methyl]phenyl STK958229, 4-iodo-2-methylpyrazole-3-carboxylate AKOS003924934 ASN05116187, 2-{[1-(4-acetamidophenyl)-1,2,3,4-tetrazol-5-yl]sulfanyl}-N-(6-ethoxy- MolPort-000-061-068 1,3-benzothiazol-2-yl)acetamide ASN04363098, 2-[5-(4-Diethylsulfamoyl-phenyl)-[1,3,4]oxadiazol-2-ylsulfanyl]-N-(3,5- MolPort-000-040-886, dimethoxy-phenyl)-acetamide SMR000123570 AC1MKUQN ASN04363098 Oprea1_023656 Oprea1_263722 MLS000122916 MLS002536593 HMS2414H15 ZINC06512029 AKOS000710916 ASN05343143, N-(6-ethoxybenzothiazol-2-yl)-2-[[5-(4-methylsulfonylaminophenyl)-1,3, MolPort-000-068-903 4-oxadiazol-2-yl]sulfanyl]ethanamide ASN04363145, Ethyl2-[[2-[[5-[4-(diethylsulfamoyl)phenyl-1,3, MolPort-000-040-916 4-oxadiazol-2-yl]sulfanyl]acetyl]amino]-4, 5-dimethylthiophene-3-carboxylate BAS01074227, 2-(2,4-Dihydroxyphenyl)-3-{[(Z)-(2-hydroxy-4-oxo-2,5-cyclohexadien-1- ylidene)methyl]amino}-2,3-dihydro-4(1H)-quinazolinone ASN03776561, 1-(3-chlorophenyl)-3-[2-(morpholin-4-yl)ethyl]-3-({7-oxo-2H,3H,6H- MolPort-000-027-875 [1,4]dioxino[2,3-g]quinolin-8-yl}methyl)thiourea MolPort-001-670-311 3-[(1E)-({2-[(6-ethoxy-1,3-benzothiazol-2- yl)sulfanyl]acetamido}imino)methyl]phenyl4-iodo-1-methyl-1H- pyrazole-5-carboxylate Ulinastatin,UTI, AVLPQEEEGSGGGQLVTEVTKKEDSCQLGYSAGPCMGMTSRYFYNGTSMACETFQYGGCMGNGNNFVTEKECL Bikunin,Uristatin, QTCRTVAACNLPIVRGPCRAFIQLWAFDAVKGKCVLFPYGGCQGNGNKFYSEKECREYCGVPGDGDEELL Ulinastatin,AMBP, (SEQIDNO:425) EDC1,HI30,ITIL, IATIL,ITILC,Urinary TyrpsinInhibitor Bowman-Birkinhibitor, MPSTWGAAGGGLKLGRTGNSNCPVTVLQDYSEIFRGTPVKFSIPGISPGIIFTGTPLEIEFAEKPYCAESSKW Soybeantrypsin VAFVDNEIQKACVGIGGPEGHPGQQTFSGTFSIQKYKFGYKLVFCITGSGTCLDIGRFDAKNGEGGRRLNLTE inhibitor HEAFDIVFIEASKVDGIIKSVV (SEQIDNO:426)

(207) Additional exemplary putative inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity include, but are not limited to, those described in Abbente, G. et al., Medicinal Chem. 1:71-104, 2005.

(208) Recombinant Expression of Proteins and Nucleic Acids

(209) The term expressed refers to transcription of a nucleic acid sequence to produce a corresponding mRNA and/or translation of the mRNA to produce the corresponding protein. Expression constructs can be generated recombinantly or synthetically or by DNA synthesis using well-known methodology to express a desired nucleic acid and/or protein. The term expression construct is used herein to refer to a double-stranded recombinant DNA molecule containing a nucleic acid sequence desired to be expressed and containing appropriate regulatory elements necessary or desirable for the transcription of the operably linked nucleic acid sequence in vitro or in vivo. The term recombinant is used to indicate a nucleic acid construct in which two or more nucleic acids are linked and which are not found linked in nature. The term nucleic acid as used herein refers to RNA or DNA molecules having more than one nucleotide in any form including single-stranded, double-stranded, oligonucleotide or polynucleotide. The term nucleotide sequence is used to refer to the ordering of nucleotides in an oligonucleotide or polynucleotide in a single-stranded form of nucleic acid.

(210) An expression construct is introduced into a cell using well-known methodology, such as, but not limited to, by introduction of a vector containing the expression construct into the cell. A vector is a nucleic acid molecule that transfers an inserted nucleic acid molecule into and/or between host cells, becoming self-replicating. The term includes vectors that function primarily for insertion of a nucleic acid molecule into a cell, replication of vectors that function primarily for the replication of nucleic acid, and expression vectors that function for transcription and/or translation of the DNA or RNA. Also included are vectors that provide more than one of the above functions.

(211) Vectors include plasmids, viruses, BACs, YACs, and the like. Particular viral vectors illustratively include those derived from adenovirus, adeno-associated virus and lentivirus.

(212) The term regulatory element as used herein refers to a nucleotide sequence which controls some aspect of the expression of an operably linked nucleic acid sequence. Exemplary regulatory elements illustratively include an enhancer, an internal ribosome entry site (IRES), an intron; an origin of replication, a polyadenylation signal (pA), a promoter, a transcription termination sequence, and an upstream regulatory domain, which contribute to the replication, transcription, post-transcriptional processing of a nucleic acid sequence. Those of ordinary skill in the art are capable of selecting and using these and other regulatory elements in an expression construct with no more than routine experimentation.

(213) The term signal peptide refers to a protein, typically about 3-60 amino acids in length, that directs localization of a second protein to which the signal peptide is operably linked to a particular location within a cell. A nucleic acid encoding a signal peptide may be included in an expression construct and may encode a signal peptide operably linked to the naturally occurring protein or may be an exogenous signal peptide. Signal peptides and their use are well-known in the art.

(214) The term operably linked as used herein refers to a nucleic acid in functional relationship with a second nucleic acid. The term operably linked encompasses functional connection of two or more nucleic acid molecules, such as an oligonucleotide or polynucleotide to be transcribed and a regulatory element such as a promoter or an enhancer element, which allows transcription of the oligonucleotide or polynucleotide to be transcribed.

(215) The term promoter as used herein refers to a DNA sequence operably linked to a nucleic acid sequence to be transcribed such as a nucleic acid sequence encoding a desired molecule. A promoter is generally positioned upstream of a nucleic acid sequence to be transcribed and provides a site for specific binding by RNA polymerase and other transcription factors. In specific embodiments, a promoter is generally positioned upstream of the nucleic acid sequence transcribed to produce the desired molecule, and provides a site for specific binding by RNA polymerase and other transcription factors.

(216) In addition to a promoter, one or more enhancer sequences may be included such as, but not limited to, cytomegalovirus (CMV) early enhancer element and an SV40 enhancer element. Additional included sequences are an intron sequence such as the beta globin intron or a generic intron, a transcription termination sequence, and an mRNA polyadenylation (pA) sequence such as, but not limited to SV40-pA, beta-globin-pA, the human growth hormone (hGH) pA and SCF-pA. The term polyA or p(A) or pA refers to nucleic acid sequences that signal for transcription termination and mRNA polyadenylation. A polyA sequence is characterized by the hexanucleotide motif AAUAAA. Commonly used polyadenylation signals are the SV40 pA, the human growth hormone (hGH) pA, the beta-actin pA, and beta-globin pA. The sequences can range in length from 32 to 450 bp. Multiple pA signals may be used.

(217) Method for In-Vivo Screening for an Inhibitor of a Borrelia burgdorferi Sensu Lato HtrA Protease Activity

(218) Methods for in-vivo screening for an inhibitor of a Borrelia burgdorferi sensu lato HtrA protease activity are provided according to the present invention which include expressing the Borrelia burgdorferi sensu lato HtrA protein in a non-human organism; contacting the Borrelia burgdorferi sensu lato HtrA protein with a test agent under conditions that promote protease activity of the Borrelia burgdorferi sensu lato HtrA protein; and detecting a specific effect of the test agent to decrease protease activity of the Borrelia burgdorferi sensu lato HtrA protein, thereby identifying the test agent as an inhibitor of Borrelia burgdorferi sensu lato HtrA

(219) Assays for inhibitor activity described herein are optionally performed using a transgenic non-human animal, such as a transgenic mouse modified to express Borrelia burgdorferi sensu lato HtrA, for example to test efficacy and specificity of inhibitor compounds.

(220) Any of various methods can be used to introduce a transgene into a non-human animal to assay for inhibitors. Such techniques are well-known in the art and include, but are not limited to, pronuclear microinjection, viral infection and transformation of embryonic stem cells and iPS cells. Methods for generating transgenic animals that can be used include, but are not limited to, those described in J. P. Sundberg and T. Ichiki, Eds., Genetically Engineered Mice Handbook, CRC Press; 2006; M. H. Hofker and J. van Deursen, Eds., Transgenic Mouse Methods and Protocols, Humana Press, 2002; A. L. Joyner, Gene Targeting: A Practical Approach, Oxford University Press, 2000; Manipulating the Mouse Embryo: A Laboratory Manual, 3rd edition, Cold Spring Harbor Laboratory Press; 2002, ISBN-10: 0879695919; K. Turksen (Ed.), Embryonic stem cells: methods and protocols in Methods Mol Biol. 2002; 185, Humana Press; Current Protocols in Stem Cell Biology, ISBN: 978047015180; Meyer et al. PNAS USA, vol. 107 (34), 15022-15026; U.S. Pat. Nos. 5,994,618 and 6,891,082; and Pinkert, C. A., Transgenic Animal Technology, A Laboratory Handbook, 2.sup.nd ed., Academic Press, 2002.

(221) Assays for inhibitor activity described herein are optionally performed using a non-human animal infected with Borrelia burgdorferi sensu lato, for example to test efficacy and specificity of inhibitor compounds.

(222) Methods and pharmaceutical compositions for treating Lyme disease in a subject in need thereof are provided according to the present invention.

(223) Pharmaceutical compositions according to embodiments of the present invention include a pharmaceutically acceptable carrier. The term pharmaceutically acceptable carrier refers to a carrier which is substantially non-toxic to a subject and substantially inert to the active agent. A pharmaceutically acceptable carrier is a solid, liquid or gel in form and is typically sterile and pyrogen free.

(224) Methods of treating Lyme disease in a subject in need thereof are provided according to the present invention which include administering a therapeutically effective dose of an inhibitor of protease activity of a Borrelia burgdorferi sensu lato HtrA to the subject.

(225) Methods and compositions of the present invention can be used for prophylaxis as well as amelioration of signs and/or symptoms of Lyme disease. The terms treating and treatment used to refer to treatment of Lyme disease in a subject include: preventing, inhibiting or ameliorating Lyme disease in the subject, such as slowing progression of Lyme disease and/or reducing or ameliorating a sign or symptom of Lyme disease.

(226) Methods of diagnosis, assessment and/or treating a subject according to aspects of the present invention including assay of a sample obtained from a subject having or suspected of having Lyme disease and detection of one or more Borrelia burgdorferi sensu lato HtrA cleavage product and/or one or more cytokines and chemokines indicative of active Borrelia burgdorferi sensu lato infection according to methods of the present invention optionally includes treating a subject having Lyme disease or at risk of having Lyme disease by administration of a therapeutically effective amount of an antibiotic effective to kill or inhibit Borrelia burgdorferi sensu lato. Examples of such antibiotics include but are not limited to amoxicillin, cefotaxime, ceftriaxone, cefuroxime, doxycycline, erythromycin, penicillin and tetracycline.

(227) Antibiotics that can be used in treatment are described, for example, in Goodman et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th Ed., Macmillan Publishing Co., 1990. Guidelines for the antibiotic treatment of Lyme disease are found in Wormser G P, et al., Clin. Infect. Dis. 2006; 43:1089-134; and Halperin, J. J. et al., Neurology, 2007, 69(1):91-102.

(228) A therapeutically effective amount of a vaccine composition or a composition including an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity of the present invention is an amount which has a beneficial effect in a subject being treated.

(229) Pharmaceutical compositions suitable for delivery of an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity to a subject may be prepared in various forms illustratively including physiologically acceptable sterile aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, and sterile powders for reconstitution into sterile injectable solutions or dispersions. Examples of suitable aqueous and nonaqueous carriers include water, ethanol, polyols such as propylene glycol, polyethylene glycol, glycerol, and the like, suitable mixtures thereof; vegetable oils such as olive oil; and injectable organic esters such as ethyloleate. Proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants, such as sodium lauryl sulfate. Additional components illustratively including a buffer, a solvent, or a diluent may be included.

(230) Such formulations are administered by a suitable route including parenteral and oral administration. Administration may include systemic or local injection, and particularly intraarticular or intravenous injection.

(231) These compositions may also contain adjuvants such as preserving, wetting, emulsifying, and dispensing agents. Prevention of the action of microorganisms can be ensured by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, and the like. It may also be desirable to include isotonic agents, for example, sugars, sodium chloride, and substances similar in nature. Prolonged delivery of an injectable pharmaceutical form can be brought about by the use of agents delaying absorption, for example, aluminum monostearate and gelatin.

(232) Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity is admixed with at least one inert customary excipient (or carrier) such as sodium citrate or dicalcium phosphate or (a) fillers or extenders, as for example, starches, lactose, sucrose, glucose, mannitol, and silicic acid, (b) binders, as for example, carboxymethylcellulose, alignates, gelatin, polyvinylpyrrolidone, sucrose, and acacia, (c) humectants, as for example, glycerol, (d) disintegrating agents, as for example, agar-agar, calcium carbonate, plant starches such as potato or tapioca starch, alginic acid, certain complex silicates, and sodium carbonate, (e) solution retarders, as for example, paraffin, (f) absorption accelerators, as for example, quaternary ammonium compounds, (g) wetting agents, as for example, cetyl alcohol, glycerol monostearate, and glycols (h) adsorbents, as for example, kaolin and bentonite, and (i) lubricants, as for example, talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, or mixtures thereof. In the case of capsules, tablets, and pills, the dosage forms may also include a buffering agent.

(233) Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethyleneglycols, and the like.

(234) Solid dosage forms such as tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells, such as enteric coatings and others well known in the art. They may contain opacifying agents, and can also be of such composition that they release the active compound or compounds in a certain part of the intestinal tract in a delayed manner. Examples of embedding compositions which can be used are polymeric substances and waxes. The active compounds can also be in micro-encapsulated form, if appropriate, with one or more of the above-mentioned excipients.

(235) Liquid dosage forms for oral administration include a pharmaceutically acceptable carrier formulated as an emulsion, solution, suspension, syrup, or elixir. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art, such as water or other solvents, solubilizing agents and emulsifiers, as for example, ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butyleneglycol, dimethylformamide, oils, in particular, cottonseed oil, groundnut oil, corn germ oil, olive oil, castor oil and sesame oil, glycerol, tetrahydrofurfuryl alcohol, polyethyleneglycols and fatty acid esters of sorbitan or mixtures of these substances, and the like.

(236) Besides such inert diluents, the composition can also include adjuvants, such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.

(237) Suspensions, in addition to an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity, may contain suspending agents, as for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitol esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar or tragacanth, or mixtures of these substances, and the like.

(238) In particular aspects, compositions of the present invention are formulated for topical application, for example to the site of a tick bite. In further particular aspects, compositions of the present invention are formulated for topical application and are characterized by less than 10% absorption of an active ingredient in the composition into the system of an individual treated topically. In still further particular aspects, compositions of the present invention are formulated for topical application and are characterized by less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% absorption of an active ingredient in the composition into the system of an individual treated topically. Absorption into the system of an individual can be measured by any of various methods, particularly assay for the active ingredient, a metabolite and/or a breakdown product of the active ingredient in a sample obtained from an individual treated with the topical formulation. For example, a blood, plasma or serum sample can be assayed for presence of the active ingredient, a metabolite of the active ingredient and/or a breakdown product of the active ingredient.

(239) A topical formulation can be an ointment, lotion, cream or gel in particular aspects. Topical dosage forms such as ointment, lotion, cream or gel bases are described in Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins, 2006, p. 880-882 and p. 886-888; and in Allen, L. V. et al., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, 8th Ed., Lippincott Williams & Wilkins, 2005, p. 277-297.

(240) Pharmaceutically acceptable carriers and formulation of pharmaceutical compositions are known in the art, illustratively including, but not limited to, as described in Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott, Williams & Wilkins, Philadelphia, Pa., 2006; and Allen, L. V. et al., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, 8th Ed., Lippincott, Williams & Wilkins, Philadelphia, Pa., 2005.

(241) A pharmaceutical composition according to the present invention is suitable for administration to a subject by a variety of systemic and/or local routes including, but not limited to, intravenous, intraarticular, intramuscular, subcutaneous, intraperitoneal, oral, otic, rectal, vaginal, topical, parenteral, pulmonary, ocular, nasal, and mucosal.

(242) An inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity may be administered acutely or chronically. For example, a composition as described herein may be administered as a unitary dose or in multiple doses over a relatively limited period of time, such as seconds-hours. In a further embodiment, administration may include multiple doses administered over a period of days-years, such as for extended treatment of Lyme disease.

(243) A therapeutically effective amount of a pharmaceutical composition according to the present invention will vary depending on the particular pharmaceutical composition used, the severity of the condition to be treated, the species of the subject, the age and sex of the subject and the general physical characteristics of the subject to be treated. One of skill in the art could determine a therapeutically effective amount in view of these and other considerations typical in medical practice. In general it is contemplated that a therapeutically effective amount would be in the range of about 0.001 mg/kg-100 mg/kg body weight, optionally in the range of about 0.01-10 mg/kg, and further optionally in the range of about 0.1-5 mg/kg. Further, dosage may be adjusted depending on whether treatment is to be acute or continuing.

(244) Inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity are optionally formulated to achieve lipid-solubility and/or aqueous-solubility.

(245) In particular aspects, a pharmaceutically acceptable carrier is a particulate carrier such as lipid particles including liposomes, micelles, unilamellar or mulitlamellar vesicles; polymer particles such as hydrogel particles, polyglycolic acid particles or polylactic acid particles; inorganic particles such as calcium phosphate particles such as described in for example U.S. Pat. No. 5,648,097; and inorganic/organic particulate carriers such as described for example in U.S. Pat. No. 6,630,486.

(246) A particulate pharmaceutically acceptable carrier can be selected from among a lipid particle; a polymer particle; an inorganic particle; and an inorganic/organic particle. A mixture of particle types can also be included as a particulate pharmaceutically acceptable carrier.

(247) A particulate carrier is typically formulated such that particles have an average particle size in the range of about 1 nm-10 microns. In particular aspects, a particulate carrier is formulated such that particles have an average particle size in the range of about 1 nm-100 nm.

(248) Combination Treatments

(249) Combinations of therapeutic agents are administered according to embodiments of the present invention. For example, an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity and at least one additional therapeutic agent are administered to a subject to treat Lyme disease in a subject in need thereof.

(250) The term additional therapeutic agent is used herein to denote a chemical compound, a mixture of chemical compounds, a biological macromolecule (such as a nucleic acid, an antibody, a protein or portion thereof, e.g., a peptide), or an extract made from biological materials such as bacteria, plants, fungi, or animal (particularly mammalian) cells or tissues which is a biologically, physiologically, or pharmacologically active substance (or substances) that acts locally or systemically in a subject.

(251) Additional therapeutic agents included in aspects of methods and compositions of the present invention include, but are not limited to, antibiotics, analgesics, antipyretics, antidepressants, antipsychotics, antihistamines, anti-osteoporosis agents, anti-osteonecrosis agents, antiinflammatory agents, anxiolytics, chemotherapeutic agents, diuretics, growth factors, hormones, non-steroidal antiinflammatory agents, steroids and vasoactive agents.

