Methods of generating and screening for lytic chimeric polypeptides

Abstract

The present invention relates to novel methods of generating and screening for chimeric polypeptides, which can be used in the treatment and prophylaxis of pathogenic bacterial contamination, colonisation and infection. The novel methods are based on random recombination of protein domains, and the chimeric polypeptides obtainable by the methods according to the invention are characterized in that they comprise at least one enzymatic active domain (EAD) and at least one cell binding domain (CBD). The present invention also relates to a library of chimeric polypeptides obtainable by the methods of the present invention.

Claims

1. A method of generating a chimeric polypeptide having at least one cell binding domain (CBD) and at least one enzymatic active domain (EAD), the method comprising the steps of: (a) providing one or more DNA sequences each encoding at least one CBD and one or more DNA sequences each encoding at least one EAD, and optionally one or more DNA sequences each encoding at least one CBD and at least one EAD, wherein the EAD is selected from the group consisting of (i) the lytic domain of a bacteriophage lysin; and (ii) a bacteriophage tail-associated protein having lytic activity; (b) amplifying a first (1.sup.st) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce different restriction sites at the 5-end and at the 3-end, and a tag labeling at the 5-end or at the 3-end; (c) amplifying a second (2.sup.nd) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce: (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the first domain, and at the 3-end a restriction site different from the restriction sites introduced into the 1.sup.st domain sequence, (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the 1.sup.st domain, and at the 5-end a restriction site different from the restriction sites introduced into the 1.sup.st domain sequence; (d) amplifying a third (3.sup.rd) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce: (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the preceding 2.sup.nd domain, and at the 3-end a restriction site that is different from that at the 5-end of the 1.sup.st domain, (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the preceding 2.sup.nd domain, and at the 5-end a restriction site that is different from that at the 3-end of the 1.sup.st domain; wherein the pair of primers is further designed such that the restriction sites are different at the 5-end and the 3-end of the 3.sup.rd domain sequence; (e) optionally amplifying one or more further domain sequences selected from the domain sequences of (a) for extending the series of domain sequences according to steps (b) to (d), using for each of said one or more further domain sequences a pair of primers designed following the principle of steps (c) and (d) so as to introduce: (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the preceding domain, and at the 3-end a restriction site that is different from that at the 5-end of the 1.sup.st domain, (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the preceding domain, and at the 5-end a restriction site that is different from that at the 3-end of the 1.sup.st domain; wherein the pair of primers is further designed such that the restriction sites are different at the 5-end and the 3-end of each of said one or more further domain sequences; (f) performing a restriction digest of the amplified domain sequences of any of steps (b) to (e) using restriction enzymes targeting the restriction sites introduced in any of steps (b) to (e), wherein a restriction digest is not performed on the restriction site introduced to an end carrying a tag labelling; (g) ligating the digested 1.sup.st and 2.sup.nd domain sequence obtained in step (f) to obtain a ligation product comprising the 1.sup.st and 2.sup.nd domain sequence; (h) binding the ligation products of step (g) to a solid support using the tag labeling of the 1.sup.st domain sequence to obtain a bound ligation product comprising the 1.sup.st and 2.sup.nd domain sequence; (j) optionally ligating the digested 3.sup.rd domain sequence of (d) obtained in step (f) to the bound ligation product of step (h) to obtain a bound ligation product comprising the 1.sup.st, 2.sup.nd and 3.sup.rd domain sequence; (k) optionally ligating one or more digested domain sequences of (e) obtained in step (f) to the bound ligation product of step (j) to obtain a bound ligation product comprising one or more further domain sequences of (e); (l) releasing the ligation product obtained in any one of steps (h) to (k) from the solid support; and (m) characterizing the ligation product obtained in step (l) and identifying chimeric polypeptides having at least one CBD and at least one EAD.

2. The method of claim 1, further comprising a washing step after binding the first ligation product to the solid support in step (h) to remove unbound ligation products and/or non-ligated domain sequences.

3. The method of claim 1, wherein steps (g) and (h) are replaced by a step of binding the digested 1.sup.st domain sequence to a solid support using the tag labeling at the 5-end or 3-end, respectively, and a subsequent step of ligating the digested 2.sup.nd domain sequence of (c) obtained in step (f) to the bound 1.sup.st domain sequence to obtain a bound ligation product comprising the 1.sup.st and 2.sup.nd domain sequence.

4. The method of claim 3, further comprising a step of removing unbound domain sequences after binding the first ligation product to the solid support, and optionally a further step of removing non-ligated domain sequences after ligating the second domain sequence to the bound first domain sequence.

5. The method of claim 1, further comprising a step of removing non-ligated domain sequences after each ligation step performed in steps (j) and (k).

6. The method of claim 1, wherein the domain sequences of (a) are cloned into a vector prior to amplification.

7. The method of claim 1, wherein the step of releasing the ligation product or ligation products from the solid support is carried out using a restriction enzyme targeting the restriction site at that end of the 1.sup.st domain, which is carrying the tag labelling.

8. The method of claim 1, wherein in case of repeated ligation steps optionally after any repeated ligation step part of the obtained bound ligation product is separated from the method prior to performing a subsequent ligation step.

9. The method of claim 1, wherein the solid support is a particle, a surface of a device, a foil or a fleece.

10. The method of claim 9, wherein the particle is a silica bead or an organic polymer bead being magnetic.

11. The method of claim 1, wherein step (a) further includes providing one or more DNA sequences each encoding at least one CBD and at least one EAD.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 shows a scheme of the modified cloning vector pET14b. The 5 end of the insert will be ligated to the NcoI site, the 3 end of the insert will be ligated to the SpeI site of the vector. Downstream of the SpeI site lies the sequence for the synthetic linker. For the insert carries no stop codon the translation will include the synthetic linker and a stop at a vector intrinsic codon behind the BamHI-site.