(252) Combination therapies utilizing one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity and one or more additional therapeutic agents may show synergistic effects, e.g., a greater therapeutic effect than would be observed using either the one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity or one or more additional therapeutic agents alone as a monotherapy.

(253) According to aspects, combination therapies include: (1) pharmaceutical compositions that include one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity in combination with one or more additional therapeutic agents; and (2) co-administration of one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity of the present invention with one or more additional therapeutic agents wherein the one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity and the one or more additional therapeutic agents have not been formulated in the same composition. When using separate formulations, the one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity may be administered at the same time, intermittent times, staggered times, prior to, subsequent to, or combinations thereof, with reference to the administration of the one or more additional therapeutic agents.

(254) Combination treatments can allow for reduced effective dosage and increased therapeutic index of the one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity and the one or more additional therapeutic agents used in methods of the present invention.

(255) According to embodiments, a method of treating a subject having Lyme disease or at risk of having Lyme disease includes administration of a therapeutically effective amount of one or more inhibitors of Borrelia burgdorferi sensu lato HtrA protease activity and further includes a therapeutically effective amount of an antibiotic effective to kill or inhibit Borrelia burgdorferi sensu lato. Examples of such antibiotics include but are not limited to amoxicillin, cefotaxime, ceftriaxone, cefuroxime, doxycycline, erythromycin, penicillin and tetracycline.

(256) Antibiotics are described, for example, in Goodman et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th Ed., Macmillan Publishing Co., 1990. Guidelines for the antibiotic treatment of Lyme disease are found in Wormser G P, et al., Clin. Infect. Dis. 2006; 43:1089-134.

(257) Commercial Packages for Treatment

(258) Commercial packages are provided according to aspects of the present invention for treating Lyme disease in a subject in need thereof, including an inhibitor of Borrelia burgdorferi sensu lato HtrA protease activity. One or more auxiliary components are optionally included in commercial packages of the present invention, such as a pharmaceutically acceptable carrier exemplified by, but not limited to, a buffer, diluent or a reconstituting agent. An adjunct therapeutic is optionally included in commercial packages of the present invention, such as an antibiotic.

(259) Vaccine Methods and Compositions

(260) Methods for producing a detectable immune response in a subject are provided according to the present invention.

(261) Methods for producing a detectable immune response in a subject are provided according to the present invention which include administering an amount of proteolytically inactive Borrelia burgdorferi sensu lato HtrA and/or an immunogenic fragment of Borrelia burgdorferi sensu lato HtrA to a subject to produce a detectable immune response to Borrelia burgdorferi sensu lato HtrA in the subject.

(262) Borrelia burgdorferi sensu lato HtrA is rendered proteolytically inactive by any of various inactivation methods, illustratively including, but not limited to, denaturation by heat and/or chemical treatment such as cross-linking or use of a proteolytically inactive mutant protein, such as, but not limited to BbHtrA.sup.S226A.

(263) Administration of a vaccine composition according to a method of the present invention includes administration of one or more doses of a vaccine composition to a subject at one time in particular embodiments. Alternatively, two or more doses of a vaccine composition are administered at time intervals of weeks-years. A suitable schedule for administration of vaccine composition doses depends on several factors including age and health status of the subject, type of vaccine composition used and route of administration, for example. One of skill in the art is able to readily determine a dose and schedule of administration to be administered to a particular subject.

(264) Vaccines and methods for their use to induce active immunity and protection against Lyme disease in a subject are provided according to the present invention.

(265) In particular embodiments, vaccine compositions for enhancing immunological protection against Lyme disease in a subject are provided according to the present invention which includes Borrelia burgdorferi sensu lato HtrA and/or an immunogenic fragment thereof admixed with a pharmaceutically acceptable carrier.

(266) The term vaccine composition is used herein to refer to a composition including proteolytically inactive Borrelia burgdorferi sensu lato HtrA and/or an immunogenic fragment thereof capable of inducing an immune response in a subject inoculated with the vaccine composition.

(267) A vaccine composition of the present invention may be in any form suitable for administration to a subject.

(268) A vaccine composition is administered by any suitable route of administration including oral and parenteral such as intradermal, intramuscular, mucosal, nasal, or subcutaneous routes of administration.

(269) For example, a vaccine composition for parenteral administration may be formulated as an injectable liquid including proteolytically inactive Borrelia burgdorferi sensu lato HtrA and/or an immunogenic fragment thereof and a pharmaceutically acceptable carrier. Examples of suitable aqueous and nonaqueous carriers include water, ethanol, polyols such as propylene glycol, polyethylene glycol, glycerol, and the like, suitable mixtures thereof; vegetable oils such as olive oil; and injectable organic esters such as ethyloleate. Proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of a desirable particle size in the case of dispersions, and/or by the use of a surfactant, such as sodium lauryl sulfate. A stabilizer is optionally included such as, for example, sucrose, EDTA, EGTA, and an antioxidant.

(270) A solid dosage form for administration or for suspension in a liquid prior to administration illustratively includes capsules, tablets, powders, and granules. In such solid dosage forms, proteolytically inactive Borrelia burgdorferi sensu lato HtrA and/or an immunogenic fragment thereof is admixed with at least one carrier illustratively including a buffer such as, for example, sodium citrate or an alkali metal phosphate illustratively including sodium phosphates, potassium phosphates and calcium phosphates; a filler such as, for example, starch, lactose, sucrose, glucose, mannitol, and silicic acid; a binder such as, for example, carboxymethylcellulose, alignates, gelatin, polyvinylpyrrolidone, sucrose, and acacia; a humectant such as, for example, glycerol; a disintegrating agent such as, for example, agar-agar, calcium carbonate, plant starches such as potato or tapioca starch, alginic acid, certain complex silicates, and sodium carbonate; a solution retarder such as, for example, paraffin; an absorption accelerator such as, for example, a quaternary ammonium compound; a wetting agent such as, for example, cetyl alcohol, glycerol monostearate, and a glycol; an adsorbent such as, for example, kaolin and bentonite; a lubricant such as, for example, talc, calcium stearate, magnesium stearate, a solid polyethylene glycol or sodium lauryl sulfate; a preservative such as an antibacterial agent and an antifungal agent, including for example, sorbic acid, gentamycin and phenol; and a stabilizer such as, for example, sucrose, EDTA, EGTA, and an antioxidant.

(271) Solid dosage forms optionally include a coating such as an enteric coating. The enteric coating is typically a polymeric material. Preferred enteric coating materials have the characteristics of being bioerodible, gradually hydrolyzable and/or gradually water-soluble polymers. The amount of coating material applied to a solid dosage generally dictates the time interval between ingestion and drug release. A coating is applied having a thickness such that the entire coating does not dissolve in the gastrointestinal fluids at pH below 3 associated with stomach acids, yet dissolves above pH 3 in the small intestine environment. It is expected that any anionic polymer exhibiting a pH-dependent solubility profile is readily used as an enteric coating in the practice of the present invention to achieve delivery of the active agent to the lower gastrointestinal tract. The selection of the specific enteric coating material depends on properties such as resistance to disintegration in the stomach; impermeability to gastric fluids and active agent diffusion while in the stomach; ability to dissipate at the target intestine site; physical and chemical stability during storage; non-toxicity; and ease of application.

(272) Suitable enteric coating materials illustratively include cellulosic polymers such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose, methyl cellulose, ethyl cellulose, cellulose acetate, cellulose acetate phthalate, cellulose acetate trimellitate, hydroxypropylmethyl cellulose phthalate, hydroxypropylmethyl cellulose succinate and carboxymethylcellulose sodium; acrylic acid polymers and copolymers, preferably formed from acrylic acid, methacrylic acid, methyl acrylate, ammonium methylacrylate, ethyl acrylate, methyl methacrylate and/or ethyl; vinyl polymers and copolymers such as polyvinyl pyrrolidone, polyvinyl acetate, polyvinylacetate phthalate, vinylacetate crotonic acid copolymer, and ethylene-vinyl acetate copolymers; shellac; and combinations thereof. A particular enteric coating material includes acrylic acid polymers and copolymers described for example U.S. Pat. No. 6,136,345.

(273) The enteric coating optionally contains a plasticizer to prevent the formation of pores and cracks that allow the penetration of the gastric fluids into the solid dosage form. Suitable plasticizers illustratively include, triethyl citrate (Citroflex 2), triacetin (glyceryl triacetate), acetyl triethyl citrate (Citroflec A2), Carbowax 400 (polyethylene glycol 400), diethyl phthalate, tributyl citrate, acetylated monoglycerides, glycerol, fatty acid esters, propylene glycol, and dibutyl phthalate. In particular, a coating composed of an anionic carboxylic acrylic polymer typically contains approximately 10% to 25% by weight of a plasticizer, particularly dibutyl phthalate, polyethylene glycol, triethyl citrate and triacetin. The coating can also contain other coating excipients such as detackifiers, antifoaming agents, lubricants (e.g., magnesium stearate), and stabilizers (e.g. hydroxypropylcellulose, acids or bases) to solubilize or disperse the coating material, and to improve coating performance and the coated product.

(274) Liquid dosage forms for oral administration include inactivated Borrelia burgdorferi sensu lato HtrA and/or an immunogenic fragment thereof and a pharmaceutically acceptable carrier formulated as an emulsion, solution, suspension, syrup, or elixir. A liquid dosage form of a vaccine composition of the present invention may include a wetting agent, an emulsifying agent, a suspending agent, a sweetener, a flavoring, or a perfuming agent.

(275) Detailed information concerning customary ingredients, equipment and processes for preparing dosage forms is found in Pharmaceutical Dosage Forms: Tablets, eds. H. A. Lieberman et al., New York: Marcel Dekker, Inc., 1989; and in L. V. Allen, Jr. et al., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, 8th Ed., Philadelphia, Pa.: Lippincott, Williams & Wilkins, 2004, throughout and in chapter 16; A. R. Gennaro, Remington: The Science and Practice of Pharmacy, Lippincott Williams & Wilkins, 21st ed., 2005, particularly chapter 89; and J. G. Hardman et al., Goodman & Gilman's The Pharmacological Basis of Therapeutics, McGraw-Hill Professional, 10th ed., 2001.

(276) An adjuvant is optionally included in a vaccine composition according to embodiments of the present invention. Adjuvants are known in the art and illustratively include Freund's adjuvant, aluminum hydroxide, aluminum phosphate, aluminum oxide, saponin, dextrans such as DEAE-dextran, vegetable oils such as peanut oil, olive oil, and/or vitamin E acetate, mineral oil, bacterial lipopolysaccharides, peptidoglycans, polylactides, CpG containing oligonucleotides and proteoglycans.

(277) In particular aspects, a vaccine composition includes a particulate carrier adjuvant such as lipid particles including liposomes, micelles, unilamellar or mulitlamellar vesicles; polymer particles such as hydrogel particles, polyglycolic acid particles or polylactic acid particles such as poly(lactic-co-glycolic acid) microspheres and other carriers described in Hanes, J. et al., Adv. Drug. Delivery Rev., 28:97-119, 1997; inorganic particles such as calcium phosphate particles such as described in for example U.S. Pat. No. 5,648,097; and inorganic/organic particulate carriers such as described for example in U.S. Pat. No. 6,630,486.

(278) Induction of an immunological response in a subject can be determined by any of various techniques known in the art, illustratively including detection of anti-Borrelia burgdorferi sensu lato HtrA antibodies, measurement of anti-Borrelia burgdorferi sensu lato HtrA antibody titer and/or lymphocyte proliferation assay. Signs and symptoms of Lyme disease may be monitored to detect induction of an immunological response to administration of a vaccine composition of the present invention in a subject. For example, induction of an immunological response is detected by preventing or reducing skin, neural, cardiac, and/or arthritic abnormalities characteristic of Lyme disease in a subject.

(279) Embodiments of inventive compositions and methods are illustrated in the following examples. These examples are provided for illustrative purposes and are not considered limitations on the scope of inventive compositions and methods.

EXAMPLES

Example 1

(280) BbHtrA and BbHtrA.sup.S226A

(281) BbHtrA contains a 37 amino acid signal sequence, the cleavage of which results in a mature protein of 437 amino acids with an amino terminus beginning at amino acid .sup.38Glu. BbHtrA is homologous to other DegP/HtrA proteases and sequence alignment indicates that BbHtrA serine 226 is part of the catalytic triad (His119, Asp149, and Ser226). Mutation of Ser226 to alanine is expected to abolish proteolytic activity. Wild type BbHtrA and BbHtrA.sup.S226A full length genes were codon optimized for expression in E. coli, synthesized, sequenced, and cloned into pUC57. For protein production, the sequence for the mature proteins (amino acids 38-474) were sub-cloned into expression vectors using the following primers:

(282) TABLE-US-00002 Forward: (SEQIDNO:25) CTTTAAGAAGGAGATATACATATGGAAGAAAAAGATAACACCGTG; Reverse: (SEQIDNO:26) ATACAGCTGTGCGGCCGCAAGCTTTCATTAGTGATGGTGATGGTGATGAA.

(283) FIG. 1A shows BbHtrA (3 g) shows as visualized by Coomassie stain (left panel) and anti-His tag Western (right panel). FIG. 1B shows BbHtrA.sup.S226A (2 g) as visualized by Coomassie stain (left panel) and anti-His tag Western (right panel). BbHtrA and BbHtrA.sup.S226A were purified from the soluble cellular fraction by application to a nickel column and eluted with imidazole. Preparations were then further purified by size exclusion chromatography and dialyzed into a storage buffer (TBS, 10% glycerol). ProteoSpin endotoxin removal kits (Norgen) were used, per the product insert, to reduce the lipopolysaccharide (LPS) in the recombinant proteins. Proteins were aliquoted and stored at 80 C. until use.

Example 2

(284) Polyclonal Rabbit and Mouse Anti-BbHtrA Antibodies

(285) Rabbit and mouse polyclonal anti-BbHtrA antibodies, directed against a BbHtrA KLH-conjugated peptide (306-VSAAIIASLYPGSPAVKSG-324) (SEQ ID NO:27), were generated for detection of BbHtrA.

Example 3

(286) BbHtrA is Accessible to Proteinase K in B. burgdorferi

(287) Protease accessibility studies on intact spirochetes were used to examine the exposure of BbHtrA to proteinase K. B. burgdorferi (strain B31) was cultured in complete BSK II medium to early log phase (4.510.sup.6/ml) and harvested by centrifugation at 2,000g for 20 min. Borrelia were washed to remove media components, and resuspended in phosphate buffered saline (PBS) containing 5 mM MgCl.sub.2. The sample was divided equally, half was incubated with proteinase K (20 g, Qiagen) and the other half was stored on ice. After 40 minutes, the reaction was stopped by addition of a protease inhibitor cocktail (HALT, Pierce) and incubated for an additional 5 min. The cells were pelleted, washed with PBS/Mg.sup.2+ to remove excess proteinase K and resuspended in non-reducing SDS-PAGE sample buffer and -110.sup.8 Borrelia were loaded per lane in pre-cast Tris-glycine gels (BioRad). Proteins separated by electrophoresis were transferred to a nitrocellulose membrane which was stained to reveal total protein (FIG. 2A). After total protein stain removal, the membrane was blocked (Starting Block, Pierce) and then probed with antibodies for a known surface protein (anti-OspA, H5332, 1 g/ml) and a periplasmic internal protein (anti-FlaB, H9724, 0.025 g/ml). Unbound primary antibody was removed by washing with TBS Tween. An appropriate alkaline phosphatase labeled secondary antibody (5 ng/ml) was applied for sixty minutes after which the membrane was washed to remove unbound antibody. A chemiluminescent phosphatase substrate was applied to enable visualization of the antibody complexes and images were captured with a chemiluminescence imaging system (BioRad). The membrane was stripped of antibodies (Restore, Pierce) and reprobed overnight with polyclonal rabbit anti-BbHtrA (0.2 g/ml) followed by an appropriate secondary antibody (KPL, alkaline phosphatase-conjugated, 50 ng/ml) (FIG. 2B). All antibodies were diluted in Starting Block (Pierce). Signals were detected by chemiluminescence. As expected, the signal for OspA was greatly diminished and that of FlaB was retained after exposure to the protease. The BbHtrA signal was greatly diminished upon treatment, indicating that part of the cellular pool was accessible to proteinase K and part was protected by intracellular localization.

(288) FIG. 2A shows total protein stain demonstrating equivalent loading levels and the efficacy of the proteinase K (PK) treatment. FIG. 2B is an image of a Western blot showing loss of surface protein signal (OspA), retention of internal protein signal (FlaB) and diminished BbHtrA signal.

Example 4

(289) BbHtrA is Expressed During Infection of Humans and is an Immunogenic Protein

(290) Western blot strips of purified recombinant BbHtrA were probed with sera from the CDC Lyme disease reference panel and demonstrate that antibodies against this protease are generated during infection of humans (FIGS. 3A and 3B). Recombinant BbHtrA (FIG. 3A) or BbHtrA.sup.S226A (FIG. 3B) was electrophoretically separated in precast Tris-HCl gels (BioRad). BbHtrA degrades itself, resulting in more than one band in FIG. 3A, whereas a single band was observed when the mutant protease was used (FIG. 3B). Protein was transferred to a nitrocellulose membrane (BioRad) (100 Volts, 60 minutes) and the membrane was blocked (Starting Block, Pierce) for 60 minutes. The membrane was cut into strips which were was probed with anti-borrelial antibodies from human sera (1:100, CDC Lyme disease reference panel or 1:250, ViraMed diagnostic kit positive control sera, 60 minutes) or control sera from healthy blood donors living in U.S. regions non-endemic for Lyme disease, washed with TBS-Tween to remove excess primary antibody, and incubated with alkaline phosphatase conjugated goat anti-human antibody (1:6,000, ViraMed, 60 minutes, room temperature). Protein/antibody complexes were visualized by the addition of colorimetric alkaline phosphatase substrate (BCIP/NBT, BioRad). Given the similarity of BbHtrA to HtrA1 (33% identity, 54% similarity) and to lesser degrees to HtrAs 2-4, strips were also probed with commercially available rabbit polyclonal anti-HtrAs 1-4, all of which were negative (FIGS. 3A and 3B). Rabbit polyclonal antibody against a BbHtrA peptide served as a positive control.

Example 5

(291) Proteolysis Assays

(292) For proteolysis assays described in Examples herein, purified protein substrates (200-600 nM) and proteases (100-150 nM) were diluted in assay buffer (50 mM HEPES, pH 7.4, 5 mM CaCl.sub.2) and incubated overnight at 37 C. Samples were boiled for 4 minutes to inactivate the proteases. Proteoglycans were deglycosylated by overnight incubation at 37 C. with 0.01 U chondroitinase ABC (Seikagaku). Reactions were stopped by the addition of SDS/PAGE sample buffer, boiled for 4 minutes, and electrophoresed on pre-cast Tris-glycine gels (BioRad). Reaction products were visualized by silver staining.

Example 6

(293) BbHtrA Degrades Recombinant and Full Length Aggrecan

(294) Purified ECM components were incubated with wild type BbHtrA or the inactive mutant BbHtrA.sup.S226A (FIGS. 4A-4C). BbHtrA cleaved recombinant human aggrecan (G1-IGD-G2 domains) within the IGD (FIG. 4A). Cleavage of recombinant aggrecan generated three high molecular weight proteolytic fragments which migrated at 110 kd, 60 kd and -50 kd. These fragments were dependent on the presence of proteolytically active BbHtrA as incubation of recombinant aggrecan (FIG. 4A, lane 1) alone or with the inactive mutant (FIG. 4A, lane 6) failed to generate these fragments.

(295) BbHtrA also degraded native, fully glycosylated aggrecan (FIG. 4B, lane 5). Again, this degradation required BbHtrA catalytic activity (FIG. 4B, lane 6). The BbHtrA-generated aggrecan fragments appear to be a doublet, unlike those generated by HtrA1.

(296) BbHtrA shows a temperature dependent increase in activity against recombinant aggrecan (FIG. 4C). There is a concentration dependency. Increased aggrecan degradation is observed upon incubation with increasing concentrations of BbHtrA (FIG. 4C).

(297) BbHtrA degrades itself after proteolysis (FIG. 4A, lane 5, 43 kD band; FIG. 8, lane 1, gray arrows). The cleavage site was identified between .sup.80Phe-Phe.sup.81.

(298) FIG. 4 shows images of SDS-PAGE analyses FIG. 4A shows degradation of recombinant human aggrecan. Aggrecan was incubated with: lane 1, buffer alone; lane 2, ADAMTS-5; lane 3, MMP2; lane 4, HtrA1; lane 5, BbHtrA; and 6, BbHtrA.sup.S226A. Digestion products were separated by SDS-PAGE and silver stained. Black arrows, cleavage products; gray arrows, protease. FIG. 4B shows degradation of native bovine aggrecan. The numbering is the same as in FIG. 4A. Black arrow, cleavage products. FIG. 4C shows BbHtrA proteolytic activity is increased at elevated temperatures and is concentration dependent.

Example 7

(299) BbHtrA Degrades Extracellular Matrix Proteins

(300) Purified proteins were incubated with BbHtrA or BbHtrA.sup.S226A as described herein. HtrA (also known as DegP) proteases belong to the family of serine proteases which contain a highly reactive serine residue in their active site. This serine (Ser210 in DegP) is part of the canonical His-Ser-Asp catalytic triad and mutation of the catalytic serine abolishes proteolytic activity (Skorko-Glonek et al., 1995). In BbHtrA, residues His119, Ser226 and Asp149 form the catalytic triad and mutation of serine 226 to alanine abolished proteolytic activity as expected (FIG. 5).

(301) Reaction products were separated by SDS-PAGE and silver stained. Native collagen II and recombinant tenascin C were not degraded by BbHtrA indicating selectivity for proteoglycans, E-cadherin and fibronectin. FIG. 5 is an image of SDS-PAGE analysis showing that BbHtrA degrades aggrecan, neurocan, versican, brevican, biglycan, decorin, E-cadherin, and casein.

(302) Table II summarizes BbHtrA protease assays using various substrates.

(303) TABLE-US-00003 TABLE II Substrate Source Proteolytic activity Proteoglycans Aggrecan nB, rH + Brevican rH + Neurocan rH + Versican rH + Decorin nB, rH + Biglycan nB, rH + Other ECM Components Plasma fibronectin nH + E-cadherin rH + Casein nB + Collagen type II nH ND Laminin LAMB I nH ND Tenascin C nH ND TGF-3 rH ND nB = native bovine; rH = recombinant human; nH = native human; ND = degradation not detected

Example 8

(304) Identification of BbHtrA Cleavage Sites within Aggrecan Using Amino Terminal Sequence Analysis and Western Blotting

(305) Cleavage within the aggrecan IGD by ADAMTS-5, MMP-2 and HtrA1 is very specific and, consequently, monoclonal antibodies to the newly exposed termini (neoepitopes) have been developed. Currently, neoepitope antibodies are commercially available to detect the activity of aggrecanases and MMPs (FIG. 6A). Given the similarity in the sizes of the aggrecan fragments, BbHtrA reaction products were probed with three of these antibodies. To examine cleavage at the MMP site, the reaction products were also probed with the DIPEN neoepitope antibody. Cleavage at DIPEN.sup.342 (SEQ ID NO:28); was not detected (FIG. 6B). The amino terminus at the aggrecanase site (.sup.374ARGS, SEQ ID NO:29) was weakly identified by the BC-3 antibody in the BbHtrA-generated degradation products (FIG. 6B). The carboxyl terminal neoepitope (.sup.373NITEGE, SEQ ID NO:30) was not detected (FIG. 6B). BbHtrA may cleave at .sup.356VQTV (SEQ ID NO:31) releasing the peptide fragment 357-373 containing the NITEGE (SEQ ID NO:30) neoepitope.

(306) FIG. 6A is an image showing Western blot analysis of BbHtrA-generated recombinant aggrecan fragments recognized by monoclonal antibody BC-3, indicating cleavage between amino acids 373 and 374 within the aggrecan IGD.

(307) FIG. 6B is a schematic showing the proteolytic sites within the IGD and the epitopes for the antibodies raised against the neoepitopes.

(308) Amino terminal sequence analysis of the reaction products was performed. For Edman degradation and N-terminal sequencing, following SDS-PAGE and electroblotting onto PVDF membranes, the protein bands visualized with Coomassie Brilliant Blue were sequenced using model cLC-Procise sequencer (Applied Biosystems, Foster City, Calif.) applying manufacturer's PVDF chemistry cycles. The N-terminal sequences were identified for the main PTH signal that was assigned against the known template protein sequence. The major signals detected for all products were consistent with the amino terminus of recombinant aggrecan (.sup.20VETSDHDNSLS, SEQ ID NO:32) (FIG. 7A). Several minor signals were identified in the band detected by the BC-3 antibody (FIG. 7B) which is consistent with cleavage at or near the aggrecanase site (FIG. 7B). Additionally, minor signals in the 60 kD band could be consistent with cleavage at the HtrA1 site (FIG. 7B).

(309) The abundance of recombinant aggrecan amino terminal fragments reflects processive degradation of substrates from their carboxyl terminus. However, the very reproducible and characteristic bands generated by BbHtrA suggest that the protease cleaves a minimum of two distinct points within the IGD and then releases the substrate. The protease may be halted by variable post-translational modifications of the aggrecan IGD. In support of this hypothesis, there are potential O-linked keratan sulfate attachment sites very near the proteolytic sites (FIG. 7B) and, at least in calf and steer aggrecan, of these are modified with KS Hering, T. M., et al., Arch Biochem Biophys, 1997. 345(2): 259-70. There is 100% inter-species conservation of Asn.sup.368 at the aggrecanase site and glycosylation at Asn.sup.368 has a proposed regulatory role for aggrecanases Miwa, H. E., et al., Biochim Biophys Acta, 2009. 1790(3): 161-72.

(310) BbHtrA is not a purely processive protease. BbHtrA cleaves aggrecan internally at the .sup.374ARGS aggrecanase site and processively from the carboxyl terminus until it reaches distinct points within the IGD.

(311) FIG. 7A shows major and minor amino acid residues identified by Edman degradation of the aggrecan fragments. * indicates that no amino acid could be assigned to that position.

(312) FIG. 7B is a schematic diagram of the pathologic proteolytic cleavage sites within the aggrecan IGD showing possible location of BbHtrA-generated minor signals.

Example 9

(313) Identification of BbHtrA-Generated Fibronectin Fragments Using Mass Spectrometry

(314) BbHtrA generates pro-inflammatory amino terminal (Fnf-29) and carboxyl terminal (FnIII.sub.13-14) fibronectin fragments. BbHtrA degradation of fibronectin yielded distinct product bands. Fibronectin was incubated with BbHtrA overnight (FIG. 8A, lane 1) or for 96 hours (FIG. 8A, lane 3). Reaction products were separated electrophoretically, and the bands were excised and analyzed by tandem LC MS/MS, FIG. 8B.

(315) For mass spectrometry analysis, peptides are purified and concentrated using an on-line enrichment column (Agilent Zorbax C18, 5 m, 50.3 mm). Subsequent chromatographic separation is performed on a reverse phase nanospray column (Agilent 1100 nanoHPLC, Zorbax C18, 5 m, 75 m ID150 mm column) using a 42 minute linear gradient from 25%-55% buffer B (90% ACN, 0.1% formic acid) at a flow rate of 300 nanoliters/min. Peptides are eluted directly into the mass spectrometer (Thermo Scientific LTQ linear ion trap) and spectra are collected over a m/z range of 200-2000 Da using a dynamic exclusion limit of 2 MS/MS spectra of a given peptide mass for 30 s (exclusion duration of 90 s). Compound lists of the resulting spectra were generated using Bioworks 3.0 software (Thermo Scientific) with an intensity threshold of 5,000 and 1 scan/group. MS/MS spectra are searched against the appropriate protein database using the Mascot database search engine (version 2.1).

(316) The majority of the fibronectin tryptic peptides identified map to the carboxyl terminus and, with prolonged incubation amino terminal fragments were also observed. The most abundant carboxyl terminal fragment (37 kD) yielded fragments that span from fibronectin type three repeat 13 (FnIII.sub.13) to the terminus.

(317) FIGS. 8A and 8B show results indicating that BbHtrA degradation of fibronectin generates amino terminal Fnf-29, and carboxyl terminal FnIII.sub.13-14. FIG. 8A shows an image of an SDS-PAGE analysis of an experiment in which fibronectin was incubated with: lane 1, BbHtrA 15 hours; lane 2, fibronectin alone; lane 3, BbHtrA 96 hours. Black arrows indicate proteolytic fragments; gray arrows indicate BbHtrA. FIG. 8B is a table showing BbHtrA-generated fibronectin fragments identified by mass spectrometry. All peptides had peptide identity scores of greater than 95% yielding a 100% protein identity.

Example 10

(318) BbHtrA Induces Inflammatory Cytokine and Chemokine Expression in Cultured Chondrocytes

(319) Chondrocyte aggregate cultures are used which form an extensive extracellular matrix with components characteristic of articular cartilage including aggrecan and type II collagen as described in Welter, J. et al, BioTechniques, 2007, 42(6):732-737; and Solchaga, L. A. et al., Chondrogenic Differentiation of Bone Marrow-Derived Mesenchymal Stem Cells: Tips and Tricks, 2011, 698:253-278.

(320) To form the chondrocyte aggregate cultures, 110.sup.6 human mesenchymal stem cells (passage one, Lonza, catalog #PT-2501) were plated in a T150 flask (Corning) and cultured in growth media: mesenchymal stem cell basal media (MSCBM, Lonza, #PT-3238), mesenchymal growth supplements (SingleQuots, Lonza, #PT-4105), and 5 ng/ml recombinant human fetal growth factor (Shenandoah Biotechnology). When confluent, cells were trypsin-released (0.5% trypsin EDTA, Gibco), expanded to two T150 flasks and fed with growth media every three days. When confluent, cells were harvested, resuspended in fresh growth media containing 5% DMSO and aliquots of 110.sup.6 cells were cryopreserved in liquid nitrogen.

(321) Human mesenchymal stem cells were used to promote chondrogenesis and chondrocyte aggregate formation for use in these studies. Two vials of passage three cryopreserved cells were thawed, plated in growth media in two T150 flasks and then expanded to six T150 flasks as above. Cells were harvested (0.5% trypsin EDTA, Gibco), pooled, enumerated and induced to chondrogenic differentiation as follows. Cells were resuspended in defined chondrocyte differentiation media: high glucose DMEM (Gibco), 50 g/ml ascorbic acid-2-phosphate (Sigma), 39.3 ng/ml dexamethasone (Sigma), 40 g/ml L-proline (Sigma), ITS+Premix (BD Biosciences), 10 ng/ml transforming growth factor -3 (Shenandoah Biotechnology) and 30 g/ml gentamicin sulfate+15 ng/ml amphotericin-B (GA-1000, Lonza, #PT-4504E). High density aggregates were obtained by plating, on average, 310.sup.5 cells per well in a conical bottom 96 well plate (Thermo Scientific), pelleting by centrifugation (5 minutes at 600 g), and incubation at 37 C. and 5% CO.sub.2. Pellets formed coherent spherical aggregates by day two of culture. After seven days, wide bore tips were used to transfer aggregates to V-bottom 96 well plates (Corning). Aggregates were maintained in differentiation media at 37 C. and 5% CO.sub.2 for 3-5 weeks and fed every two days until experimentation.

(322) For chondrocyte cytokine induction assays, 24 hours prior to experimentation, dexamethasone containing media was removed, aggregates were rinsed with DPBS (Gibco) and dexamethasone-free differentiation media was added. For experimentation, aggregates were transferred to 24 well plates (24 aggregates per condition), spent media was removed and fresh warmed dexamethasone-free media containing samples was added. Aggregates were then incubated at 37 C. and 5% CO.sub.2 for two days.

(323) Recombinant BbHtrA or BbHtrA.sup.S226A was added to culture medium and incubated with chondrocyte aggregate cultures. BbHtrA and BbHtrA.sup.S226A were purified using an E. coli system and was expected to contain endotoxin which would have a stimulatory effect on the chondrocytes. To control for endotoxin contamination (lipopolysaccharide, LPS), an endotoxin removal kit (Noragen) was used to remove the bulk of LPS from recombinant BbHtrAs. The relative toxicity of the amount remaining in the BbHtrA and BbHtrA.sup.S226A samples was determined by a chromogenic Limulus Amoebocyte Lysate (LAL) method (Lonza, Walkersville, Md.). Prior to addition to aggregates, LPS (44 ng, 200 EU), BbHtrA.sup.WT (20 g, 27.9 EU LPS) and BbHtrA.sup.S226A(20 g, 1.99 EU LPS) were incubated in 1 mg/ml polymyxin B sulfate (Sigma) on ice for 30 min with occasional mixing. Warmed dexamethasone-free medium was then added to each test condition to a final volume of 1 ml. Control aggregates were maintained in untreated medium also containing polymyxin B sulfate. The final concentration for all test conditions was 60 g/ml polymyxin B sulfate. For chondrocyte cytokine induction, equivalent numbers of aggregates per test condition were transferred to individual wells of 24 well plates, spent medium was removed and 1 ml freshly warmed dexamethasone-free medium containing test components was added. Aggregates were incubated at 37 C. and 5% CO.sub.2 for 48 hours. (FIGS. 9A-9B and FIG. 10).

(324) Proteome Profiler Cytokine Arrays (R&D Systems, #ARY005) were used to detect 32 cytokines released in response to various conditions and were performed per product inserts. Briefly, spent media from chondrocyte assays was immediately diluted 1:5 in assay buffer containing biotinylated cytokine detection antibodies and incubated at room temperature for 60 minutes. The capture antibodies are spotted in duplicate on nitrocellulose membranes which were blocked with supplied buffer for 60 minutes. The samples were added to the blocked membranes and incubated overnight at 4 C. with mixing. After washing to remove unbound cytokines, membranes were incubated with 0.05 g/ml phosphatase-labeled streptavidin (KPL) for 30 minutes. After washing to remove unbound streptavidin, precipitating phosphatase substrate (BioRad) was added. Membranes were developed simultaneously to control for development time. Pixel densities for each spot on a membrane were measured, the averaged background values from the negative controls for that membrane were subtracted and then the duplicate values for a particular cytokine were averaged.

(325) Comparison of BbHtrA, Heat-denatured BbHtrA and LPS-induced Cytokine Responses. Initial experiments compared BbHtrA, heat denatured BbHtrA and LPS (FIG. 9A). The medium alone condition demonstrated that chondrocytes constitutively expressed cytokines MIF and Serpin E1 and very low levels of several others. LPS induced TLR4-mediated release of the cytokines CXCL1, IL-6 and IL-8 and very low levels of CCL5. BbHtrA, like LPS, stimulated release of CXCL1, IL-6, IL-8 and CCL5. Unlike LPS, however, CCL2 and sICAM-1 were also released in response to BbHtrA. The level of LPS used in these experiments was 7-fold greater than the residual LPS in recombinant BbHtrA, yet many of the cytokine signals were stronger from the BbHtrA treated chondrocytes and two were unique to the response to BbHtrA. The requirement of BbHtrA proteolytic activity for these responses was demonstrated by the near loss of all induced signals upon heat denaturation of BbHtrA. Cytokines were determined to be released in response to BbHtrA if the signals were greater than that seen in the control condition and greatly diminished by heat denaturation of BbHtrA. Six inflammatory cytokines and chemokines were stimulated in response to BbHtrA; CXCL1, CCL1, sICAM-1, IL-6, IL-8 and CCL2. A guide to the identities of the signals detected by the proteome profiler are shown in FIG. 9B.

(326) Comparison of BbHtrA, BbHtrAS226A and LPS-induced Cytokine Responses. To examine the impact of BbHtrA proteolytic activity on the observed responses, additional experiments compared BbHtrA.sup.WT, BbHtrA.sup.S226A, LPS and medium alone (FIG. 10). Results were very similar to the previous experiments (FIG. 9A). Inter-assay variability was observed in the strength of the responses although the cytokines induced were consistent. Chondrocytes released CCL5, CCL2, CXCL1, CCL1, sICAM-1, IL-6 and IL-8 in response to BbHtrA. Results with BbHtrA.sup.S226A demonstrated that catalytic activity was required for most of these responses. BbHtrA.sup.S226A stimulated release of IL-8 and CXCL1 which may suggest direct BbHtrA interaction with surface receptors or the displacement of a receptor agonist from the ECM. IL6, IL8 and low levels of CXCL1 were observed upon LPS stimulation of TLR4. Cytokines CXCL1, CCL1, sICAM-1, IL-6, IL-8, CCL2, and CCL5 were elevated in response to BbHtrA protease compared with BbHtrA inactivated by heat (FIG. 9A) or mutation of its active site (FIG. 10). Pixel densities of each of the cytokines induced by BbHtrA and controls are shown in Table III

(327) Table III Shows Results of Cytokine Assays

(328) TABLE-US-00004 TABLE III Cytokine Condition Mean StdDev N RANTES/CCL5 Medium 0.246 0.053 6 BbHtrA 0.736 0.393 8 BbHtrA.sup.S226A 0.265 0.056 6 LPS 0.365 0.084 6 MCP-1/CCL2 Medium 0.055 0.031 6 BbHtrA 0.452 0.275 8 BbHtrA.sup.S226A 0.050 0.041 6 LPS 0.082 0.028 6 GRO/CXCL1 Medium 0.174 0.044 6 BbHtrA 1.349 0.095 8 BbHtrA.sup.S226A 0.647 0.251 6 LPS 0.631 0.431 6 I-309/CCL1 Medium 0.123 0.033 6 BbHtrA 0.535 0.138 8 BbHtrA.sup.S226A 0.163 0.017 6 LPS 0.132 0.037 6 sICAM-1/CD54 Medium 0.173 0.035 6 BbHtrA 0.890 0.598 8 BbHtrA.sup.S226A 0.257 0.070 6 LPS 0.166 0.022 6 IL-8 Medium 0.402 0.089 6 BbHtrA 1.581 0.126 8 BbHtrA.sup.S226A 1.187 0.422 6 LPS 1.063 0.667 6 IL-6 Medium 0.253 0.041 6 BbHtrA 0.627 0.310 8 BbHtrA.sup.S226A 0.309 0.147 6 LPS 0.353 0.199 6 Positive control Medium 1.392 0.181 18 BbHtrA 1.438 0.118 24 BbHtrA.sup.S226A 1.406 0.138 18 LPS 1.298 0.135 18

Example 11

(329) BbHtrA undergoes partial self-degradation generating a lower molecular weight form of the protease often referred to the short-form and designated by an s preceding the protease name. FIG. 11A shows a silver stain of self-digested BbHtrA electrophoretically separated by SDS-PAGE. Amino terminal sequence analysis by Edman degradation of the 43 kD band established that s-BbHtrA arises from self-cleavage between .sup.80Phe-Phe.sup.81 (FIG. 11A). This cleavage removes 43 residues from the mature protein (amino acids 38-80) resulting in a predicted 5 kD mass change which is consistent with the observed changes in the protein bands. It is likely that the 23 and 28 kD bands result from consistent C processing of the protein. In addition to s-BbHtrA, other self-degradation products are observed in FIG. 11A. Mass spectrometric analysis identified additional self-cleavage sites between .sup.313Ser-Leu.sup.314, .sup.334Val-Asn.sup.335, .sup.385Ser-Ser.sup.386, and .sup.416Val-Val.sup.417. * indicates BbHtrA self-cleavage products.