(2) FIG. 2 shows a scheme for the introduction of position specific restriction sites by position specific primer combinations. In particular, FIG. 2 shows the cloning vector pET14b with an insert (here: EAD) from NcoI to BamHI site. The forward PCR primer overlaps 3 with the insert and introduces for position 1 a NcoI site and a biotin tag, for position 2 a PstI site and for position 3 a SalI site. The reverse PCR primer overlaps 5 with the insert and introduces for position 1 a PstI site, for position 2 a SalI site and for position 3 a EcoRV site.

(3) FIG. 3: PCR of EAD500 with position specific primer combinations and thus restriction sites of position 1, 2 and 3. FIG. 3 shows the agarose gel with the PCR products of EAD500 of position 1, position 2 and position 3. The products were generated with the position specific PCR primers and the cloned EAD500 as template. The generated fragments have the same size but carry the different, position specific restriction sites.

(4) FIG. 4: Agarose gel analysis of S1, S2 and Beads. FIG. 4 shows a binding experiment of biotinylated and non-biotinylated DNA and streptavidin coated beads. The biotin tags can be cut off by NcoI digest. S1 is the supernatant after incubation of DNA with streptavidin coated beads and contains biotinylated DNA with 1400 bp and 600 bp as well as non-biotinylated DNA with 700 bp. The non-biotinylated DNA could not bind to the streptavidin beads because of the lack of a biotin tag. The biotinylated DNA exceeded the binding capacity of the streptavidin beads and was thus in the supernatant. The beads were washed and resuspended in buffer and a restriction digest with NcoI was performed. The supernatant was removed (=S2). S2 contains only DNA with 1400 bp and 600 bp. These fragments were biotinylated and could bind to the beads. The Beads themselves showed no DNA bands at the agarose gel.

(5) FIG. 5 shows the 16 possible constructs of the ligation of the 4 N-terminal EADs (EAD511, EADP35, EADP40 and EADPSA) combined with the 4 C-terminal CBDs (CBD006, CBD500, CBD511, CBDP40 variant A). In the random ligation every EAD should be ligated to every CBD.

(6) FIG. 6: PCR fragments of EADs and CBDs for position 1 and position 2, respectively. E: EAD, C: CBD. FIG. 6 shows an agarose gel with the PCR products of the EADs (E) for position 1 (EAD511: 640 bp, EADP40: 730 bp, EADPSA: 601 bp, EADP35: 505 bp) amplified with the specific primers for position 1 and the CBDs (C) for position 2 (CBD511: 550 bp, CBDP40 variant A: 463 bp, CBD500: 532 bp, CBD006: 337 bp) amplified with the specific primers for position 2.

(7) FIG. 7: Analysis of ligation and DNA-capture on 1.5% agarose gel. L: Ligation, NS: Supernatant after NcoI digest, D: pooled domains. FIG. 7 shows an agarose gel of the random ligation of the 4 N-terminal EADs and the 4 C-terminal CBDs. About 0.06 pmol of each fragment were applicated in lane D as indicated by the arrows. Lane L shows the ligation products with 0.06 pmol of each fragment. Lane NS shows the ligation products out of 0.06 pmol of each fragment that were captured via biotin tag by streptavidin coated beads and cut off the beads by NcoI.

(8) FIG. 8: Scheme of pQE60-lib with modified cloning site. FIG. 8 shows a scheme of the pQE60-lib vector. The multiple cloning site was adapted for cloning of inserts with an 5 NcoI site and a 3 PstI, SalI or EcoRV site. The translation begins with the ATG of the NcoI site and ends at a vector intrinsic stop codon between the EcoRV site and HindIII site.

(9) FIG. 9: Induced E. coli M15 cells show lysis after plasmid transformation and colony growth. FIG. 9 shows a lysis selection plate with induced endolysin expressing E. coli M15 tranformants. Transformed E. coli cells were plated on lysis plates with heat inactivated Listeria cells WSLC 2011 (Listeria innocua, serotype 6a). The lysis selection plate contains LB Top Agar, heat inactivated Listeria cells WSLC 2011 (Listeria innocua, serotype 6a), IPTG and Ampicillin. E. coli M15 were transformed with pQE60-lib carrying endolysins and plated. E. coli cells that express a soluble and active protein are surrounded by a clearance of the Listeria cells.

(10) FIG. 10: Confirmation of the 16 possible variants. FIG. 10 shows the confirmation of the 16 possible variants A to P of the 4 N-terminal EADs (EADP40, EADP35, EAD511, EADPSA) and the 4 C-terminal CBDs (CBD511, CBD500, CBDP40 variant A, CBD006). Colony PCR was performed with pQE forward and pQE reverse primer and digested at the PstI site where the domains were ligated together during the cloning procedure. The resulting fragments were analysed by agarose gel electrophoresis. The separated domains can be identified by the individual domain sizes. The domain sizes include also fragments from the domain borders to the priming sites of pQE forward and pQE reverse primer. CBDP40 means CBDP40-A construct of Table 1.

(11) FIG. 11 shows the SDS gel analysis of protein expression of the 16 variants A-P. All proteins have the correct size. Hence, the domain fragments are ligated correctly without frame shifts. The numeration is the same as in FIG. 10.

(12) FIG. 12: Lytic spectrum of the 16 variants follows the behaviour of corresponding CBDs.

(13) FIG. 12 shows the lytic behaviour of the variants A-P against Listeria serovars 6a (L. innocua WSLC2011), 1/2a (L. monocytogenes EGDe) and 4b (L. monocytogenes ScottA). The proteins behave corresponding to the CBD binding spectra: variants A, D, F and K have CBD511 and lyse all three serovars, the CBD511 binds all three serovars. Variants with CBD500 (B, E, G and L) lyse only serovars 6a and 4b, variants with CBD006 (I, M, O P) lyse mainly serovars 1/2a. Candidates with CBDP40 are not lytic active against the tested Listeria cells what means that this CBDP40-variant A is not functionable. Sv 6a: L. innocua WSLC2011, 1/2a: L. monocytogenes EGDe, 4b: L. monocytogenes ScottA.