(330) Comparison of the BbHtrA sequence aligned with that of E. coli DegQ (FIG. 11B) demonstrates that these paired phenylalanines are conserved. FIG. 11B shows a ClustalW alignment of BbHtrA and E. coli DegQ showing conserved paired phenylalanines.

Example 12

(331) Survey of Species of Borrelia for Presence of Borrelia burgdorferi Sensu Lato HtrA

(332) Proteolytic activity was studied by zymography of lysates of the prototype strains of each of the major genospecies of Borrelia that cause Lyme disease. Borrelia burgdorferi (passage 4, non-clonal, infectious strain B31), Borrelia garinii (unknown passage, infectious strain FR-20047) and Borrelia afzelii (unknown passage, infectious strain ACA-1) were grown in Barbour-Stoenner-Kelly media (BSK II) supplemented with 6% rabbit serum at 37 C. Borrelial lysates (110.sup.8 B. garinii, B. afzelii; 510.sup.7 B. burgdorferi) and recombinant BbHtrA proteins (1 g) were subjected to SDS-PAGE electrophoresis using 12% -casein Zymogram Ready Gels (Bio-Rad). Following electrophoresis, the gels were renatured in 2.5% Triton X-100 (Sigma) for 60 min at 37 C. with a buffer change at 15 min. The gels were developed in Zymogram Development Buffer (BioRad) for 40 h at 37 C. with a buffer change at 15 min. Gels were stained (0.5% Coomassie Brilliant Blue R-250, 40% methanol, 10% glacial acetic acid) for 60 min at room temperature and then destained (40% methanol, 10% glacial acetic acid).

(333) Recombinant BbHtrA was proteolytically active against -casein as evidenced by clearing around the protein band whereas BbHtrA.sup.S226A was not (FIG. 12A, lanes 1 and 2). Within the lysates, proteases displaying caseinolytic activity migrated at positions similar to the recombinant BbHtrA bands (FIG. 12A, lanes 3-5). All three species contained Western blot bands reactive with anti-BbHtrA peptide IgG antibodies (FIG. 12B), which likely represent the HtrA homologs. Black arrowhead indicates recombinant BbHtrA.sup.WT self-degradation product. FIG. 12C demonstrates the relative loading of the samples by immunoblot probed with anti-flagellar protein antibody (FlaB). Total protein was stained with silver (FIG. 12D). B. burgdorferi sensu stricto, B. garinii, and B. afzelii each possess an active HtrA.

Example 13

(334) Mass Spectrometry of Fibronectin Fragments

(335) In-gel reduced, alkylated, and trypsin digested peptides were purified and concentrated using an on-line enrichment column (Agilent Zorbax C18, 5 m, 50.3 mm). Subsequent chromatographic separation was performed on a reverse phase nanospray column (Agilent 1100 nano HPLC, Zorbax C18, 5 m, 75 m ID150 mm column) using a 42 min linear gradient from 25%-55% buffer B (90% ACN, 0.1% formic acid) at a flow rate of 300 nanoliters/min. Peptides were eluted directly into the mass spectrometer (Thermo Scientific LTQ linear ion trap) and spectra were collected over a m/z range of 200-2000 Da using a dynamic exclusion limit of 2 MS/MS spectra of a given peptide mass for 30 s (exclusion duration of 90 s). Compound lists of the resulting spectra were generated using Bioworks 3.0 software (Thermo Scientific) with an intensity threshold of 5,000 and 1 scan/group. MS/MS spectra were searched against the International Protein Index (IPI) human database (56,555 sequence entries) using the Mascot database search engine (version 2.2.1). The following parameters were employed in the database searches: peptide mass tolerance of 2 Da, fragment ion mass tolerance of 1.5 Da, fully tryptic digestion allowing for 1 missed cleavage, variable modification of methionine oxidation, and a fixed modification of cysteine carbamidomethylation. Protein identifications from all samples were combined using probabilistic protein identification algorithms implemented in Scaffold software (Proteome Software, Portland, Oreg.). Peptide and protein probability thresholds of 95% and 95%, respectively, were applied to the results (2.2% FDR as calculated by Scaffold based on probability statistics). A minimum of 2 unique peptides were required for protein identification. Proteins containing shared peptides are grouped by Scaffold to satisfy the laws of parsimony. Manual validation of MS/MS spectra was performed for all protein identifications above these thresholds that were based on one or two peptides. Criteria for manual validation included the following: 1) The peptide must be identified by all three search engines (Sequest, Mascot, and X! Tandem); 2) there must be a minimum of 80% coverage of theoretical y or b ions (at least 5 in consecutive order); 3) there must be an absence of prominent unassigned peaks greater than 5% of the maximum intensity; and 4) indicative residue specific fragmentation, such as intense ions N-terminal to proline and immediately C-terminal to aspartate and glutamate, were used as additional parameters of confirmation.

Example 14

(336) Mass Spectrometry of Proteolysis Assays

(337) Protease reactions were resuspended in 50 uL 0.1% formic acid (EMD, Gibbstown, N.J.) in 3% acetonitrile (Fisher Scientific) and transferred into sample vials. Liquid chromatography was carried out using an Agilent 1200 series HPLC equipped with a capillary pump and a nano pump (Agilent, Santa Clara, Calif.). Eluted peptides were analyzed on an Agilent quadrupole time of flight system (QTOF, model 6510) mass spectrometer with an HPLC-chip interface. A long HPLC chip was used with a 40-nL enrichment column and a 75-um150-mm analytical column combined on a single chip. Buffer A for the nano pump consisted of 0.1% formic acid in HPLC grade water; buffer B contained 90% acetonitrile, 10% HPLC grade water, and 0.1% formic acid. The buffer for the capillary pump contained 3% acetonitrile, 97% HPLC grade water, and 0.1% formic acid. QTOF parameters were as follows: voltage, 1920; drying gas, 5 L/min; temperature, 350 C.; m/z (mass to charge ratio) range (ms), 300 to 1600; m/z range (ms/ms), 50 to 2200; precursor ions, 4; active exclusion, yes; and scan rate, ultra (26,000 m/z per second). Gradient conditions for the nano pump were as follows: 3% B from 0 to 1 minute, from 15% B to 40% B between minutes 1 to 7, 100% B from minutes 7.1 to 11, and 3% B from 11.1 to 18.1 minutes. A total of 4 uL of the resuspended protease reactions were injected onto the enrichment column for concentration/purification. The chip cube was switched to redirect the flow from the nano pump to elute the enrichment column onto the analytical column from 0 to 50 minutes. Flow rates were 0.45 uL/min for the nano pump and 4 uL/min for the capillary pump. All samples were run in duplicate. Standards were run at the beginning of each day and at the end of a set of analyses for quality control purposes. Raw data were extracted and analyzed by using the Spectrum Mill database searching program (Rev A.03.03.080 SR1; Agilent, Santa Clara, Calif.). Peak picking was performed within Spectrum Mill with the following parameters: MH.sup.+ between 200 and 4000 Da, a maximum charge state of 7 was allowed (z7), and the program was directed to attempt to find a precursor charge state. During searching, the following parameters were applied: searches were performed with the Swiss-Prot Bovine database (Release 2010_11 of 2 Nov. 2010 of UniProtKB/Swiss-Prot contains 522019 sequence entries, comprising 184241293 amino acids abstracted from 192744 references.), oxidized methionine and deamidated asparagine as variable modifications, no enzyme search, precursor mass tolerance of 30 PPM, product mass tolerance 60 PPM, maximum ambiguous precursor charge of 4, and dynamic peak thresholding. Data were evaluated and protein identifications were considered significant if the following confidence thresholds were met: minimum of 2 peptides per protein, protein score >20, individual peptide scores of at least 10, and Scored Percent Intensity (SPI) of at least 70%. A reverse (random) database search was simultaneously conducted, and manual inspection of spectra was used to validate the match of the spectrum to the predicted peptide fragmentation pattern.

(338) Peptides found are listed in Table IV.

(339) TABLE-US-00005 TABLEIV Bovine Amino- Substrate/ terminal Measured Matched SEQIDNO UniprotID aminoacid BbHtrA-generatedPeptides (Da) (Da) SEQIDNO:33 Decorin/ 72 GLEKVPKDLPPDTALLDLQNNKITEI 719.40 2874.58 P21793 SEQIDNO:34 Decorin/ 179 VVELGTNPLKS 578.83 1156.66 P21793 SEQIDNO:35 Decorin/ 179 VVELGTNPLKSSGIENGAFQGMKKLS 676.86 2704.43 P21793 SEQIDNO:36 Decorin/ 179 VVELGTNPLKSSGIENGAFQGMKKLSYIRI 813.44 3249.77 P21793 SEQIDNO:37 Decorin/ 179 VVELGTNPLKSSGIENGAFQGMKKL 655.10 2617.40 P21793 SEQIDNO:38 Biglycan/ 296 GLPDLKLL 434.78 868.55 P21809 SEQIDNO:39 Biglycan/ 296 GLPDLKLLQV 548.34 1095.68 P21809 SEQIDNO:40 Biglycan/ 296 GLPDLKLLQVV 597.88 1194.75 P21809 SEQIDNO:41 Aggrecan/ 105 TLPNYPAIPSDA 629.82 1258.63 P13608 SEQIDNO:42 Aggrecan/ 105 TLPNYPAIPSDATLEI 857.95 1714.89 P13608 SEQIDNO:43 Aggrecan/ 907 GWLADQTVRYPI 709.88 1418.74 P13608 SEQIDNO:44 Fibromodulin/ 319 YLQGNRINEFSI 727.38 1453.74 P13605 SEQIDNO:45 Fibromodulin/ 336 VVDVMNFSKLQV 689.88 1378.74 P13605 SEQIDNO:46 Fibromodulin/ 337 VDVMNFSKLQV 640.34 1279.67 P13605 SEQIDNO:47 COMP/ 611 VMWKQMEQT 590.78 1180.55 P35445 SEQIDNO:48 COMP/ 612 MWKQMEQTYWQA 815.36 1629.72 P35445 SEQIDNO:49 COMP/ 612 MWKQMEQTYWQANPFRA 739.01 2215.02 P35445 SEQIDNO:50 COMP/ 654 WHTGDTASQV 551.25 1101.50 P35445 SEQIDNO:51 COMP/ 654 WHTGDTASQVRL 457.57 1370.68 P35445

(340) Both human and bovine substrates were degraded by BbHtrA (Table II). Mass spectrometry data (Table IV) were generated using native, fully glycosylated bovine substrates. Sequence alignments demonstrate the high degree of sequence conservation at the observed cleavage sites indicating cleavage will occur at these sites within the human substrates. Cleavage will also occur at the homologous positions within the human substrates (Table V) based on analysis of 93 known BbHtrA cleavage sites to generate a model of BbHtrA substrate characteristics. Corresponding peptides of the corresponding human proteins are listed in Table V.

(341) TABLE-US-00006 TABLEV Human Amino- SEQ Substrate/ terminal Humanpeptidesatpositionsanalogousto IDNO UniprotID aminoacid BbHtrA-generatedbovinepeptidesinTableIII SEQID Decorin/ 71 GLDKVPKDLPPDTTLLDLQNNKITEI NO:52 P07585 SEQID Decorin/ 178 VIELGTNPLKS NO:53 P07585 SEQID Decorin/ 178 VIELGTNPLKSSGIENGAFQGMKKLS NO:54 P07585 SEQID Decorin/ 178 VIELGTNPLKSSGIEnGAFQGMKKLSYIRI NO:55 P07585 SEQID Biglycan/ 295 GLPDLKLL NO:56 P21810 SEQID Biglycan/ 295 GLPDLKLLQV NO:57 P21810 SEQID Biglycan/ 295 GLPDLKLLQVV NO:58 P21810 SEQID Aggrecan/ 105 SLPNYPAIPSDA NO:59 P16112 SEQID Aggrecan/ 105 SLPNYPAIPSDATLEV NO:60 P16112 SEQID Aggrecan/ 202 GWLADQTVRYPI NO:61 P16112 SEQID Fibromodulin/ 319 YLQGNRINEFSI NO:62 Q06828 SEQID Fibromodulin/ 336 VVDVVNESKLQV NO:63 Q06828 SEQID Fibromodulin/ 337 VDVVNFSKLQV NO:64 Q06828 SEQID COMP/ 612 VMWKQMEQT NO:65 P49747 SEQID COMP/ 613 MWKQMEQTYWQA NO:66 P49747 SEQID COMP/ 613 MWKQMEQTYWQANPFRA NO:67 P49747 SEQID COMP/ 655 WHTGDTESQV NO:68 P49747 SEQID COMP/ 655 WHTGDTESQVRL NO:69 P49747

(342) A list of empirically derived BbHtrA protease cleavage sites is presented in Table VI. Each listed cleavage site is represented by the generic formula (P4P3P2P1)P1P2P3P4 where P4, P3, P2 and P1 represent the ordered sequence of the four amino acids on the side of the BbHtrA protease cleavage site closer to the N-terminal of the full-length protein and P1, P2, P3 and P4 represent the ordered sequence of the four amino acids on the side of the BbHtrA protease cleavage site closer to the C-terminal of the full-length protein. Protease cleavage breaks molecular bonds between amino acids P1 and P1, represented as x to generate fragments of the full-length protein, wherein one fragment has the amino acid sequence P4P3P2P1 at the C-terminus and the second fragment has the amino acid sequence P1P2P3P4 at the N-terminus. Parentheses are provided around the amino acid sequence P4P3P2P1 in Table VI solely to aid in visualization of these cleavage sites. These cleavage sites are depicted in isolation from the larger context of the proteins in which they are found. As will be recognized by those of skill in the art, conservative amino acid substitutions may be made in these cleavage sites without affecting the ability of BbHtrA to cleave at the sites.

(343) TABLE-US-00007 TABLEVI (P4P3P2P1)x SEQIDNO P1P2P3P4 SEQIDNO:70 (AFQT)VVLD SEQIDNO:71 (AIEL)EDLL SEQIDNO:72 (AKLT)GIPK SEQIDNO:73 (AVKS)STGP SEQIDNO:74 (CIEM)GGNP SEQIDNO:75 (CSDL)GLEK SEQIDNO:76 (CVYV)RAAV SEQIDNO:77 (DIKA)QLNL SEQIDNO:78 (DTNI)TTIP SEQIDNO:79 (FCTV)VDVM SEQIDNO:80 (FEPG)AFDG SEQIDNO:81 (FQTV)VLDP SEQIDNO:82 (FRAV)AEPG SEQIDNO:83 (FRCV)TDRL SEQIDNO:84 (FYVV)MWKQ SEQIDNO:85 (GISL)ENNP SEQIDNO:86 (GLKL)NYLR SEQIDNO:87 (GLPS)ALEQ SEQIDNO:88 (GVVV)DYID SEQIDNO:89 (HEKA)FSPL SEQIDNO:90 (HLYA)LVLV SEQIDNO:91 (HNNV)FSVP SEQIDNO:92 (IEMG)GNPL SEQIDNO:93 (IHQL)YLDS SEQIDNO:94 (IIAS)LYPG SEQIDNO:95 (IMKV)NGVS SEQIDNO:96 (IPFF)FEDM SEQIDNO:97 (IQEV)GSSM SEQIDNO:98 (ISEA)KLTG SEQIDNO:99 (ISKI)SPGA SEQIDNO:100 (ISLF)NNPV SEQIDNO:101 (ISPG)AFAP SEQIDNO:102 (IVQT)MNSD SEQIDNO:103 (KDKT)SYRW SEQIDNO:104 (KELS)SSKM SEQIDNO:105 (KGVV)VDYI SEQIDNO:106 (KIQA)IELE SEQIDNO:107 (KLQV)LRLD SEQIDNO:108 (KLYI)SKNH SEQIDNO:109 (KVDA)ASLK SEQIDNO:110 (LENL)YLQG SEQIDNO:111 (LENS)GFEP SEQIDNO:112 (LILI)NNKI SEQIDNO:113 (LKAV)KSST SEQIDNO:114 (LPPS)LTEL SEQIDNO:115 (LQNS)AIIA SEQIDNO:116 (LRNA)LWHT SEQIDNO:117 (MCSA)GWLA SEQIDNO:118 (MEQT)YWQA SEQIDNO:119 (MKKL)SYIR SEQIDNO:120 (MNCI)EMGG SEQIDNO:121 (NGIS)LENN SEQIDNO:122 (NHLV)EIPP SEQIDNO:123 (NKLS)RVPA SEQIDNO:124 (NLPS)SLVE SEQIDNO:125 (NNKI)SKIS SEQIDNO:126 (NNKL)SRVP SEQIDNO:127 (NQMI)VVEL SEQIDNO:128 (NQTG)LLDP SEQIDNO:129 (NRNL)KYLP SEQIDNO:130 (NWVV)LNQG SEQIDNO:131 (PDTA)LLDL SEQIDNO:132 (PDTT)LLDL SEQIDNO:133 (PFRA)VAEP SEQIDNO:134 (PNWV)VLNQ SEQIDNO:135 (PSRM)KYVY SEQIDNO:136 (PVST)NLEN SEQIDNO:137 (QCDA)GWLA SEQIDNO:138 (QDKV)TLPN SEQIDNO:139 (QLKA)VKSS SEQIDNO:140 (QTVV)LDPE SEQIDNO:141 (RNAL)WHTG SEQIDNO:142 (RNWI)KGVV SEQIDNO:143 (RSLI)LLDL SEQIDNO:144 (RVPA)GLPD SEQIDNO:145 (SFCT)VVDV SEQIDNO:146 (SFYV)VMWK SEQIDNO:147 (SKNH)LVEI SEQIDNO:148 (SKSV)SNLR SEQIDNO:149 (SLSV)SIPE SEQIDNO:150 (SPGA)FAPL SEQIDNO:151 (TKKA)SYSG SEQIDNO:152 (TSYI)SDFY SEQIDNO:153 (VFYA)TSPE SEQIDNO:154 (VKRA)YYNG SEQIDNO:155 (VVDV)MNFS SEQIDNO:156 (VVEL)GTNP SEQIDNO:157 (YIRV)RFYE SEQIDNO:158 (YLRI)SEAK SEQIDNO:159 (YNGI)SLFN SEQIDNO:160 (YSGV)SLFS SEQIDNO:161 (YVRA)AVQL SEQIDNO:162 (YWQA)NPFR

Example 15

(344) BbHtrA Cleavage Sites within Human Aggrecan, Biglycan, Decorin, Cartilage Oligomeric Matrix Protein and Fibromodulin

(345) SitePrediction, an internet-based protease cleavage site prediction tool, described in detail in Verspurten, J., et al., Trends Biochem Sci, 2009, 34(7):319-23, was used to predict BbHtrA cleavage sites in human aggrecan (Table VII), human biglycan (Table VIII), human cartilage oligomeric matrix protein (Table IX), human decorin (Table X) and human fibromodulin (Table XI). Ninety-three unique BbHtrA cleavage sites, identified by mass spectrometry from BbHtrA self-degradation and bovine aggrecan, biglycan, decorin, cartilage oligomeric matrix protein, were used as the training data-set to analyze BbHtrA substrate cleavage motifs, see Table VI. For each of the 93 sites, eight amino acids (four on either side of the cut site; generically described as (P4P3P2P1)P1P2P3P4 as indicated above,) were entered into the SitePrediction known sites input box. UniProt identifier codes for human aggrecan, biglycan, decorin, cartilage oligomeric matrix protein and fibromodulin were entered into the substrate input box. SitePrediction default parameters (0.1 penalty and BLOSUM62 amino acid substitution sequence alignment matrix) were used to predict 50 cleavage sites for each candidate human protein. The plot of true positive versus the false positive values (ROC curve) for the known BbHtra P sites yielded an area under the curve (AUC) of 0.945.

Example 16

(346) Table VII lists predicted BbHtrA-generated peptides of Human Aggrecan (Uniprot Identifier P16112).

(347) TABLE-US-00008 TABLEVII Amino-Terminal PredictedHumanAggrrecan SEQIDNO AminoAcid (UniprotIdentifierP16112)Peptides SEQIDNO:163 31 VSIPQPSPLRVLLGTSLTIPCYFIDPMHPVTTAP SEQIDNO:164 32 SIPQPSPLRVLLGTSLTIPCYFIDPMHPVTTAPS SEQIDNO:165 86 LLVATEGRVRVNSAYQDKVSLPNYPAIPSDATLE SEQIDNO:166 105 SLPNYPAIPSDATLEVQSLRSNDSGVYRCEVMHG SEQIDNO:167 117 TLEVQSLRSNDSGVYRCEVMHGIEDSEATLEVVV SEQIDNO:168 191 AYEDGFHQCDAGWLADQTVRYPIHTPREGCYGDK SEQIDNO:169 202 GWLADQTVRYPIHTPREGCYGDKDEFPGVRTYGI SEQIDNO:170 259 TSPEKFIFQEAANECRRLGARLATTGHVYLAWQA SEQIDNO:171 300 GWLADRSVRYPISKARPNCGGNLLGVRTVYVHAN SEQIDNO:172 336 GYPDPSSRYDAICYTGEDFVDIPENFFGVGGEED SEQIDNO:173 408 SPSPLEPEEPFITAPEIGATAFAEVENETGEATR SEQIDNO:174 516 AYEAGYEQCDAGWLRDQTVRYPIVSPRTPCVGDK SEQIDNO:175 624 GWLADGSLRYPIVTPRPACGGDKPGVRTVYLYPN SEQIDNO:176 660 GLPDPLSRHHAFCFRGISAVPSPGEEEGGTPTSP SEQIDNO:177 891 SGLPSGDLDSSGLTSTVGSGLTVESGLPSGDEER SEQIDNO:178 916 GLPSGDEERIEWPSTPTVGELPSGAEILEGSASG SEQIDNO:179 920 GDEERIEWPSTPTVGELPSGAEILEGSASGVGDL SEQIDNO:180 955 GLPSGEVLETSASGVGDLSGLPSGEVLETTAPGV SEQIDNO:181 974 GLPSGEVLETSASGVGDLSGLPSGEVLETTAPGV SEQIDNO:182 1296 SGLPSGEVLETTAPGVDEISGLPSGEVLETTAPG SEQIDNO:183 1334 SGLPSGEVLETTAPGVDEISGLPSGEVLETTAPG SEQIDNO:184 1354 GLPSGEVLETSASGVGDLSGLPSGEVLETTAPGV SEQIDNO:185 1365 SVSGVEDISGLPSGEVVETSASGIEDVSELPSGE SEQIDNO:186 1368 GVEDISGLPSGEVVETSASGIEDVSELPSGEGLE SEQIDNO:187 1392 SELPSGEGLETSASGVEDLSRLPSGEEVLEISAS SEQIDNO:188 1448 GTDLSGLPSGREGLETSASGAEDLSGLPSGKEDL SEQIDNO:189 1453 GLPSGREGLETSASGAEDLSGLPSGKEDLVGSAS SEQIDNO:190 1497 GTLGSGQAPETSGLPSGFSGEYSGVDLGSGPPSG SEQIDNO:191 1509 GLPSGFSGEYSGVDLGSGPPSGLPDFSGLPSGFP SEQIDNO:192 1530 GLPDFSGLPSGFPTVSLVDSTLVEVVTASTASEL SEQIDNO:193 1545 SLVDSTLVEVVTASTASELEGRGTIGISGAGEIS SEQIDNO:194 1550 TLVEVVTASTASELEGRGTIGISGAGEISGLPSS SEQIDNO:195 1561 SELEGRGTIGISGAGEISGLPSSELDISGRASGL SEQIDNO:196 1593 GLPSGTELSGQASGSPDVSGEIPGLFGVSGQPSG SEQIDNO:197 1597 GTELSGQASGSPDVSGEIPGLEGVSGQPSGEPDT SEQIDNO:198 1686 GLPGFSGATSGVPDLVSGTTSGSGESSGITFVDT SEQIDNO:199 1720 SLVEVAPTTFKEEEGLGSVELSGLPSGEADLSGK SEQIDNO:200 1741 SGLPSGEADLSGKSGMVDVSGQFSGTVDSSGFTS SEQIDNO:201 1742 GLPSGEADLSGKSGMVDVSGQFSGTVDSSGFTSQ SEQIDNO:202 1820 SLVDSTLVEVVTASTASELEGRGTIGISGAGEIS SEQIDNO:203 1875 GLIEPSGEPPGTPYFSGDFASTTNVSGESSVAMG SEQIDNO:204 1881 GEPPGTPYFSGDFASTTNVSGESSVAMGTSGEAS SEQIDNO:205 1915 GLPEVTLITSEFVEGVTEPTISQELGQRPPVTHT SEQIDNO:206 1979 SSVPESSSETSAYPEAGFGASAAPEASREDSGSP SEQIDNO:207 1980 SVPESSSETSAYPEAGFGASAAPEASREDSGSPD SEQIDNO:208 1990 AYPEAGFGASAAPEASREDSGSPDLSETTSAFHE SEQIDNO:209 2030 SGLGVSGSTLTFQEGEASAAPEVSGESTTTSDVG SEQIDNO:210 2101 SIPESEWTQQTQRPAETHLEIESSSLLYSGEETH SEQIDNO:211 2195 SLLYSGEETHTVETATSPTDASIPASPEWKRESE SEQIDNO:212 2127 LYSGEETHTVETATSPTDASIPASPEWKRESEST SEQIDNO:213 2244 VTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSD

(348) Table VIII lists predicted BbHtrA-generated peptides of Human Biglycan (Uniprot Identifier P21810)

(349) TABLE-US-00009 TABLEVIII Amino-Terminal PredictedHumanBiglycan SEQIDNO AminoAcid (UniprotIdentifierP21810)Peptides SEQIDNO:214 8 VSLLALSQALPFEQRGEWDFTLDDGPFMMNDEEA SEQIDNO:215 10 LLALSQALPFEQRGEWDFTLDDGPFMMNDEEASG SEQIDNO:216 11 LALSQALPFEQRGFWDFTLDDGPFMMNDEEASGA SEQIDNO:217 12 ALSQALPFEQRGFWDFTLDDGPFMMNDEEASGAD SEQIDNO:218 13 LSQALPFEQRGEWDFTLDDGPFMMNDEEASGADT SEQIDNO:219 17 LPFEQRGEWDFTLDDGPFMMNDEEASGADTSGVL SEQIDNO:220 48 GVLDPDSVTPTYSAMCPFGCHCHLRVVQCSDLGL SEQIDNO:221 49 VLDPDSVTPTYSAMCPFGCHCHLRVVQCSDLGLK SEQIDNO:222 50 LDPDSVTPTYSAMCPFGCHCHLRVVQCSDLGLKS SEQIDNO:223 80 GLKSVPKEISPDTTLLDLQNNDISELRKDDFKGL SEQIDNO:224 94 LLDLQNNDISELRKDDFKGLQHLYALVLVNNKIS SEQIDNO:225 103 SELRKDDFKGLQHLYALVLVNNKISKIHEKAFSP SEQIDNO:226 119 LVLVNNKISKIHEKAFSPLRKLQKLYISKNHLVE SEQIDNO:227 122 VNNKISKIHEKAFSPLRKLQKLYISKNHLVEIPP SEQIDNO:228 123 NNKISKIHEKAFSPLRKLQKLYISKNHLVEIPPN SEQIDNO:229 127 SKIHEKAFSPLRKLQKLYISKNHLVEIPPNLPSS SEQIDNO:230 134 FSPLRKLQKLYISKNHLVEIPPNLPSSLVELRIH SEQIDNO:231 146 SKNHLVEIPPNLPSSLVELRIHDNRIRKVPKGVF SEQIDNO:232 152 EIPPNLPSSLVELRIHDNRIRKVPKGVFSGLRNM SEQIDNO:233 160 SLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGN SEQIDNO:234 161 LVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNP SEQIDNO:235 162 VELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPL SEQIDNO:236 163 ELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLE SEQIDNO:237 179 FSGLRNMNCIEMGGNPLENSGFEPGAFDGLKLNY SEQIDNO:238 192 GNPLENSGFEPGAFDGLKLNYLRISEAKLTGIPK SEQIDNO:239 199 GFEPGAFDGLKLNYLRISEAKLTGIPKDLPETLN SEQIDNO:240 204 AFDGLKLNYLRISEAKLTGIPKDLPETLNELHLD SEQIDNO:241 211 NYLRISEAKLTGIPKDLPETLNELHLDHNKIQAI SEQIDNO:242 216 SEAKLTGIPKDLPETLNELHLDHNKIQAIELEDL SEQIDNO:243 219 KLTGIPKDLPETLNELHLDHNKIQAIELEDLLRY SEQIDNO:244 222 GIPKDLPETLNELHLDHNKIQAIELEDLLRYSKL SEQIDNO:245 231 LNELHLDHNKIQAIELEDLLRYSKLYRLGLGHNQ SEQIDNO:246 244 IELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLP SEQIDNO:247 245 ELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLPT SEQIDNO:248 247 EDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLR SEQIDNO:249 256 YRLGLGHNQIRMIENGSLSFLPTLRELHLDNNKL SEQIDNO:250 274 SFLPTLRELHLDNNKLARVPSGLPDLKLLQVVYL SEQIDNO:251 275 FLPTLRELHLDNNKLARVPSGLPDLKLLQVVYLH SEQIDNO:252 279 LRELHLDNNKLARVPSGLPDLKLLQVVYLHSNNI SEQIDNO:253 290 ARVPSGLPDLKLLQVVYLHSNNITKVGVNDFCPM SEQIDNO:254 291 RVPSGLPDLKLLQVVYLHSNNITKVGVNDFCPMG SEQIDNO:255 295 GLPDLKLLQVVYLHSNNITKVGVNDFCPMGFGVK SEQIDNO:256 305 VYLHSNNITKVGVNDFCPMGFGVKRAYYNGISLF SEQIDNO:257 313 TKVGVNDFCPMGFGVKRAYYNGISLFNNPVPYWE SEQIDNO:258 316 GVNDFCPMGFGVKRAYYNGISLENNPVPYWEVQP SEQIDNO:259 331 YYNGISLFNNPVPYWEVQPATFRCVTDRLAIQFG SEQIDNO:260 336 SLFNNPVPYWEVQPATFRCVTDRLAIQFGNYKK SEQIDNO:261 338 FNNPVPYWEVQPATFRCVTDRLAIQFGNYKK SEQIDNO:262 339 NNPVPYWEVQPATFRCVTDRLAIQFGNYKK SEQIDNO:263 356 TDRLAIQFGNYKK

(350) Table IX lists predicted BbHtrA-generated peptides; Cartilage oligomeric matrix protein (COMP, Uniprot Identifier P49747)

(351) TABLE-US-00010 TABLEIX Predicted BbHtrA-Generated Peptides; Amino-Terminal Cartilageoligomericmatrixprotein SEQIDNO AminoAcid (COMP,UniprotIdentifierP49747) SEQIDNO:264 10 LLTLAALGASGQGQSPLGSDLGPQMLRELQETNA SEQIDNO:265 11 LTLAALGASGQGQSPLGSDLGPQMLRELQETNAA SEQIDNO:266 13 LAALGASGQGQSPLGSDLGPQMLRELQETNAALQ SEQIDNO:267 14 AALGASGQGQSPLGSDLGPQMLRELQETNAALQD SEQIDNO:268 15 ALGASGQGQSPLGSDLGPQMLRELQETNAALQDV SEQIDNO:269 19 SGQGQSPLGSDLGPQMLRELQETNAALQDVRELL SEQIDNO:270 27 GSDLGPQMLRELQETNAALQDVRELLRQQVREIT SEQIDNO:271 28 SDLGPQMLRELQETNAALQDVRELLRQQVREITF SEQIDNO:272 29 DLGPQMLRELQETNAALQDVRELLRQQVREITFL SEQIDNO:273 49 RELLRQQVREITFLKNTVMECDACGMQQSVRTGL SEQIDNO:274 60 TFLKNTVMECDACGMQQSVRTGLPSVRPLLHCAP SEQIDNO:275 81 GLPSVRPLLHCAPGFCFPGVACIQTESGARCGPC SEQIDNO:276 85 VRPLLHCAPGFCFPGVACIQTESGARCGPCPAGF SEQIDNO:277 117 GFTGNGSHCTDVNECNAHPCFPRVRCINTSPGFR SEQIDNO:278 258 GWAGNGILCGRDTDLDGFPDEKLRCPERQCRKDN SEQIDNO:279 294 TVPNSGQEDVDRDGIGDACDPDADGDGVPNEKDN SEQIDNO:280 331 VRNPDQRNTDEDKWGDACDNCRSQKNDDQKDTDQ SEQIDNO:281 332 RNPDQRNTDEDKWGDACDNCRSQKNDDQKDTDQD SEQIDNO:282 487 VPNPGQEDADRDGVGDVCQDDFDADKVVDKIDVC SEQIDNO:283 514 VDKIDVCPENAEVTLTDFRAFQTVVLDPEGDAQI SEQIDNO:284 525 EVTLTDFRAFQTVVLDPEGDAQIDPNWVVLNQGR SEQIDNO:285 537 VVLDPEGDAQIDPNWVVLNQGREIVQTMNSDPGL SEQIDNO:286 538 VLDPEGDAQIDPNWVVLNQGREIVQTMNSDPGLA SEQIDNO:287 539 LDPEGDAQIDPNWVVLNQGREIVQTMNSDPGLAV SEQIDNO:288 553 VLNQGREIVQTMNSDPGLAVGYTAFNGVDFEGTF SEQIDNO:289 554 LNQGREIVQTMNSDPGLAVGYTAFNGVDFEGTFH SEQIDNO:290 564 MNSDPGLAVGYTAFNGVDFEGTFHVNTVTDDDYA SEQIDNO:291 565 NSDPGLAVGYTAFNGVDFEGTFHVNTVTDDDYAG SEQIDNO:292 570 LAVGYTAFNGVDFEGTFHVNTVTDDDYAGFIFGY SEQIDNO:293 573 GYTAFNGVDFEGTFHVNTVTDDDYAGFIFGYQDS SEQIDNO:294 581 DFEGTFHVNTVTDDDYAGFIEGYQDSSSFYVVMW SEQIDNO:295 591 VTDDDYAGFIFGYQDSSSFYVVMWKQMEQTYWQA SEQIDNO:296 592 TDDDYAGFIFGYQDSSSFYVVMWKQMEQTYWQAN SEQIDNO:297 611 VVMWKQMEQTYWQANPFRAVAEPGIQLKAVKSST SEQIDNO:298 612 VMWKQMEQTYWQANPFRAVAEPGIQLKAVKSSTG SEQIDNO:299 621 YWQANPFRAVAEPGIQLKAVKSSTGPGEQLRNAL SEQIDNO:300 630 VAEPGIQLKAVKSSTGPGEQLRNALWHTGDTESQ SEQIDNO:301 631 AEPGIQLKAVKSSTGPGEQLRNALWHTGDTESQV SEQIDNO:302 638 KAVKSSTGPGEQLRNALWHTGDTESQVRLLWKDP SEQIDNO:303 640 VKSSTGPGEQLRNALWHTGDTESQVRLLWKDPRN SEQIDNO:304 641 KSSTGPGEQLRNALWHTGDTESQVRLLWKDPRNV SEQIDNO:305 643 STGPGEQLRNALWHTGDTESQVRLLWKDPRNVGW SEQIDNO:306 644 TGPGEQLRNALWHTGDTESQVRLLWKDPRNVGWK SEQIDNO:307 654 LWHTGDTESQVRLLWKDPRNVGWKDKKSYRWFLQ SEQIDNO:308 667 LWKDPRNVGWKDKKSYRWELQHRPQVGYIRVRFY SEQIDNO:309 675 GWKDKKSYRWELQHRPQVGYIRVREYEGPELVAD SEQIDNO:310 693 GYIRVREYEGPELVADSNVVLDTTMRGGRLGVFC SEQIDNO:311 698 RFYEGPELVADSNVVLDTTMRGGRLGVECFSQEN SEQIDNO:312 707 ADSNVVLDTTMRGGRLGVECFSQENIIWANLRYR SEQIDNO:313 712 VLDTTMRGGRLGVECFSQENIIWANLRYRCNDTI SEQIDNO:314 713 LDTTMRGGRLGVECFSQENIIWANLRYRCNDTIP

(352) Table X lists predicted BbHtrA-generated peptides; Human Decorin (Uniprot Identifier P07585)