(14) FIG. 13A-B: FIGS. 13A and 13B shows the claimed methods using either 5-labeling (FIG. 13A) or 3-labeling (FIG. 13B) of the 1.sup.st domain according to the first aspect of the invention. According to the first aspect of the invention, the claimed methods comprise performing a restriction digest on the amplified domain sequences of any of steps (b) to (e) with restriction enzymes targeting the restriction sites introduced in any of steps (b) to (e), wherein a restriction digest is not performed on the restriction site introduced to an end carrying a tag labelling.

(15) FIG. 14A-B: FIGS. 14A and 14B shows the claimed methods using either 5-labeling (FIG. 14A) or 3-labeling (FIG. 14B) of the 1.sup.st domain according to the second aspect of the invention. According to the second aspect of the invention, the claimed methods comprise performing a restriction digest on the domain sequences of any of steps (b) to (e) as follows:

(16) (i) in case of 5-end labelling of the 1.sup.st domain (FIG. 14A): performing a restriction digest of the domain sequence of step (b) with a restriction enzyme targeting the restriction site at the 3-end and performing a restriction digest of the domain sequences of any of steps (c) to (e) with restriction enzymes targeting the restriction sites at the 5-ends,

(17) (ii) in case of 3-end labelling of the 1.sup.st domain (FIG. 14B): performing a restriction digest of the domain sequence of step (b) with a restriction enzyme targeting the restriction site at the 5-end and performing a restriction digest of the domain sequences of any of steps (c) to (e) with restriction enzymes targeting the restriction sites at the 3-ends.

(18) Furthermore, according to the second aspect of the invention, the claimed methods further comprise performing a further restriction digest on the bound ligation product as follows:

(19) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the domain ligated to the bound ligation product,

(20) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5-end of the domain ligated to the bound ligation product.

DETAILED DESCRIPTION OF THE INVENTION

(21) The foregoing has outlined the features of various embodiments in order that the detailed description that follows may be better understood. Additional features and advantages of various embodiments will be described hereinafter which form the subject of the claims of the invention.

(22) The prior art describes lytic chimeric polypeptides, which may comprise a CBD and an EAD. WO 2010/020657 describes the combination of different fragments of polypeptides from different wild-type enzymes into new chimeric polypeptide constructs (shuffling). As mentioned therein, the fragments are combined by molecular biological methods on the nucleic acid level. There are several differences between WO 2010/020657 and the novel methods of the present invention. In particular, in contrast to WO 2010/020657 the methods of the present invention comprise the use of a solid support. This provides for an improvement of the efficiency and accuracy of the methods of generating and screening for a chimeric polypeptide according to the present invention. In addition, the use of a solid support provides for accelerating the generation of novel chimeric polypeptides. Furthermore, the methods of the present invention follow a cyclic process, which has the effect that only those constructs are formed that have the desired length, i.e., chimeric polypeptides having, for example, 3 or 4 domains. In connection with this it is of note that the constructs as such are not generated in a directed manner. That is, the sequence (i.e., chronological order) of the domains in the chimeric polypeptides obtained from the methods is not predetermined (combinatorial approach). Here, the approach followed in the prior art, in particular in WO 2010/020657, is completely different. In particular, in the chimeric polypeptides generated in the prior art the domains are predetermined (directed cloning approach), and the domains used in the cloning methods were known domains having specific favourable characteristics and advantageous properties/activities. This is not surprising given that it was desired in the prior art to combine EADs, which were known for their favourable lytic activity. In other words, the prior art was following the principle of considering which combination of known fully characterized domains may be desirous. In contrast, the domains applied in the methods of the present invention are independent of any such previous knowledge, even though of course known domain sequences may be applied to the methods of the present invention. However, basically there is no prior knowledge necessary with respect to the characteristics, the relative positions, and activities/properties of the domains applied in the methods of the present invention. The chimeric polypeptides obtained from the methods of the present invention are characterized using the lytic activity of the resulting constructs. Therefore, the claimed methods allow selecting those variants, which have desired superior properties. This approach followed by the methods of the present invention is a hypothesis-free approach (discovery-driven). There is no need to identify and characterize the domain sequences prior to conducting the methods of the present invention. This is in clear contrast to the prior art methods. The prior art neither teaches nor suggest or foreshadows the approach that is underlying the methods of the present invention.

(23) In essence, the methods of the present invention allow generating and screening for improved domain combinations that could not have been expected from considering the single domains in isolation. This effectiveness of the claimed methods has been demonstrated in the examples of the present application (Examples 5 and 6). Therefore, the present application provides evidence for the quality of the claimed methods. There is no method whatsoever in the prior art that would generate results similar to those achieved with the methods of the present invention.

(24) In addition, the following Table shows the number of variants that can be obtained with the methods of the present invention:

(25) TABLE-US-00001 Number of DNA possible 2- sequences domain possible 3- possible 4- (domains) variants domain variants domain variants Total 5 25 125 625 775 10 100 1000 10000 11100 20 400 8000 160000 168400 25 625 15625 390625 406875

(26) Therefore, the methods of the present invention provide for a rapid and accurate generation of all variants resulting from a specific number of DNA sequences applied to the methods.

(27) Enormous time-consuming, laborious efforts are required if all possible variants would have to be generated using conventional cloning methods.

(28) Furthermore, the methods of the present invention have the effect that undesired by-products are eliminated during the method steps, thereby providing for a high efficiency of the methods and improving the likelihood that all possible variants are present in the resulting library.