(353) TABLE-US-00011 TABLEX Amino-Terminal PredictedBbHtrA-GeneratedPeptides; SEQIDNO AminoAcid HumanDecorin(UniprotIdentifierP07585) SEQIDNO:315 7 LLLLAQVSWAGPFQQRGLFDFMLEDEASGIGPEV SEQIDNO:316 9 LLAQVSWAGPFQQRGLEDFMLEDEASGIGPEVPD SEQIDNO:317 10 LAQVSWAGPFQQRGLFDFMLEDEASGIGPEVPDD SEQIDNO:318 50 LGPVCPFRCQCHLRVVQCSDLGLDKVPKDLPPDT SEQIDNO:319 71 GLDKVPKDLPPDTTLLDLQNNKITEIKDGDFKNL SEQIDNO:320 85 LLDLQNNKITEIKDGDFKNLKNLHALILVNNKIS SEQIDNO:321 94 TEIKDGDFKNLKNLHALILVNNKISKVSPGAFTP SEQIDNO:322 105 KNLHALILVNNKISKVSPGAFTPLVKLERLYLSK SEQIDNO:323 114 NNKISKVSPGAFTPLVKLERLYLSKNQLKELPEK SEQIDNO:324 118 SKVSPGAFTPLVKLERLYLSKNQLKELPEKMPKT SEQIDNO:325 119 KVSPGAFTPLVKLERLYLSKNQLKELPEKMPKTL SEQIDNO:326 121 SPGAFTPLVKLERLYLSKNQLKELPEKMPKTLQE SEQIDNO:327 124 AFTPLVKLERLYLSKNQLKELPEKMPKTLQELRA SEQIDNO:328 125 FTPLVKLERLYLSKNQLKELPEKMPKTLQELRAH SEQIDNO:329 135 YLSKNQLKELPEKMPKTLQELRAHENEITKVRKV SEQIDNO:330 137 SKNQLKELPEKMPKTLQELRAHENEITKVRKVTF SEQIDNO:331 142 KELPEKMPKTLQELRAHENEITKVRKVTFNGLNQ SEQIDNO:332 169 TFNGLNQMIVIELGTNPLKSSGIENGAFQGMKKL SEQIDNO:333 178 VIELGTNPLKSSGIENGAFQGMKKLSYIRIADTN SEQIDNO:334 182 GTNPLKSSGIENGAFQGMKKLSYIRIADTNITSI SEQIDNO:335 183 TNPLKSSGIENGAFQGMKKLSYERIADTNITSIP SEQIDNO:336 189 SGIENGAFQGMKKLSYIRIADTNITSIPQGLPPS SEQIDNO:337 190 GIENGAFQGMKKLSYIRIADTNITSIPQGLPPSL SEQIDNO:338 195 AFQGMKKLSYIRIADTNITSIPQGLPPSLTELHL SEQIDNO:339 203 SYIRIADTNITSIPQGLPPSLTELHLDGNKISRV SEQIDNO:340 223 LTELHLDGNKISRVDAASLKGLNNLAKLGLSFNS SEQIDNO:341 234 SRVDAASLKGLNNLAKLGLSFNSISAVDNGSLAN SEQIDNO:342 239 ASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLR SEQIDNO:343 240 SLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRE SEQIDNO:344 244 LNNLAKLGLSENSISAVDNGSLANTPHLRELHLD SEQIDNO:345 245 NNLAKLGLSFNSISAVDNGSLANTPHLRELHLDN SEQIDNO:346 248 AKLGLSFNSISAVDNGSLANTPHLRELHLDNNKL SEQIDNO:347 249 KLGLSFNSISAVDNGSLANTPHLRELHLDNNKLT SEQIDNO:348 253 SFNSISAVDNGSLANTPHLRELHLDNNKLTRVPG SEQIDNO:349 258 SAVDNGSLANTPHLRELHLDNNKLTRVPGGLAEH SEQIDNO:350 260 VDNGSLANTPHLRELHLDNNKLTRVPGGLAEHKY SEQIDNO:351 266 ANTPHLRELHLDNNKLTRVPGGLAEHKYIQVVYL SEQIDNO:352 282 TRVPGGLAEHKYIQVVYLHNNNISVVGSSDFCPP SEQIDNO:353 283 RVPGGLAEHKYIQVVYLHNNNISVVGSSDFCPPG SEQIDNO:354 287 GLAEHKYIQVVYLHNNNISVVGSSDFCPPGHNTK SEQIDNO:355 297 VYLHNNNISVVGSSDFCPPGHNTKKASYSGVSLF SEQIDNO:356 305 SVVGSSDFCPPGHNTKKASYSGVSLFSNPVQYWE SEQIDNO:357 307 VGSSDFCPPGHNTKKASYSGVSLFSNPVQYWEIQ SEQIDNO:358 308 GSSDFCPPGHNTKKASYSGVSLFSNPVQYWEIQP SEQIDNO:359 323 SYSGVSLFSNPVQYWEIQPSTERCVYVRSAIQLG SEQIDNO:360 326 GVSLFSNPVQYWEIQPSTERCVYVRSAIQLGNYK SEQIDNO:361 328 SLFSNPVQYWEIQPSTERCVYVRSAIQLGNYK SEQIDNO:362 330 FSNPVQYWEIQPSTFRCVYVRSAIQLGNYK SEQIDNO:363 331 SNPVQYWEIQPSTFRCVYVRSAIQLGNYK SEQIDNO:364 352 AIQLGNYK

(354) Table XI lists predicted BbHtrA-generated peptides; Human Fibromodulin (Uniprot Identifier Q06828).

(355) TABLE-US-00012 TABLEXI Amino-Terminal PredictedBbHtrA-GeneratedPeptides; SEQIDNO AminoAcid HumanFibromodulin(UniprotIdentifierQ06828) SEQIDNO:365 5 SLLLLAGLFSLSQAQYEDDPHWWFHYLRSQQSTY SEQIDNO:366 6 LLLLAGLFSLSQAQYEDDPHWWFHYLRSQQSTYY SEQIDNO:367 8 LLAGLFSLSQAQYEDDPHWWFHYLRSQQSTYYDP SEQIDNO:368 9 LAGLFSLSQAQYEDDPHWWFHYLRSQQSTYYDPY SEQIDNO:369 11 GLFSLSQAQYEDDPHWWFHYLRSQQSTYYDPYDP SEQIDNO:370 12 LFSLSQAQYEDDPHWWFHYLRSQQSTYYDPYDPY SEQIDNO:371 38 YYDPYDPYPYETYEPYPYGVDEGPAYTYGSPSPP SEQIDNO:372 98 KYLPFVPSRMKYVYFQNNQITSIQEGVFDNATGL SEQIDNO:373 118 TSIQEGVEDNATGLLWIALHGNQITSDKVGRKVF SEQIDNO:374 124 VFDNATGLLWIALHGNQITSDKVGRKVESKLRHL SEQIDNO:375 129 TGLLWIALHGNQITSDKVGRKVFSKLRHLERLYL SEQIDNO:376 151 FSKLRHLERLYLDHNNLTRMPGPLPRSLRELHLD SEQIDNO:377 161 YLDHNNLTRMPGPLPRSLRELHLDHNQISRVPNN SEQIDNO:378 169 RMPGPLPRSLRELHLDHNQISRVPNNALEGLENL SEQIDNO:379 178 LRELHLDHNQISRVPNNALEGLENLTALYLQHNE SEQIDNO:380 189 SRVPNNALEGLENLTALYLQHNEIQEVGSSMRGL SEQIDNO:381 196 LEGLENLTALYLQHNEIQEVGSSMRGLRSLILLD SEQIDNO:382 205 LYLQHNEIQEVGSSMRGLRSLILLDLSYNHLRKV SEQIDNO:383 216 GSSMRGLRSLILLDLSYNHLRKVPDGLPSALEQL SEQIDNO:384 225 LILLDLSYNHLRKVPDGLPSALEQLYMEHNNVYT SEQIDNO:385 227 LLDLSYNHLRKVPDGLPSALEQLYMEHNNVYTVP SEQIDNO:386 231 SYNHLRKVPDGLPSALEQLYMEHNNVYTVPDSYF SEQIDNO:387 245 ALEQLYMEHNNVYTVPDSYFRGAPKLLYVRLSHN SEQIDNO:388 246 LEQLYMEHNNVYTVPDSYFRGAPKLLYVRLSHNS SEQIDNO:389 257 YTVPDSYFRGAPKLLYVRLSHNSLTNNGLASNTF SEQIDNO:390 259 VPDSYFRGAPKLLYVRLSHNSLTNNGLASNTFNS SEQIDNO:391 271 LYVRLSHNSLTNNGLASNTFNSSSLLELDLSYNQ SEQIDNO:392 274 RLSHNSLTNNGLASNTFNSSSLLELDLSYNQLQK SEQIDNO:393 276 SHNSLTNNGLASNTENSSSLLELDLSYNQLQKIP SEQIDNO:394 281 TNNGLASNTENSSSLLELDLSYNQLQKIPPVNTN SEQIDNO:395 282 NNGLASNTFNSSSLLELDLSYNQLQKIPPVNTNL SEQIDNO:396 290 FNSSSLLELDLSYNQLQKIPPVNTNLENLYLQGN SEQIDNO:397 293 SSLLELDLSYNQLQKIPPVNTNLENLYLQGNRIN SEQIDNO:398 294 SLLELDLSYNQLQKIPPVNTNLENLYLQGNRINE SEQIDNO:399 295 LLELDLSYNQLQKIPPVNTNLENLYLQGNRINEF SEQIDNO:400 296 LELDLSYNQLQKIPPVNTNLENLYLQGNRINEFS SEQIDNO:401 297 ELDLSYNQLQKIPPVNTNLENLYLQGNRINEFSI SEQIDNO:402 302 YNQLQKIPPVNTNLENLYLQGNRINEFSISSFCT SEQIDNO:403 312 NTNLENLYLQGNRINEFSISSECTVVDVVNESKL SEQIDNO:404 314 NLENLYLQGNRINEFSISSECTVVDVVNESKLQV SEQIDNO:405 319 YLQGNRINEFSISSFCTVVDVVNFSKLQVLRLDG SEQIDNO:406 336 VVDVVNFSKLQVLRLDGNEIKRSAMPADAPLCLR SEQIDNO:407 337 VDVVNFSKLQVLRLDGNEIKRSAMPADAPLCLRL SEQIDNO:408 340 VNFSKLQVLRLDGNEIKRSAMPADAPLCLRLASL SEQIDNO:409 346 QVLRLDGNEIKRSAMPADAPLCLRLASLIEI SEQIDNO:410 348 LRLDGNEIKRSAMPADAPLCLRLASLIEI SEQIDNO:411 349 RLDGNEIKRSAMPADAPLCLRLASLIEI SEQIDNO:412 359 AMPADAPLCLRLASLIEI SEQIDNO:413 371 ASLIEI SEQIDNO:414 372 SLIEI

Example 17

(356) Enzyme Linked Immunosorbent Assay (ELISA) for BbHtrA-Generated Protein Fragments (Biomarkers) from Mammalian Samples

(357) An exemplary ELISA is described here but other formulations embodying these principles also may be used, including multiplex ELISAs. Microtiter plate wells are coated with 100 L of up to 20 g/mL capture antibody (a monoclonal or polyclonal antibody (or a mixture of antibodies directed against several substrates) specifically immunoreactive with a BbHtrA substrate including, but not limited to, brevican, neurocan, versican, E-cadherin decorin, biglycan, fibromodulin, cartilage oligomeric matrix protein, and/or aggrecan in 0.1M bicarbonate buffer, pH 9.2, covered, and held at 4 C. for 16-18 h. Coating buffers may vary in type and pH, wash solutions may vary in constituents such as salt and detergent, or blocking agents may be vary to include reagents such as dry milk powder. Wells are washed 5 times in 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound capture antibodies, followed by the addition of 300 L of blocking buffer containing 100 mM phosphate buffer, 150 mM NaCl and 0.2% BSA per well. The plates are incubated for 1 h at RT with rotation (150 rpm) followed by 5 washes with 100 mM phosphate buffer, 150 mM NaCl. 100 L of each sample (whole blood, plasma, serum, urine, synovial fluid, cerebrospinal fluid) diluted in 100 mM phosphate buffer, 150 mM NaCl and 0.2% BSA is added to duplicate wells, and plates are incubated for 1 h at RT or 16 h at 4 C. with rotation. Wells are washed with 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound antigens, and then 100 L per well of up to 10 g/mL detection antibody in 150 mM NaCl and 0.2% BSA is added and incubated 1 h at RT with rotation. Detection antibodies include monoclonal antibodies conjugated with a detectable label such as horse radish peroxidase (HRP) or alkaline phosphatase (AP), but not limited to these enzymes, that are specifically immunoreactive with the BbHtrA-generated candidate substrate protein terminus which is exposed after BbHtrA digestion of a candidate substrate protein including, but not limited to, brevican, neurocan, versican, E-cadherin decorin, biglycan, fibromodulin, cartilage oligomeric matrix protein, and/or aggrecan Wells are washed with 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound detection antibody. Biomarker-detection antibody complexes are detected by the addition of 100 L per well of 2 mg/mL p-nitrophenyl phosphate (for AP labeled detection antibodies) or 3,5,3,5-tetramethylbenzidine (for HRP labeled detection antibodies). The reaction is stopped by the addition of 100 L per well of 0.75M NaOH (for AP) or 2M H.sub.2SO.sub.4 (for HRP) and a spectrophotometer is used to measure the optical density of wells at 405 nm (for AP) or 450 nm (for HRP). Quantitation of biomarker levels in samples is achieved by comparing values obtained from samples with those generated by a standard curve of serial dilutions of known concentrations of BbHtrA-generated biomarkers diluted in control uninfected body fluid. Values from subject samples are then compared to samples from healthy individuals and patients with other diseases.

Example 18

(358) Enzyme Linked Immunosorbent Assay (ELISA) for BbHtrA-Induced Cytokines from Mammalian Samples

(359) An exemplary ELISA is described here but other formulations embodying these principles also may be used, including multiplex ELISAs. Microtiter plate wells are coated with 100 L of up to 20 g/mL capture antibody (a monoclonal or polyclonal antibody (or a mixture of antibodies directed against several substrates) specifically immunoreactive with a BbHtrA-induced cytokine including, but not limited to CXCL1, CCL1, CCL2, CCL5, sICAM-1, IL-6, IL-8 in 0.1M bicarbonate buffer, pH 9.2, covered, and held at 4 C. for 16-18 h. Coating buffers may vary in type and pH, wash solutions may vary in constituents such as salt and detergent, or blocking agents may be vary to include reagents such as dry milk powder. Wells are washed 5 times in 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound capture antibodies, followed by the addition of 300 L of blocking buffer containing 100 mM phosphate buffer, 150 mM NaCl and 0.2% BSA per well. The plates are incubated for 1 h at RT with rotation (150 rpm) followed by 5 washes with 100 mM phosphate buffer, 150 mM NaCl. 100 L of each sample (whole blood, plasma, serum, urine, synovial fluid, cerebrospinal fluid) diluted in 100 mM phosphate buffer, 150 mM NaCl and 0.2% BSA is added to duplicate wells, and plates are incubated for 1 h at RT or 16 h at 4 C. with rotation. Wells are washed with 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound antigens, and then 100 L per well of up to 10 g/mL detection antibody in 150 mM NaCl and 0.2% BSA is added and incubated 1 h at RT with rotation. Detection antibodies include monoclonal antibodies conjugated with a detectable label such as horse radish peroxidase (HRP) or alkaline phosphatase (AP), but not limited to these enzymes, that are specifically immunoreactive with a BbHtrA-induced cytokine including but not limited to CXCL1, CCL1, CCL2, CCL5, sICAM-1, IL-6, IL-8. Wells are washed with 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound detection antibody. Cytokine-detection antibody complexes are detected by the addition of 100 L per well of 2 mg/mL p-nitrophenyl phosphate (for AP labeled detection antibodies) or 3,5,3,5-tetramethylbenzidine (for HRP labeled detection antibodies). The reaction is stopped by the addition of 100 L per well of 0.75M NaOH (for AP) or 2M H.sub.2SO.sub.4 (for HRP) and a spectrophotometer is used to measure the optical density of wells at 405 nm (for AP) or 450 nm (for HRP). Quantitation of cytokine levels in samples is achieved by comparing values obtained from samples with those generated by a standard curve of serial dilutions of known concentrations of BbHtrA-induced bytokines diluted in control uninfected body fluid. Values from subject samples are then compared to samples from healthy individuals and patients with other diseases.

(360) BbHtrA-generated protein fragment biomarkers and BbHtrA-induced cytokines optionally can be measured independently or at the same time in microplate, membrane, or glass-based microarray immunoassays or multi-plex bead based immunoassay.

Example 19

(361) Assay for Activity of BbHtrA Isolated from Mammalian Samples

(362) An exemplary activity assay is described here but other formulations embodying these principles also may be used. Microtiter plates or magnetic beads are coated with 100 L of up to 20 g/mL capture antibody (a monoclonal or polyclonal antibody) specifically immunoreactive with Borrelia burgdorferi sensu lato BbHtrA. in 0.1M bicarbonate buffer, pH 9.2, covered, and held at 4 C. for 16-18 h. Coating buffers may vary in type and pH, wash solutions may vary in constituents such as salt and detergent, or blocking agents may be vary to include reagents such as dry milk powder. Wells are washed 5 times in 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound capture antibodies, followed by the addition of 300 L of blocking buffer containing 100 mM phosphate buffer, 150 mM NaCl and 0.2% BSA per well. Capture antibodies are adsorbed for 1 h at RT with rotation (150 rpm) followed by 5 washes with 100 mM phosphate buffer, 150 mM NaCl. BbHtrA isolation/enrichment: 100 L or an appropriate volume of each sample (whole blood, plasma, serum, synovial fluid, cerebrospinal fluid) or control (serial dilutions of recombinant BbHtrA) diluted in 100 mM phosphate buffer, 150 mM NaCl and 0.2% BSA is added in duplicate and samples are incubated for 1 h at RT or 16 h at 4 C. with rotation. Wells are washed with 100 mM phosphate buffer, 150 mM NaCl, and 0.05% Tween 20 to remove unbound antigens. BbHtrA substrate is then added including but not limited to fluorescein isothiocyanate-labeled casein (FITC-casein) or para-nitro-aniline (pNA) labeled chromogenic DPMFKLV-pNA. Alternatively, a substrate composed of an FITC- or pNA-labeled peptide from a BbHtrA substrate including, but not limited to, aggrecan, decorin, biglycan, brevican, neurocan, versican, fibronectin, fibromodulin, cartilage oligomeric matrix protein, and/or E-cadherin is added. Labeled substrates are incubated with isolated BbHtrA and incubated for 1 h at RT or 16 h at 4 C. with rotation to allow for substrate degradation. Presence of BbHtrA is indicated by BbHtrA cleavage of these substrates which generates a measurable fluoroscent or colorometric signal detectable by fluorimetry or spectrophotometry. Alternatively, reactions are subjected to mass spectrometry to identify BbHtrA-generated degradation products. Quantitation of BbHtrA activity in samples is achieved by comparing values obtained from samples with those generated by a standard curve of serial dilutions of known concentrations of recombinant BbHtrA. Values from subject samples are then compared to samples from healthy individuals and patients with other diseases.

Example 20

(363) Mass Spectrometric Analysis of Mammalian Samples

(364) Prior to mass spectrometric analysis, a sample obtained from a subject having, or suspected of having, Lyme disease and intended for mass spectrometric analysis is optionally and preferably subjected to immunodepletion chromatography to remove high abundance materials, such as serum proteins. Alternatively, reverse phase chromatography is used to isolate peptides present in the sample. For absolute quantitation, samples are spiked with known concentrations of an appropriate internal standard. Mass spectrometric analysis of the subject sample is then performed, for example as described in Examples 13 and 14.

Example 21

(365) In this example, peptides of SEQ IDs 52-69 are synthesized using standard peptide synthesis methodology. The peptides are conjugated to a carrier protein such as BSA, MBP or KLH for use in production of antibodies which specifically recognize the amino terminal 5-10 amino acid residues of these peptides, a neo-epitope.

(366) Peptide-carrier protein fusions are used to immunize mice for antibody production and purification using standard methods known to those skilled in the art. Hybridoma cells are screened for those which specifically recognize the amino terminal 5-10 amino acid residues. Clones producing monoclonal antibodies specifically recognizing BbHtrA-generated neo-epitopes are identified by competition ELISAs and meet the following criteria: recognition of the BbHtrA-generated amino terminus, lack of recognition of the intact substrate or a peptide spanning the cleavage site or truncations thereof and lack of recognition of the carrier protein. Standard methods are used to obtain large quantities of the purified monoclonal anti-neo-epitope antibodies specific for BbHtrA-generated peptides.

(367) Monoclonal Antibody Production

(368) Female specific-pathogen-free inbred C57BL/6 mice can be used at 5 to 6 weeks of age. Upon arrival the mice are quarantined for 2 weeks and acclimated to a 12-hour light/dark cycle. Animals are housed in ventilated microisolator cages under environmentally controlled conditions. The animal rooms are monitored for specific pathogens through a disease surveillance and a sentinel animal program. Food and water are provided ad libitum.

(369) Mice are immunized with a BbHtrA cleavage product conjugated to a carrier protein such as Keyhole Limpet Hemocyanin by subcutaneous or intraperitoneal injection. Booster injections of the antigen are given biweekly and titers can be checked using blood drawn from the tail vein. The spleens are removed aseptically for hybridoma production days to weeks after antigen injection.

(370) Cell viability of exponentially growing myeloma cells is checked microscopically prior to use and the myeloma cultures are split at an appropriate time prior to the fusion to ensure mitotically active cells.