(29) In the present invention, the term CBD represents the abbreviation for cell binding domain, more specifically cell wall binding domain. Thus, the term CBD may also represent the abbreviation for cell wall binding domain. The terms cell binding domain and cell wall binding domain may be used interchangeably. The structural and functional definition of a CBD according to the present invention is given elsewhere in the description. In the present invention, EAD represents the abbreviation for enzymatic active domain. In the present invention, an EAD has lytic activity against bacteria. Thus, an EAD in accordance with the present invention can also be considered as a lytic domain. A more specific structural and functional definition of an EAD according to the present invention is given elsewhere here in the description. EADs in accordance with the present invention can be isolated from nature or can be produced by recombinant or synthetic means.

(30) In the literature, the terms bacteriophage lysins, phage endolysins, endolysins, virolysins and lysins are often interchangeably used. Thus, in the present invention, the terms bacteriophage lysins, phage endolysins, endolysins and lysins can be used interchangeably while defining the same kind of enzymes, namely bacterial cell wall-hydrolyzing enzymes synthesized during the late phase of gene expression in the lytic cycle of phage multiplication. By way of another definition, endolysin are enzymes encoded by double stranded (ds) DNA phage genomes that lyse bacterial cell walls. In general, in the present invention the term bacteriophage or phage means lytic bacteriophage or lysogenic bacteriophage (lytic phage or lysogenic phage).

(31) A phage or bacteriophage, as used herein, relates to the well-known category of viruses that infect bacteria. Phages include DNA or RNA sequences encapsidated in a protein envelope or coat (capsid).

(32) In the present invention, the term bacterium preferably describes a target bacterium, and refers to a bacterium that is bound by a chimeric polypeptide of the present invention and and/or whose growth, survival, or replication is inhibited by the enzymatic activity of an EAD in accordance with the present invention. Such a bacterium in accordance with the present invention is preferably a pathogenic bacterium. The inhibition of bacterial growth refers to the slowing or stopping of the rate of a bacteria cell's division or cessation of bacterial cell division, or to death of bacteria. The term target bacterium specifically includes both Gram-positive and Gram-negative target bacteria, preferably Gram-positive bacteria.

(33) In the present invention, a polypeptide obtainable by the claimed methods is chimeric because it comprises a combination of domains selected from CBDs and EADs, which is as such not found in nature. Preferably, the domains combined in a chimeric polypeptide obtainable by the methods of the present invention are of different source or origin. Thus, a chimeric polypeptide obtainable by the methods of the present invention may comprise a CBD and an EAD from the same source or origin, provided that the chimeric polypeptide comprises at least one further CBD and/or EAD from a different source or origin.

(34) Furthermore, a chimeric polypeptide obtainable by the methods of the present invention may comprise a CBD and an EAD from the same source or origin if the combination of domains from the same source or origin is as such not found in nature. In the present invention, the term heterologous may be used interchangeably with the term chimeric.

(35) In the present invention, the term domain(s) of different source or origin includes domain(s) of a different source or origin of organism and domain(s) of a different source or origin of enzyme.

(36) A chimeric polypeptide obtainable by the methods of the present invention may comprise more than one EAD and, thus, can act on different cell wall structures, and hence has the potential to treat two or more different bacterial infections at the same time.

(37) In the present invention, a pathogenic bacterial species is defined by the similarities found among its members. Properties such as biochemical reactions, chemical composition, cellular structures, genetic characteristics, and immunological features are used in defining a pathogenic bacterial species and thus differentiating different pathogenic bacterial species.

(38) An EAD in accordance with the present invention exhibits lytic activity against a bacterial cell. Thus, an EAD in accordance with the present invention exhibits the activity of inhibition of bacterial growth, including the slowing or stopping of the rate of cell division of bacteria or cessation of bacterial cell division, or to death of bacteria (killing colonizing bacteria).

(39) In various embodiments of the present invention, the EAD is the lytic domain of a bacteriophage endolysin, including bacteriophage endolysins against Gram-positive and Gram-negative bacteria. More preferably, the EAD is the lytic domain of a bacteriophage endolysin, wherein the endolysin is from a bacteriophage that infects a Gram-positive bacterium. In various embodiments the EAD is the lytic domain of a bacteriophage endolysin, wherein the endolysin is from a bacteriophage that infects a Gram-negative bacterium.

(40) As mentioned before, in the present invention bacteriophage lysins (or lysins) are bacterial cell wall-hydrolyzing enzymes synthesized during the late phase of gene expression in the lytic cycle of phage multiplication. As peptidoglycan is the major structural component of bacterial cell walls, in the present invention bacteriophage lysins are preferably peptidoglycan-hydrolysing enzymes. More preferably, in the present invention a bacteriophage lysine is a glycosidase, amidase, or endopeptidase, depending on the type of chemical bond they cleave within the peptidoglycan. Still more preferably, a bacteriophage lysine to be used in the present invention exhibits muramidase activity, glucosaminidase activity, or transglycosylase activity. Thus, in the present invention, a bacteriophage lysine provides at least one of the following enzymatic activities against a peptidoglycan substrate: muramidase activity, glucosaminidase activity, N-acetylmuramyl-L-alanine amidase activity and endopeptidase activity.

(41) By way of another definition, bacteriophage endolysin are enzymes encoded by double stranded (ds) DNA phage genomes that lyse bacterial cell walls. This definition of bacteriophage endolysins is encompassed by the present invention, too.

(42) In various embodiments of the present invention, the EAD is the lytic domain of a bacteriocin, including the lytic domain of a bacteriocin from Gram-positive and Gram-negative bacteria. Preferably, the EAD is the lytic domain of a bacteriocin from a Gram-positive bacterium. In various embodiments, the EAD is the lytic domain of a bacteriocin from a Gram-negative bacterium.

(43) In various embodiments of the present invention, the EAD is the lytic domain of a bacterial autolysin, including autolyins from both Gram-positive and Gram-negative bacteria.