(371) Hybridomas are produced using standard polyethyleneglycol-based cell fusion techniques. Cell cultures can be maintained in Dulbecco's Modified Eagle Medium, supplemented with 1 mM pyruvate, 100 units/mL penicillin, 100 g/mL streptomycin and 0.292 mg/mL L-glutamine, 100 M sodium hypoxanthine, 16 M thymidine and 10% fetal calf serum and 100 units/mL IL-6.

(372) After about seven days, culture fluid is recovered from each well and screened for BbHtrA cleavage product-reactive IgG, such as by ELISA.

(373) Sequences

(374) SEQ ID NO:1 Borrelia burgdorferi HtrA (BB0104, BbHtrA) amino acid sequence, Catalytic triad is at amino acid positions 119H, 149D and 226S.

(375) TABLE-US-00013 MEKKFFSGFLLSFLALSIGFFIGMHYLASNRSNIVFAEEKDNTVRALQD SFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEFDSERKSNWAGS GVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKHKAKLIGKDEK KDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQFSFTVTAGI VSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNIKGEVIGINAWIA SNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYPLKTRDSE VLKSLGVESNDVSAAIIASLYPGSPAVKSGLRAGDIIMKVNGVSMSVFQ DVTSYISDFYAGEKVNVEILRGNVKKNIEIVLAVRPKDKELSSSKMLPG FVVYPLVEDIKAQLNLRNWIKGVVVDYIDKNLASNIKMKSGDVILSVNS KSVSNLREFYDALEVGKNTYKILRGNDSFKITF

(376) SEQ ID NO:2 Borrelia burgdorferi HtrA (BB0104, BbHtrA) nucleic acid sequence

(377) TABLE-US-00014 CTAAAATGTAATTTTAAAAGAATCGTTTCCTCTCAAAATTTTATAAGTA TTTTTTCCAACCTCAAGAGCATCATAAAATTCTCTTAAATTAGAAACAC TTTTTGAATTTACAGAAAGAATTACATCTCCTGATTTCATTTTAATATT TGATGCTAAATTTTTATCAATATAATCAACAACAACACCTTTAATCCAA TTTCTTAAATTAAGCTGAGCTTTAATATCCTCAACCAATGGATACACAA CAAAGCCTGGAAGCATCTTTGAAGAAGAAAGCTCTTTATCCTTAGGTCT AACAGCAAGAACAATCTCAATATTTTTTTTGACATTGCCTCTTAAGATT TCTACATTTACTTTCTCACCAGCATAAAAATCACTAATATATGATGTAA CATCTTGAAAAACGCTCATGGAAACCCCATTAACCTTCATAATAATATC CCCTGCCCTAAGCCCTGATTTAACAGCGGGTGAACCCGGATAAAGAGAA GCAATAATTGCAGCTGAAACATCATTACTTTCAACCCCTAAGCTTTTTA GCACCTCAGAATCTCTTGTCTTTAGCGGATAAAAAGAAATTCCAAGCCA AGCCGATTCAATTTTTTTACCTTTAAGGAAAAAATCTAGCAGTGCTTTT AATATTGTTAACAGGAATTGCAAAACCCAACCCAATATTTCCGCCAGAA TTTGAAGCTATCCAAGCATTAATTCCAATAACCTCGCCCTTTATATTTA CAAGAGGACCACCTGAATTACCCCTGTTGATTGCAGCATCGGTTTGAAT AAACAGATTCCTTGATTGCAAATTAGGATTTGCAGAACGTTGCAATCCA CTTACAATACCTGCTGTAACTGTAAAACTAAATTGAAAAGGGCTGCCCA CTGCCATAACCCAATCACCTATTTCAAGCTTATCACTATCTCCAAGATC AGCTACTTTAATAGTTGCGTCATCACTTTCAAAGCTAATAAGGGCAATA TCCTTTTTTTCATCTTTGCCAATTAACTTAGCCTTGTGCTTTTTTTTAT CATAAGATACAACTTCAAGTTCAGTTGCCTTATCTACCACATGACTATT CGTAACCACATAAAATAATGATTTTTTTTGAGAATCTCTACCAATTATT ACTCCAGACCCCGCCAATTGCTTTTTCTCTCAGAATCAAATTCTGGCAT ATCAAAAAAGAAAAATGGAATAGGAAAACTCTGCTTGATTACCCCTGTT GCATGAACTTCCACAGATGATGGTAAAATTTTCTTGGAAACCTCTCTAA AAGAATCTTGTAAGGCTCGTACGGTATTGTCCTTTTCTTCTGCAAAAAC AATGTTGCTTCTATTAGAAGCTAAATAATGCATCCCAATAAAAAATCCA ATACTCAAAGCCAAAAAACTAAGAAGAAATCCAGAAAAAAACTTTTTTT CCAC

(378) SEQ ID NO:3 Borrelia burgdorferi HtrA (BB0104, BbHtrA.sup.S226A) amino acid sequence. Mutation site S.fwdarw.A is at position 226. In this sequence the signal peptide is amino acids 1-37 and the mature protein is amino acid 38-474.

(379) TABLE-US-00015 MEKKFFSGFLLSFLALSIGFFIGMHYLASNRSNIVFAEEKDNTVRALQD SFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEFDSERKSNWAGS GVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKHKAKLIGKDEK KDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQFSFTVTAGI VSGLQRSANPNLQSRNLFIQTDAAINRGNAGGPLVNIKGEVIGINAWIA SNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYPLKTRDSE VLKSLGVESNDVSAAIIASLYPGSPAVKSGLRAGDIIMKVNGVSMSVFQ DVTSYISDFYAGEKVNVEILRGNVKKNIEIVLAVRPKDKELSSSKMLPG FVVYPLVEDIAKQLNLRNWIKGVVVDYIDKNLASNIKMKSGDVILSVNS KSVSNLREFYDALEVGKNTYKILRGNDSFKITF

(380) SEQ ID NO:4 Borrelia burgdorferi HtrA (BB0104, BbHtrA.sup.S226A) Nucleic Acid Sequence

(381) TABLE-US-00016 CTAAAATGTAATTTTAAAAGAATCGTTTCCTCTCAAAATTTTATAAGTAT TTTTTCCAACCTCAAGAGCATCATAAAATTCTCTTAAATTAGAAACACTT TTTGAATTTACAGAAAGAATTACATCTCCTGATTTCATTTTAATATTTGA TGCTAAATTTTTATCAATATAATCAACAACAACACCTTTAATCCAATTTC TTAAATTAAGCTGAGCTTTAATATCCTCAACCAATGGATACACAACAAAG CCTGGAAGCATCTTTGAAGAAGAAAGCTCTTTATCCTTAGGTCTAACAGC AAGAACAATCTCAATATTTTTTTTGACATTGCCTCTTAAGATTTCTACAT TTACTTTCTCACCAGCATAAAAATCACTAATATATGATGTAACATCTTGA AAAACGCTCATGGAAACCCCATTAACCTTCATAATAATATCCCCTGCCCT AAGCCCTGATTTAACAGCGGGTGAACCCGGATAAAGAGAAGCAATAATTG CAGCTGAAACATCATTACTTTCAACCCCTAAGCTTTTTAGCACCTCAGAA TCTCTTGTCTTTAGCGGATAAAAAGAAATTCCAAGCCAAGCCGATTCAAT TTTTTTACCTTTAAGGAAAAAATCTACAGTGCTTTTAATATTGTTAACAG GAATTGCAAAACCCAACCCAATATTTCCGCCAGAATTTGAAGCTATCCAA GCATTAATTCCAATAACCTCGCCCTTTATATTTACAAGAGGACCACCTGC ATTACCCCTGTTGATTGCAGCATCGGTTTGAATAAACAGATTCCTTGATT GCAAATTAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTA ACTGTAAAACTAAATTGAAAAGGGCTGCCCACTGCCATAACCCAATCACC TATTTCAAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCGT CATCACTTTCAAAGCTAATAAGGGCAATATCCTTTTTTTCATCTTTGCCA ATTAACTTAGCCTTGTGCTTTTTTTTATCATAAGATACAACTTCAAGTTC AGTTGCCTTATCTACCACATGACTATTCGTAACCACATAAAATAATGATT TTTTTTGAGAATCTCTACCAATTATTACTCCAGACCCCGCCAATTGCTTT TTCTCTCAGAATCAAATTCTGGCATATCAAAAAGAAAAATGGAATAGGAA AACTCTGCTTGATTACCCCTGTTGCATGAACTTCCACAGATGATGGTAAA ATTTTCTTGGAAACCTCTCTAAAAGAATCTTGTAAGGCTCGTACGGTATT GTCCTTTTCTTCTGCAAAAACAATGTTGCTTCTATTAGAAGCTAAATAAT GCATCCCAATAAAAAATCCAATACTCAAAGCCAAAAAACTAAGAAGAAAT CCAGAAAAAAACTTTTTTTCCAC

(382) SEQ ID NO:5 Borrelia garinii HtrA (BG0105) Amino Acid Sequence

(383) TABLE-US-00017 MEKKFFSGFILSFLALGIGFFIGMHYLDSNRSNIVFAEEKDNTVQALQD SFREVSKKILSSSVEVHATGVIKQSFPIPFFFFDMPEFDSERKSNWAGS GVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKHKAKLIGKDEK KDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQFSFTVTAGI VSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNIKGEVIGINAWIA SNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYPLKTRDSE VLKSLGVEGKDVSAAIIASLYPGSPAVKSGLKAGDIIVKVNGVSMSVFQ DVTSYISDFYAGEKVNVEILRGNVKKNIEIVLAVRPKDKELSSSKMLPG FIVYPLVEDIKAQLNLRNWIKGVVVDYIDKNLASNIKMKSGDVILSVNS QSVSNLREFYDALKIGKNTYKILRGNDSFKISF

(384) SEQ ID NO:6 Borrelia garinii HtrA (BG0105) Nucleic Acid Sequence

(385) TABLE-US-00018 CTAAAACGAAATTTTAAAAGAATCATTTCCTCTTAAAATTTTATAAGTA TTTTTTCCAATCTTAAGAGCATCATAAAATTCTCTTAAATTAGAAACAC TTTGTGAATTTACAGAAAGAATCACATCTCCTGATTTCATCTTAATATT TGATGCTAAATTTTTATCAATATAATCAACAACAACGCCTTTAATCCAA TTTCTTAAATTAAGCTGAGCTTTAATATCCTCAACTAATGGATACACAA TAAAACCTGGAAGCATTTTGGAAGAAGAAGTTCTTTATCCTTAGGTCTA ACAGCAAGAACAATCTCAATATTTTTTTTGACATTACCTCTTAAAATTT CTACATTTACTTTCTCACCAGCATAAAAATCGCTAATATATGATGTAAC ATCTTGAAAAACACTCATAGAAACCCCATTAACCTTAACAATAATATCG CCTGCTTTAAGCCCTGACTTAACGGCAGGTGAACCTGGATAAAGAGAGG CAATAATTGCAGCTGAAACATCCTTACCTTCAACTCCTAAGCTTTTTAG TACTTCAGAATCTCTTGTCTTTAAAGGATAAAAAGAAATTCCAAGCCAT GCTGATTCAATTTTTTTACCTTTAAGAAAAAAATCTACAGTACTTTTAA TATTATTAACAGGAATTGCAAAACCTAACCCAATATTTCCTCCAGAATT TGAAGCTATCCAAGCATTAATTCCAATAACTTCACCTTTTATATTTACA AGAGGACCGCCTGAATTACCTCTGTTGATTGCAGCATCAGTTTGAATAA ATAAATGCTGTAACTGTAAAACTAAATTGAAAAGGACTACCTACTGCCA TAACCCAATCACCTATTTCAAGCTTATCACTATCTCCAAGATCAGCTAC TTTAATAGTTGCATCATCACTTTCAAAGCTAATAAGAGCAATATCTTTT TTTTCATCTTTGCCAATTAACTTAGCCTTGTGCTTTTTTTTATCATAAG ACACAACTTCAAGTTCAGTTGCCTTATCTACTACATGACTATTTGTAAC CACATAAAATAATGATTTTTTTTGAGAATCCCACCAATTATTACTCCAG ACCCTGCCCAATTGCTTTTTCTCTCAGAATCAAATTCTGGCATATCAAA AAAGAAAAATGGAATAGGAAAACTCTGTTTAATTACCCCGGTTGCATGA ACTTCTACGGACGATGATAAAATTTTCTTGGAAACTTCCCTAAAAGAAT CTTGTAAGGCTTGTACTGTATTGTCTTTTTCTTCTGCAAAAACAATATT GCTTCTATTAGAATCTAAGTAATGCATTCCAATAAAAAAACCAATACCT AAAGCCAAAAAACTGAGAATAAATCCAGAAAAAAACTTTTTTTCCAC

(386) SEQ ID NO:7 Borrelia afzelii HtrA (BafACA1_0105) Amino Acid Sequence

(387) TABLE-US-00019 MEKKFFSGFILSFLALGIGFFIGMHYLDSNRSNIVFAEEKGNTVQTLQD SFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEFDSERKSNWAGS GVIIGRDSKNKSLFYVVTNSHVVDKATELEVVSYDKKKHKAKLIGKDEK KDIALISFESDDATIKVADLGDSKDLEIGDWVMAVGSPFQFSFTVTAGI VSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNTKGEVIGINAWIA SNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYPLKTRDPE VLKSLGVEGDDVPAAIIASLYPGSPAIKSGLRAGDIIVKVNGVPMSVFQ DVTSYISDFYAGEKINVEILRGNVKKNIELLAVRPKDKELSSSKMFPGF FFVPLVEDIKAQLNLRNWTKGVVVDYIDKNLASNIKMKSGDVILSVNSK SVSNLREFYDALEIGKNTYNILRGNDSFKISF

(388) SEQ ID NO:8 Borrelia afzelii HtrA (BafACA1_0105) Nucleic Acid Sequence

(389) SEQ ID NO:9 Borrelia burgdorferi HtrA (BB0104, BbHtrA) amino acid sequence without signal peptide, Catalytic triad is at amino acid positions corresponding to 119H, 149D and 226S in the full-length protein; here Catalytic triad is at amino acid positions 82H, 112D and 189S.

(390) TABLE-US-00020 EEKDNTVRALQDSFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPE FDSERKSNWAGSGVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKK KHKAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGS PFQFSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNI KGEVIGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLG ISFYPLKTRDSEVLKSLGVESNDVSAAIIASLYPGSPAVKSGLRAGDII MKVNGVSMSVFQDVTSYISDFYAGEKVNVEILRGNVKKNIEIVLAVRPK DKELSSSKMLPGFVVYPLVEDIAKQLNLRNWIKGVVVDYIDKNLASNIK MKSGDVILSVNSKSVSNLREFYDALEVGKNTYKILRGNDSFKITF

(391) SEQ ID NO:10 Borrelia burgdorferi HtrA (BB0104, BbHtrA) Nucleic Acid Sequence without Signal Peptide

(392) TABLE-US-00021 CTAAAATGTAATTTTAAAAGAATCGTTTCCTCTCAAAATTTTATAAGTAT TTTTTCCAACCTCAAGAGCATCATAAAATTCTCTTAAATTAGAAACACTT TTTGAATTTACAGAAAGAATTACATCTCCTGATTTCATTTTAATATTTGA TGCTAAATTTTTATCAATATAATCAACAACAACACCTTTAATCCAATTTC TTAAATTAAGCTGAGCTTTAATATCCTCAACCAATGGATACACAACAAAG CCTGGAAGCATCTTTGAAGAAGAAAGCTCTTTATCCTTAGGTCTAACAGC AAGAACAATCTCAATATTTTTTTTGACATTGCCTCTTAAGATTTCTACAT TTACTTTCTCACCAGCATAAAAATCACTAATATATGATGTAACATCTTGA AAAACGCTCATGGAAACCCCATTAACCTTCATAATAATATCCCCTGCCCT AAGCCCTGATTTAACAGCGGGTGAACCCGGATAAAGAGAAGCAATAATTG CAGCTGAAACATCATTACTTTCAACCCCTAAGCTTTTTAGCACCTCAGAA TCTCTTGTCTTTAGCGGATAAAAAGAAATTCCAAGCCAAGCCGATTCAAT TTTTTTACCTTTAAGGAAAAAATCTACAGTGCTTTTAATATTGTTAACAG GAATTGCAAAACCCAACCCAATATTTCCGCCAGAATTTGAAGCTATCCAA GCATTAATTCCAATAACCTCGCCCTTTATATTTACAAGAGGACCACCTGA ATTACCCCTGTTGATTGCAGCATCGGTTTGAATAAACAGATTCCTTGATT GCAAATTAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTA ACTGTAAAACTAAATTGAAAAGGGCTGCCCACTGCCATAACCCAATCACC TATTTCAAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCGT CATCACTTTCAAAGCTAATAAGGGCAATATCCTTTTTTTCATCTTTGCCA ATTAACTTAGCCTTGTGCTTTTTTTTATCATAAGATACAACTTCAAGTTC AGTTGCCTTATCTACCACATGACTATTCGTAACCACATAAAATAATGATT TTTTTTGAGAATCTCTACCAATTATTACTCCAGACCCCGCCCAATTGCTT TTTCTCTCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGG AAAACTCTGCTTGATTACCCCTGTTGCATGAACTTCCACAGATGATGGTA AAATTTTCTTGGAAACCTCTCTAAAAGAATCTTGTAAGGCTCGTACGGTA TTGTCCTTTTCTTC

(393) SEQ ID NO: 11 Borrelia burgdorferi HtrA (BB0104, BbHtrA.sup.S226A) amino acid sequence without signal peptide. Mutation site S.fwdarw.A is at position 189, analogous to position 226 in the full-length protein.