(44) Preferably, the EAD is the lytic domain of an autolysin from a Gram-positive bacterium. In various embodiments, the EAD is the lytic domain of an autolysin from a Gram-negative bacterium.

(45) Bacteriophages are not only known to encode and produce lysins, but also so-called tail associated muralytic enzymes (TAMEs), which are likewise capable of hydrolysing bacterial cell walls. While lysins are produced in the final stage of the phage-life cycle to facilitate the release of progeny phage from the host bacterium, TAMEs are, in contrast, structural proteins necessary during the first stage of the process of infection of a host cell. The first stage of the phage infection process comprises the steps of adsorption to and penetration of the host cell, which is mediated using, inter alia, the TAME. Many but not all phages have tails attached to the phage head. Thus, in various embodiments of the present invention, the EAD is a bacteriophage tail-associated protein having lytic activity. Preferably, the EAD is a tail-associated protein having lytic activity of phages that infect Gram-positive hosts. In various embodiments, the EAD is a tail-associated protein having lytic activity of phages that infect Gram-negative hosts. Bacteriophage tail-associated proteins typically mediate the recognition and attachment of the phage to the target host, and some of them possess cell wall degrading activities, which assist in penetration of phage components into the host.

(46) In various embodiments of the present invention, the EAD is derived from bacteriophage tail-equivalents in caudovirales, which provide means for the phage to enter a bacterial host from the external environment.

(47) A chimeric polypeptide obtainable by the methods of the present invention may comprise more than one CBD and, thus, can bind to different cell wall structures, and hence has the potential to treat two or more different bacterial infections at the same time.

(48) In the present invention, any kind of CBD can be used in the methods of the present invention and includes cell-binding domains, which are part of proteins binding to a target bacterial cell, specifically to the cell wall of a target bacterium. Thus, in the present invention, the CBDs are specifically cell wall-binding domains. In general, a CBD in accordance with the present invention binds to bacterial cells, specifically to cell walls of target bacteria, more specifically to cell wall components produced by a target cell, which are non-covalently or covalently associated with the cell wall of a target cell. In other words, the cell-binding domain or cell wall-binding domain is that part of a cell binding protein or cell wall binding protein, which is necessary and sufficient for the binding ability to a bacterial cell or target bacterial cell, specifically for the binding ability to the cell surface of a bacterial cell or target bacterial cell. The bacterial cell or target bacterial cell includes any Gram-positive or Gram-negative bacterial cell.

(49) In various preferred embodiments of the present invention, the CBD is the cell-binding domain of a bacteriophage endolysin, including bacteriophage endolysins against Gram-positive and Gram-negative bacteria. More preferably, the CBD is the cell-binding domain of a bacteriophage endolysin, wherein the endolysin is from a bacteriophage that infects a Gram-positive bacterium. In various embodiments the CBD is the cell-binding domain of a bacteriophage endolysin, wherein the endolysin is from a bacteriophage that infects a Gram-negative bacterium.

(50) In various preferred embodiments of the present invention, the CBD is the cell-binding domain of a bacteriocin, including the cell-binding domain of a bacteriocin from Gram-positive and Gram-negative bacteria. Preferably, the CBD is the cell-binding domain of a bacteriocin from a Gram-positive bacterium. In various embodiments, the CBD is the cell-binding domain of a bacteriocin from a Gram-negative bacterium.

(51) In various preferred embodiments of the present invention, the CBD is the cell-binding domain of a bacterial autolysin, including autolysins from both Gram-positive and Gram-negative bacteria. Preferably, the CBD is the cell-binding domain of an autolysin from a Gram-positive bacterium. In various embodiments, the CBD is the cell-binding domain of an autolysin from a Gram-negative bacterium.

(52) CBDs to be used in the methods of the present invention are capable of specifically binding to bacteria. Thus, while CBDs in accordance with the present invention exhibit cell binding activity, they have no or no significant hydrolytic activity. No or no significant hydrolytic activity in this context is intended to describe the situation whereby the hydrolytic activity is not sufficient to prevent the application of a CBD to bind to a bacterial cell, more specifically to a bacterial cell wall. A CBD to be used in the methods of the present invention is supposed to be a protein, which does not have any hydrolytic activity itself. This also applies to fragments and variants of a CBD according to the present invention, which are also encompassed by the present invention.

(53) The present invention encompasses DNA sequences of any known CBDs and EADs. In the present invention, also DNA sequences coding for functional fragments of known CBDs and EADs as well as DNA sequences coding for mutants and variants of known CBDs and EADs having the same biological function or activity as the known reference CBD or EAD may be used in the methods of the present invention, i.e. binding to the cell wall of a bacterial cell and exhibiting the activity of hydrolysing a bacterial cell wall, respectively.

(54) As used herein, the terms functional fragment, mutant and variant refer to a polypeptide, which possesses biological function or activity identified through a defined functional assay and associated with a particular biologic, morphologic, or phenotypic alteration in a bacterial cell or of a bacterial cell. EADs and CBDs in accordance with the present invention specifically also encompass naturally occurring forms like, for example, alternatively spliced or modified forms and naturally-occurring variants thereof, the DNA sequences coding for which can be used in the methods of the present invention.

(55) The DNA sequences encoding fragments and variants of CBDs and EADs that can be used in the methods of the present invention include chemically synthesized DNA sequences (synthetic genes).

(56) Modifications of CBDs and EADs in accordance with the present invention may result in mutant or variant proteins having substantially equivalent activity to a reference CBD or EAD described herein. Such modifications may be deliberate, as by site-directed mutagenesis, or may occur by spontaneous changes in nucleotide and amino acid sequences where these changes produce modified polypeptides having substantially equivalent activity to the respective reference CBD or EAD. Any polypeptides produced by minor modifications of a known CBD or EAD primary amino acid sequence are included herein as long as the biological activity of a cell wall binding domain or an enzymatic active domain exhibiting lytic activity is present. DNA sequences encoding such modified CBD and EAD polypeptides may also be used in the methods according to the present invention.

(57) As used herein, substantially equivalent activity refers to polypeptides, wherein changes in one or more nucleotide bases of the respective nucleotide sequence encoding the polypeptide result in substitution of one or more amino acids, but do not affect the functional properties of the polypeptide encoded by the nucleotide sequence. Substantially equivalent activity also refers to modifications of CBD and/or EAD encoding nucleic acid sequences such as deletion or insertion that do not substantially affect the functional properties of the resulting transcript and/or protein. It is therefore understood that in the methods according to the present invention more than the nucleotide or amino acid sequences of known CBDs and EADs can be used, i.e. including functional equivalents thereof.

(58) CBDs and EADs for use in the present invention may be identified by analysis of genome sequences using the NCBI website (world wide web at ncbi.nlm.nih.gov); specifically, ORF Finder at the NCBI website may be used for identification (world wide web at ncbi.nlm.nih.gov/gorf/gorf.html). Sequences of predicted proteins can be scanned for homology with known proteins using BLAST searches via the NCBI website (world wide web at ncbi.nlm.nih.gov/BLAST). Multiple sequence alignments of homologous genes and proteins can be performed using ClustalW at the EBI website (world wide web at ebi.ac.uk/Tools/clustalw2/index.html).

(59) In particular, with respect to endolysins the skilled person is in the position to identify CBDs and EADs by homology search in the genome of bacteria and bacterial phages and/or functional screening of DNA libraries of phage genomes. Such homology searches may not only target lysine genes, but also the corresponding holin genes as the holin and lysine happen to be encoded adjacently in a particular genome. By targeting holing genes, it is thus possible to identify adjacent lysins. In addition, bacteriophage endolysin CBDs and EADs may be identified experimentally as described, for example, in Loessner et al. 2002 and Korndorfer et al. 2006, i.e. by determining the domain structure of an endolysin and elucidating the cell wall binding and lytic function of the respective domains. Bacteriophage lysins to be analyzed for CBDs and EADs may be identified by the method described in Schuch et al. 2009. As mentioned therein, the techniques described can be adapted to identify lysins from any phage infecting Gram-positive or even Gram-negative bacteria. Furthermore, endolysin CBDs and EADs may be identified using DNA libraries as described in Schmitz et al. 2008.

(60) Likewise, with respect to autolysins and bacteriocins, the skilled person is in the position to identify CBDs and EADs by homology search in the genome of bacteria. CBDs and EADs of autolysins and bacteriocins may also be identified experimentally.

(61) Basically, the methods according to the present invention are characterized by binding a first domain sequence, which may be a CBD or an EAD and which may be part of a ligation construct of two or more domain sequences selected from CBD and EAD sequences, to a solid support using a tag labelling of said first domain sequence to be bound to the solid support. Furthermore, the methods according to the present invention are basically characterized by ligating one or more domain sequences selected from CBD and EAD sequences to said first domain sequence when bound to the solid support and/or to a ligation construct of two or more domain sequences selected from CBD and EAD sequences, which is bound to the solid support phase by said first domain sequence being bound to the solid support. Thus, ligating one or more domain sequences selected from CBD and EAD sequences includes not only ligating one or more domain sequences selected from CBD and EAD sequences to a single first domain sequence originally bound to the solid support, but also ligating one or more domain sequences selected from CBD and EAD sequences to a ligation construct, which comprises two or more domain sequences and which was originally bound to the solid support by a first domain sequence. Thus, the ligation steps result in ligation products of one or more domain sequences selected from CBD and EAD sequences to a single first domain sequence bound to a solid support or one or more domain sequences selected from CBD and EAD sequences to a ligation construct of two or more domain sequences selected from CBD and EAD sequences, which was originally bound to the solid support by a first domain sequence. Still further, the methods according to the present invention are basically characterized by releasing the ligation product from the solid support after ligation of one or more domain sequences to said first domain sequence bound to the solid support and/or to the ligation construct, which was originally bound to the solid support phase by said first domain sequence being bound to the solid support. Thus, the step of releasing a ligation product from the solid support after performing one or more steps of ligation of one or more domain sequences selected from CBD and EAD sequences provides a DNA coding for a polypeptide, which can then be proven as a lytic chimeric polypeptide in accordance with the present invention.

(62) Accordingly, the present invention provides methods of generating and screening for a chimeric polypeptide comprising at least one CBD and at least one EAD comprising the steps of (i) binding a first domain sequence, which may be a CBD or an EAD and which may be part of a ligation construct of two or more domain sequences selected from CBD and EAD sequences, to a solid support using a tag labelling of the domain sequence to be bound to the solid support, (ii) ligating one or more domain sequences selected from CBD and EAD sequences to said first domain sequence bound to the solid support and/or to said ligation construct comprising one or more domain sequences selected from CBD and EAD sequences, which is bound to the solid support phase by said first domain sequence bound to the solid support, and (iii) releasing from the solid support the ligation product resulting from ligation of one or more domain sequences to the first domain sequence bound to the solid support and/or resulting from ligation of one or more domain sequences to said ligation construct, which was originally bound to the solid support phase by the said first domain sequence bound to the solid support.

(63) In the present invention, one or more domain sequences selected from CBD and EAD sequences are bound to the solid support as a first domain sequence by tag labelling. Thus, a non-limited number of different so-called first domain sequences are bound to the solid support, and to each of which one or more domain sequences selected from CBD and EAD sequences may be ligated. This allows providing a non-limited number of ligation products corresponding to all combinations of CBDs and EADs, which are statistically possible depending on the CBD and EAD sequences applied and the ligation cycles performed, and which are as such not found in nature.