(394) TABLE-US-00022 EEKDNTVRALQDSFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNAGGPLVNIKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDSEVLKSLGVESNDVSAAIIASLYPGSPAVKSGLRAGDIIMKVNGV SMSVFQDVTSYISDFYAGEKVNVEILRGNVKKNIEIVLAVRPKDKELSSS KMLPGFVVYPLVEDIKAQLNLRNWIKGVVVDYIDKNLASNIKMKSGDVIL SVNSKSVSNLREFYDALEVGKNTYKILRGNDSFKITF

(395) SEQ ID NO: 12 Borrelia burgdorferi HtrA (BB0104, BbHtrA.sup.S226A) Nucleic Acid Sequence without Signal Peptide

(396) TABLE-US-00023 CTAAAATGTAATTTTAAAAGAATCGTTTCCTCTCAAAATTTTATAAGTAT TTTTTCCAACCTCAAGAGCATCATAAAATTCTCTTAAATTAGAAACACTT TTTGAATTTACAGAAAGAATTACATCTCCTGATTTCATTTTAATATTTGA TGCTAAATTTTTATCAATATAATCAACAACAACACCTTTAATCCAATTTC TTAAATTAAGCTGAGCTTTAATATCCTCAACCAATGGATACACAACAAAG CCTGGAAGCATCTTTGAAGAAGAAAGCTCTTTATCCTTAGGTCTAACAGC AAGAACAATCTCAATATTTTTTTTGACATTGCCTCTTAAGATTTCTACAT TTACTTTCTCACCAGCATAAAAATCACTAATATATGATGTAACATCTTGA AAAACGCTCATGGAAACCCCATTAACCTTCATAATAATATCCCCTGCCCT AAGCCCTGATTTAACAGCGGGTGAACCCGGATAAAGAGAAGCAATAATTG CAGCTGAAACATCATTACTTTCAACCCCTAAGCTTTTTAGCACCTCAGAA TCTCTTGTCTTTAGCGGATAAAAAGAAATTCCAAGCCAAGCCGATTCAAT TTTTTTACCTTTAAGGAAAAAATCTACAGTGCTTTTAATATTGTTAACAG GAATTGCAAAACCCAACCCAATATTTCCGCCAGAATTTGAAGCTATCCAA GCATTAATTCCAATAACCTCGCCCTTTATATTTACAAGAGGACCACCTGC ATTACCCCTGTTGATTGCAGCATCGGTTTGAATAAACAGATTCCTTGATT GCAAATTAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTA ACTGTAAAACTAAATTGAAAAGGGCTGCCCACTGCCATAACCCAATCACC TATTTCAAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCGT CATCACTTTCAAAGCTAATAAGGGCAATATCCTTTTTTTCATCTTTGCCA ATTAACTTAGCCTTGTGCTTTTTTTTATCATAAGATACAACTTCAAGTTC AGTTGCCTTATCTACCACATGACTATTCGTAACCACATAAAATAATGATT TTTTTTGAGAATCTCTACCAATTATTACTCCAGACCCCGCCCAATTGCTT TTTCTCTCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGG AAAACTCTGCTTGATTACCCCTGTTGCATGAACTTCCACAGATGATGGTA AAATTTTCTTGGAAACCTCTCTAAAAGAATCTTGTAAGGCTCGTACGGTA TTGTCCTTTTCTTC

(397) SEQ ID NO:13 Borrelia garinii HtrA (BG0105) Amino Acid Sequence without Signal Peptide

(398) TABLE-US-00024 EEKDNTVQALQDSFREVSKKILSSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNIKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDSEVLKSLGVEGKDVSAAIIASLYPGSPAVKSGLKAGDIIVKVNGV SMSVFQDVTSYISDFYAGEKVNVEILRGNVKKNIEIVLAVRPKDKELSSS KMLPGFIVYPLVEDIKAQLNLRNWIKGVVVDYIDKNLASNIKMKSGDVIL SVNSQSVSNLREFYDALKIGKNTYKILRGNDSFKISF

(399) SEQ ID NO: 14 Borrelia garinii HtrA (BG0105) Nucleic Acid Sequence Encoding the Protein without the Signal Peptide

(400) TABLE-US-00025 CTAAAACGAAATTTTAAAAGAATCATTTCCTCTTAAAATTTTATAAGTAT TTTTTCCAATCTTAAGAGCATCATAAAATTCTCTTAAATTAGAAACACTT TGTGAATTTACAGAAAGAATCACATCTCCTGATTTCATCTTAATATTTGA TGCTAAATTTTTATCAATATAATCAACAACAACGCCTTTAATCCAATTTC TTAAATTAAGCTGAGCTTTAATATCCTCAACTAATGGATACACAATAAAA CCTGGAAGCATTTTGGAAGAAGAAAGTTCTTTATCCTTAGGTCTAACAGC AAGAACAATCTCAATATTTTTTTTGACATTACCTCTTAAAATTTCTACAT TTACTTTCTCACCAGCATAAAAATCGCTAATATATGATGTAACATCTTGA AAAACACTCATAGAAACCCCATTAACCTTAACAATAATATCGCCTGCTTT AAGCCCTGACTTAACGGCAGGTGAACCTGGATAAAGAGAGGCAATAATTG CAGCTGAAACATCCTTACCTTCAACTCCTAAGCTTTTTAGTACTTCAGAA TCTCTTGTCTTTAAAGGATAAAAAGAAATTCCAAGCCATGCTGATTCAAT TTTTTTACCTTTAAGAAAAAAATCTACAGTACTTTTAATATTATTAACAG GAATTGCAAAACCTAACCCAATATTTCCTCCAGAATTTGAAGCTATCCAA GCATTAATTCCAATAACTTCACCTTTTATATTTACAAGAGGACCGCCTGA ATTACCTCTGTTGATTGCAGCATCAGTTTGAATAAATAAATTCCTTGATT GTAAATTAGGATTTGCAGAGCGTTGTAATCCACTTACAATACCTGCTGTA ACTGTAAAACTAAATTGAAAAGGACTACCTACTGCCATAACCCAATCACC TATTTCAAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCAT CATCACTTTCAAAGCTAATAAGAGCAATATCTTTTTTTTCATCTTTGCCA ATTAACTTAGCCTTGTGCTTTTTTTTATCATAAGACACAACTTCAAGTTC AGTTGCCTTATCTACTACATGACTATTTGTAACCACATAAAATAATGATT TTTTTTGAGAATCCCTACCAATTATTACTCCAGACCCTGCCCAATTGCTT TTTCTCTCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGG AAAACTCTGTTTAATTACCCCGGTTGCATGAACTTCTACGGACGATGATA AAATTTTCTTGGAAACTTCCCTAAAAGAATCTTGTAAGGCTTGTACTGTA TTGTCTTTTTCTTC

(401) TABLE-US-00026 EEKGNTVQTLQDSFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSKNKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNTKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDPEVLKSLGVEGDDVPAAIIASLYPGSPAIKSGLRAGDIIVKVNGV PMSVFQDVTSYISDFYAGEKINVEILRGNVKKNIEIILAVRPKDKELSSS KMFPGFVVYPLVEDIKAQLNLRNWTKGVVVDYIDKNLASNIKMKSGDVIL SVNSKSVSNLREFYDALEIGKNTYNILRGNDSFKISF

(402) SEQ ID NO:16 Borrelia afzelii HtrA (BafACA1_0105) Nucleic Acid Sequence without Signal Peptide

(403) TABLE-US-00027 CTAAAACGAAATTTTAAAAGAATCGTTTCCTCTTAAAATGTTATAAGTAT TTTTTCCAATCTCAAGAGCATCATAAAATTCTCTTAAATTAGAAACACTT TTTGAATTTACAGAAAGAATTACATCTCCTGATTTCATCTTAATATTTGA TGCTAAATTTTTATCAATATAATCAACAACAACGCCTTTAGTCCAATTTC TTAAATTAAGCTGAGCTTTAATATCTTCAACTAATGGATACACAACAAAA CCTGGAAACATTTTTGAAGAAGAAAGCTCTTTGTCCTTGGGTCTAACAGC AAGAATAATCTCAATATTCTTTTTAACATTACCTCTTAAAATTTCTACAT TGATTTTCTCACCAGCATAAAAATCGCTAATATATGATGTAACGTCTTGA AAAACACTCATGGGAACTCCATTAACCTTCACAATAATGTCTCCCGCTCT AAGCCCTGACTTAATAGCAGGTGAACCTGGATAAAGAGAAGCAATAATTG CAGCTGGAACATCATCACCTTCAACCCCCAAGCTTTTTAGCACTTCAGGA TCTCTTGTCTTTAATGGGTAAAAAGAAATTCCAAGCCATGCTGATTCAAT TTTTTTACCTTTAAGGAAAAAATCTACGGTACTTTTAATATTGTTAACAG GAATTGCAAAACCTAACCCAATATTTCCACCAGAATTTGAAGCTATCCAA GCATTAATCCCAATAACTTCACCTTTTGTATTTACAAGAGGTCCACCTGA ATTACCTCTATTGATTGCAGCATCAGTTTGAATAAATAAATTTCTTGATT GTAAATTAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTA ACTGTAAAACTAAATTGAAAAGGGCTACCTACCGCCATAACCCAATCACC TATTTCAAGCTTATCACTATCCCCAAGATCAGCCACTTTAATAGTTGCAT CATCACTTTCAAAGCTAATAAGCGCAATATCCTTTTTTTCATCTTTGCCA ATTAACTTAGCCTTATGCTTTTTCTTATCATAAGATACAACTTCAAGTTC AGTTGCCTTATCTACTACATGACTATTGGTAACTACATAAAATAATGATT TATTTTTGGAATCTCTACCAATTATTACTCCAGACCCTGCCCAATTGCTT TTTCTCTCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGG AAAACTCTGCTTAATTACCCCTGTTGCATGAACTTCTACAGATGATGGTA AAATTTTCTTGGAAACTTCTCTAAAAGAGTCTTGCAAGGTTTGTACTGTA TTACCCTTTTCTTC

(404) SEQ ID NO:17 Borrelia burgdorferi HtrA (BB0104, BbHtrA) amino acid sequence without signal peptide, without the PDZ2 domain, Catalytic triad is at amino acid positions corresponding to 119H, 149D and 226S in the full-length protein, here Catalytic triad is at amino acid positions 82H, 112D and 189S.

(405) TABLE-US-00028 EEKDNTVRALQDSFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNIKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDSEVLKSLGVESNDVSAAIIASLYPGSPAVKSGLRAGDIIMKVNGV SMSVFQDVTSYISDFYAGEKVNVEILRGNVKKNIEI

(406) SEQ ID NO:18 Borrelia burgdorferi HtrA (BB0104, BbHtrA) nucleic acid sequence encoding the protein without the signal peptide and without the PDZ2 domain.

(407) TABLE-US-00029 AATCTCAATATTTTTTTTGACATTGCCTCTTAAGATTTCTACATTTACTT TCTCACCAGCATAAAAATCACTAATATATGATGTAACATCTTGAAAAACG CTCATGGAAACCCCATTAACCTTCATAATAATATCCCCTGCCCTAAGCCC TGATTTAACAGCGGGTGAACCCGGATAAAGAGAAGCAATAATTGCAGCTG AAACATCATTACTTTCAACCCCTAAGCTTTTTAGCACCTCAGAATCTCTT GTCTTTAGCGGATAAAAAGAAATTCCAAGCCAAGCCGATTCAATTTTTTT ACCTTTAAGGAAAAAATCTACAGTGCTTTTAATATTGTTAACAGGAATTG CAAAACCCAACCCAATATTTCCGCCAGAATTTGAAGCTATCCAAGCATTA ATTCCAATAACCTCGCCCTTTATATTTACAAGAGGACCACCTGAATTACC CCTGTTGATTGCAGCATCGGTTTGAATAAACAGATTCCTTGATTGCAAAT TAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTAACTGTA AAACTAAATTGAAAAGGGCTGCCCACTGCCATAACCCAATCACCTATTTC AAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCGTCATCAC TTTCAAAGCTAATAAGGGCAATATCCTTTTTTTCATCTTTGCCAATTAAC TTAGCCTTGTGCTTTTTTTTATCATAAGATACAACTTCAAGTTCAGTTGC CTTATCTACCACATGACTATTCGTAACCACATAAAATAATGATTTTTTTT GAGAATCTCTACCAATTATTACTCCAGACCCCGCCCAATTGCTTTTTCTC TCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGGAAAACT CTGCTTGATTACCCCTGTTGCATGAACTTCCACAGATGATGGTAAAATTT TCTTGGAAACCTCTCTAAAAGAATCTTGTAAGGCTCGTACGGTATTGTCC TTTTCTTC

(408) SEQ ID NO:19 Borrelia burgdorferi HtrA (BB0104, BbHtrA.sup.S226A) amino acid sequence without signal peptide, without PDZ2. Mutation site S-A is at position 189, analogous to position 226 in the full-length protein.

(409) TABLE-US-00030 EEKDNTVRALQDSFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNAGGPLVNIKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDSEVLKSLGVESNDVSAAIIASLYPGSPAVKSGLRAGDIIMKVNGV SMSVFQDVTSYISDFYAGEKVNVEILRGNVKKNIEI

(410) SEQ ID NO:20 Borrelia burgdorferi HtrA (BB0104, BbHtrA.sup.S226A) nucleic acid sequence encoding the protein without the signal peptide and without the PDZ2 domain.

(411) TABLE-US-00031 AATCTCAATATTTTTTTTGACATTGCCTCTTAAGATTTCTACATTTACTT TCTCACCAGCATAAAAATCACTAATATATGATGTAACATCTTGAAAAACG CTCATGGAAACCCCATTAACCTTCATAATAATATCCCCTGCCCTAAGCCC TGATTTAACAGCGGGTGAACCCGGATAAAGAGAAGCAATAATTGCAGCTG AAACATCATTACTTTCAACCCCTAAGCTTTTTAGCACCTCAGAATCTCTT GTCTTTAGCGGATAAAAAGAAATTCCAAGCCAAGCCGATTCAATTTTTTT ACCTTTAAGGAAAAAATCTACAGTGCTTTTAATATTGTTAACAGGAATTG CAAAACCCAACCCAATATTTCCGCCAGAATTTGAAGCTATCCAAGCATTA ATTCCAATAACCTCGCCCTTTATATTTACAAGAGGACCACCTGCATTACC CCTGTTGATTGCAGCATCGGTTTGAATAAACAGATTCCTTGATTGCAAAT TAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTAACTGTA AAACTAAATTGAAAAGGGCTGCCCACTGCCATAACCCAATCACCTATTTC AAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCGTCATCAC TTTCAAAGCTAATAAGGGCAATATCCTTTTTTTCATCTTTGCCAATTAAC TTAGCCTTGTGCTTTTTTTTATCATAAGATACAACTTCAAGTTCAGTTGC CTTATCTACCACATGACTATTCGTAACCACATAAAATAATGATTTTTTTT GAGAATCTCTACCAATTATTACTCCAGACCCCGCCCAATTGCTTTTTCTC TCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGGAAAACT CTGCTTGATTACCCCTGTTGCATGAACTTCCACAGATGATGGTAAAATTT TCTTGGAAACCTCTCTAAAAGAATCTTGTAAGGCTCGTACGGTATTGTCC TTTTCTTC

(412) SEQ ID NO:21 Borrelia garinii HtrA (BG0105) amino acid sequence without the signal peptide and without the PDZ2 domain.

(413) TABLE-US-00032 EEKDNTVQALQDSFREVSKKILSSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSQKKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNIKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDSEVLKSLGVEGKDVSAAIIASLYPGSPAVKSGLKAGDIIVKVNGV SMSVFQDVTSYISDFYAGEKVNVEILRGNVKKNIEI

(414) SEQ ID NO:22 Borrelia garinii HtrA (BG0105) nucleic acid sequence, encoding the protein without the signal peptide and without the PDZ2 domain.

(415) TABLE-US-00033 AATCTCAATATTTTTTTTGACATTACCTCTTAAAATTTCTACATTTACTT TCTCACCAGCATAAAAATCGCTAATATATGATGTAACATCTTGAAAAACA CTCATAGAAACCCCATTAACCTTAACAATAATATCGCCTGCTTTAAGCCC TGACTTAACGGCAGGTGAACCTGGATAAAGAGAGGCAATAATTGCAGCTG AAACATCCTTACCTTCAACTCCTAAGCTTTTTAGTACTTCAGAATCTCTT GTCTTTAAAGGATAAAAAGAAATTCCAAGCCATGCTGATTCAATTTTTTT ACCTTTAAGAAAAAAATCTACAGTACTTTTAATATTATTAACAGGAATTG CAAAACCTAACCCAATATTTCCTCCAGAATTTGAAGCTATCCAAGCATTA ATTCCAATAACTTCACCTTTTATATTTACAAGAGGACCGCCTGAATTACC TCTGTTGATTGCAGCATCAGTTTGAATAAATAAATTCCTTGATTGTAAAT TAGGATTTGCAGAGCGTTGTAATCCACTTACAATACCTGCTGTAACTGTA AAACTAAATTGAAAAGGACTACCTACTGCCATAACCCAATCACCTATTTC AAGCTTATCACTATCTCCAAGATCAGCTACTTTAATAGTTGCATCATCAC TTTCAAAGCTAATAAGAGCAATATCTTTTTTTTCATCTTTGCCAATTAAC TTAGCCTTGTGCTTTTTTTTATCATAAGACACAACTTCAAGTTCAGTTGC CTTATCTACTACATGACTATTTGTAACCACATAAAATAATGATTTTTTTT GAGAATCCCTACCAATTATTACTCCAGACCCTGCCCAATTGCTTTTTCTC TCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGGAAAACT CTGTTTAATTACCCCGGTTGCATGAACTTCTACGGACGATGATAAAATTT TCTTGGAAACTTCCCTAAAAGAATCTTGTAAGGCTTGTACTGTATTGTCT TTTTCTTC

(416) SEQ ID NO:23 Borrelia afzelii HtrA (BafACA1_0105) amino acid sequence without signal peptide, without the PDZ2 domain.

(417) TABLE-US-00034 EEKGNTVQTLQDSFREVSKKILPSSVEVHATGVIKQSFPIPFFFFDMPEF DSERKSNWAGSGVIIGRDSKNKSLFYVVTNSHVVDKATELEVVSYDKKKH KAKLIGKDEKKDIALISFESDDATIKVADLGDSDKLEIGDWVMAVGSPFQ FSFTVTAGIVSGLQRSANPNLQSRNLFIQTDAAINRGNSGGPLVNTKGEV IGINAWIASNSGGNIGLGFAIPVNNIKSTVDFFLKGKKIESAWLGISFYP LKTRDPEVLKSLGVEGDDVPAAIIASLYPGSPAIKSGLRAGDIIVKVNGV PMSVFQDVTSYISDFYAGEKINVEILRGNVKKNIEI

(418) SEQ ID NO:24 Borrelia afzelii HtrA (BafACA1_0105) nucleic acid sequence without signal peptide, without the PDZ2 domain.

(419) TABLE-US-00035 AATCTCAATATTCTTTTTAACATTACCTCTTAAAATTTCTACATTGATTT TCTCACCAGCATAAAAATCGCTAATATATGATGTAACGTCTTGAAAAACA CTCATGGGAACTCCATTAACCTTCACAATAATGTCTCCCGCTCTAAGCCC TGACTTAATAGCAGGTGAACCTGGATAAAGAGAAGCAATAATTGCAGCTG GAACATCATCACCTTCAACCCCCAAGCTTTTTAGCACTTCAGGATCTCTT GTCTTTAATGGGTAAAAAGAAATTCCAAGCCATGCTGATTCAATTTTTTT ACCTTTAAGGAAAAAATCTACGGTACTTTTAATATTGTTAACAGGAATTG CAAAACCTAACCCAATATTTCCACCAGAATTTGAAGCTATCCAAGCATTA ATCCCAATAACTTCACCTTTTGTATTTACAAGAGGTCCACCTGAATTACC TCTATTGATTGCAGCATCAGTTTGAATAAATAAATTTCTTGATTGTAAAT TAGGATTTGCAGAACGTTGCAATCCACTTACAATACCTGCTGTAACTGTA AAACTAAATTGAAAAGGGCTACCTACCGCCATAACCCAATCACCTATTTC AAGCTTATCACTATCCCCAAGATCAGCCACTTTAATAGTTGCATCATCAC TTTCAAAGCTAATAAGCGCAATATCCTTTTTTTCATCTTTGCCAATTAAC TTAGCCTTATGCTTTTTCTTATCATAAGATACAACTTCAAGTTCAGTTGC CTTATCTACTACATGACTATTGGTAACTACATAAAATAATGATTTATTTT TGGAATCTCTACCAATTATTACTCCAGACCCTGCCCAATTGCTTTTTCTC TCAGAATCAAATTCTGGCATATCAAAAAAGAAAAATGGAATAGGAAAACT CTGCTTAATTACCCCTGTTGCATGAACTTCTACAGATGATGGTAAAATTT TCTTGGAAACTTCTCTAAAAGAGTCTTGCAAGGTTTGTACTGTATTACCC TTTTCTTC

(420) Any patents or publications mentioned in this specification are incorporated herein by reference to the same extent as if each individual publication is specifically and individually indicated to be incorporated by reference.

(421) The compositions and methods described herein are presently representative of preferred embodiments, exemplary, and not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art. Such changes and other uses can be made without departing from the scope of the invention as set forth in the claims.