(64) The situation described above accordingly holds for constructs of two or more domain sequences selected from CBD and EAD sequences, which are bound to the solid support phase. That is, in various embodiments of the present invention a non-limited number of constructs of one or more domain sequences selected from CBD and EAD sequences may be bound to the solid support by the first domain sequence carrying a tag labelling. Thus, to each of the originally bound ligation constructs of two or more domain sequences selected from CBD and EAD sequences, one or more domain sequences selected from CBD and EAD sequences may be ligated. This allows providing a non-limited number of ligation products corresponding to all combinations of CBDs and EADs, which are statistically possible depending on the CBD and EAD sequences applied and the ligation cycles performed, and which are as such not found in nature.

(65) More specifically, the methods of the present invention may provide for a non-limited number of ligation products corresponding to all combinations of CBDs and EADs from the different sources or origins described herein. Thus, the generation and screening for lytic chimeric polypeptides provided by the present invention is based on a random shuffling of domain sequences selected from CBD and EAD sequences using a solid support, on which a non-limited number of ligation products of two or more domain sequences selected from CBD and EAD sequences is formed. Thus, the number of first domain sequences and/or ligation constructs of two or more domain sequences selected from CBD and EAD sequences, which are originally to be bound to the solid support in order to form ligation products by repeatedly performing ligation steps on said first domain sequence(s) and/or ligation construct(s), is non-limited and includes even the binding of only one such first domain sequence and/or only one such ligation construct to the solid support.

(66) In accordance with the present invention, the domain sequence originally bound to the solid support or that domain sequence of a ligation construct, which is directly bound to the solid support via tag labelling, is called the 1.sup.st domain sequence. Furthermore, in accordance with the present invention the ligation construct of two or more domain sequences selected from CBD and EAD sequences, which is originally bound to the solid support via tag labelling of the first domain sequence of such a ligation construct, may also be called a first ligation product.

(67) In the present invention, a solid support having bound first domain sequences and/or ligation constructs of two or more domain sequences selected from CBD and EAD sequences may be called solid support phase. Thus, in the present invention ligating domain sequences to first domain sequences and/or ligation constructs bound to a solid support may also be described as ligating domain sequences to the solid support phase.

(68) In various embodiments, the methods according to the present invention are characterized by the step of providing one or more DNA sequences each encoding at least one CBD, and furthermore one or more DNA sequences each encoding at least one EAD, wherein the EAD is selected from the group consisting of (i) the lytic domain of a bacteriophage lysin, (ii) the lytic domain of a bacteriocin, (iii) the lytic domain of a bacterial autolysin; and (iv) a bacteriophage tail-associated protein having lytic activity. Optionally, step (a) of the methods according to the present invention furthermore provides one or more DNA sequences, wherein each sequence encodes at least one CBD and at least one EAD, wherein the EAD is selected from the group consisting of (i) the lytic domain of a bacteriophage lysin, (ii) the lytic domain of a bacteriocin, (iii) the lytic domain of a bacterial autolysin; and (iv) a bacteriophage tail-associated protein having lytic activity. Thus, while in step (a) basically each of the DNA sequences (one or more) encodes either at least one CBD or at least one EAD, optionally step (a) furthermore includes providing one or more DNA sequences, wherein each DNA sequence encodes both at least one CBD and at least one EAD.

(69) In the present invention, the generation of ligatable, position-specific PCR fragments (see Example 2) may be performed in two ways: either with a primer which is not tag-labelled (i.e., for example, a non-biotinylated primer) or with a primer which is tag-labelled (i.e., for example, a biotinylated primer). PCR products for domain sequences, which are generated with a primer that is not tag-labelled, as well as PCR products for the first domain sequence (position 1) generated with a primer that is tag-labelled, are to be purified using common purification kits. PCR products for domain sequences except for first domain sequences generated with a primer that is tag-labelled (with, for example, a biotin-tag) may be purified by correspondingly prepared magnetic particles. That is, in case of using the biotin-streptavidin-system, such PCR products may be purified by streptavidin-coated magnetic particles. In particular, PCR products are bound to beads, which are subsequently washed for applying an appropriate buffer or change of buffer and released from the beads by restriction digest at restriction sites previously introduced into the domain sequence. PCR products for first domain sequences generated with a primer that is tag-labelled may not be purified by magnetic particles together with the use of a restriction enzyme because this would remove the tag-labelling from the first domain sequence, which is however required for binding of first domain sequences to a solid support.

(70) In the present invention, the amplification of the domain sequences follows standard procedures using PCR and position-specific primers. Alternatively, domain sequences may be obtained from plasmid preparations, i.e. for the ligation reaction a multiple of domain sequences can be prepared by restriction digest from plasmids, which carry the domain sequences and which are cultured in appropriate hosts for amplification of the plasmids. In the present invention, binding of ligation products to a solid support is performed using a tag labelling, preferably a biotin tag labelling. Various peptide tags have become popular in biotechnology, among them those essentially enabling reversible immobilization of proteins to affinity matrices.

(71) In the present invention, the introduction of a tag labelling at the 5-end or 3-end of a domain DNA sequence can be performed using standard labelling systems involving the use of, for example, 5- and 3-biotinylated primers, respectively. In various embodiments, the tag labelling may be introduced not directly at the 5-end, but at a base position located more downstream in the 3-end direction, provided that the tag labelling may still be removed by restriction enzyme digest. In the present invention, a tag labelling is a labelling which provides for a binding of a nucleic acid sequence to a solid support such as a particle, a surface of a device, a foil or a fleece, more specifically a silica bead or an organic polymer bead, which may be magnetic. Thus, in various embodiments of the present invention a tag labelling provides for a chemical tag labelling, e.g. a biotin labelling or a digoxigenin labelling. In various embodiments, the biotin-streptavidin-system is a preferred system to be used in the methods according to the present invention, wherein the binding of a domain sequence, specifically a first domain sequence in accordance with the present invention, or a ligation construct of two or more domain sequences selected from CBD and EAD sequences to a solid support is mediated by streptavidin. In various other embodiments, the digoxigenin-antibody-system is a preferred system to be used in the methods according to the present invention, wherein the binding of a domain sequence, specifically a first domain sequence in accordance with the present invention, or a ligation construct of two or more domain sequences selected from CBD and EAD sequences to a solid support is mediated by an antibody.

(72) In various embodiments of the methods of the present invention, the first domain to be ligated to the solid support may be a nonsense-domain, which is carrying a tag labelling and which may be detached after performing the ligation step(s) ligating EAD and CBD domains to the solid support phase, i.e. in accordance with the step of releasing the obtained ligation product from the solid support.

(73) In the present invention, restriction digests with restriction enzymes are performed by standard procedures and according to the manual of the manufacturer of the respective restriction enzyme.

(74) In the present invention, ligation of domain sequences follows standard procedures. In various embodiments, ligation of the 1.sup.st and 2.sup.nd domain sequence is performed in ligase buffer while ligation of the ligated 1.sup.st and 2.sup.nd domain with one or more further domain sequences is performed in restriction enzyme buffer of the respective restriction enzyme(s) under addition of ATP. In various embodiments, ligation of domains to the solid phase, i.e. ligation of domains to the solid support having bound already a ligation product, is performed using bound and free domains in a ratio of 1:5, preferably 1:10. In various embodiments, the ratio of bound and free domains is 1:15, more preferably 1:20.

(75) In the methods of the present invention, the domain sequences may be ligated to the solid support phase after a restriction digest has been performed on each of the amplified domain sequences with the appropriate restriction enzyme targeting the restriction site previously introduced into the respective domain sequences in accordance with the present invention. Alternatively, the domain sequences may be ligated to the solid support phase with only that end of the domain sequence being digested with a corresponding restriction enzyme, which is ligated to the preceding domain sequence on the solid support phase. Depending on the orientation of the growing ligation product, i.e. depending on the tag labelling of the first domain sequence being either at the 5-end or at the 3-end, the digested end of the domain sequence to be ligated may either be the 3-end or the 5-end. In this situation, a restriction digest is performed on the solid support phase, i.e., in particular, on the growing ligation product, using the appropriate restriction enzyme targeting the restriction site introduced into the most recent ligated domain sequence in order to prepare the non-ligated end of the most recent ligated domain sequence for being ligated with a further domain sequence. This alternative way of step-by-step restriction digest and ligation of a domain sequence is preferably applicable in the situation where the ligatable domain sequences are amplified using a primer which is tag-labelled (i.e., for example, a biotinylated primer). Accordingly, the resulting PCR products may be purified by correspondingly prepared magnetic particles and the PCR products are released from the beads by restriction digest, which is performed at that restriction site previously introduced into the domain sequence to be amplified, which is required for ligating the domain sequence to the growing ligation product on the solid support phase. This approach does not require performing a restriction digest on the other restriction site previously introduced at the other end (either 5 or 3) of the domain sequence to be amplified. As described above, a restriction digest on this restriction site is then performed after the domain sequence has been ligated to the solid support phase. In various embodiments of the present invention, the step of releasing the ligation product or ligation products from the solid support is carried out using a restriction enzyme targeting the restriction site at that end of the 1.sup.st domain, which is carrying the tag labelling. In various other embodiments of the present invention, the step of releasing the ligation product or ligation products from the solid support is carried out by releasing the bound tag from the solid support. In this case, the ligation product together with the tag labelling is released from the solid support. Thus, when using, for example, the biotin-streptavidin system in the methods of the present invention, this means disruption of the streptavidin-biotin bond under appropriate conditions. Where the step of releasing the ligation product from the solid support is carried out by releasing the bound tag from the solid support, subsequent cloning of the released ligation product into an expression vector requires a restriction digest of the ligation product with the respective restriction enzyme targeting the restriction site at that end of the 1.sup.st domain of the ligation product, which is carrying the tag labelling.

(76) In the present invention, introducing the expression vector carrying the ligation product released from the solid support into an expression host can be performed by methods described in standard laboratory manuals, and includes standard transformation procedures like, for example, electroporation or the use of chemically competent cells.

(77) In the present invention, the expression host, into which the expression vector carrying the ligation product is introduced, includes any host-based system, which allows expression of the ligation product released from the solid support. Host cells can be genetically engineered to incorporate expression systems or portions thereof. Representative examples of appropriate hosts include bacterial cells, such as streptococci, staphylococci, enterococci, E. coli, Streptomyces and Bacillus subtilis cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293 and Bowes melanoma cells and plant cells.

(78) In the present invention, the expression host is preferably a bacterial expression strain. More preferably, the bacterial expression strain is an inducible bacterial expression strain like, for example, the T5 or T7-expression strains. In general, expression hosts and expression vectors (plasmids) that can be used in the present invention are known to the person skilled in the art.

(79) Expression vectors to be used in the present invention provide for or are designed to allow cloning of the ligation product obtained from the solid support by appropriate restriction enzyme sites. The expression system constructs to be used in the present invention may contain control regions that regulate as well as engender expression. Generally, any system or vector suitable to express ligation products and chimeric polypeptides according to the present invention may be used for expression in this regard. The appropriate sequences may be inserted into the expression system by any of a variety of well-known and routine techniques.

(80) In various embodiments, the restriction vector carries an appropriate selection marker like, for example, an ampicillin resistance gene.

(81) In the present invention, selecting an expression clone expressing a lytic chimeric polypeptide encoded by the domain sequences of a ligation product obtained from the solid support includes, but is not limited to, picking single colonies forming a lytic halo on agar plates comprising, for example, Listeria cells. Such colonies are transformants carrying an expression vector with a ligation product and expressing a polypeptide, which is lytic to said Listeria cells. The single colonies can be isolated by, for example, picking and culturing on appropriate back-up agar plates. An appropriate back-up agar plate comprises an antibiotic in accordance with the expression vector carrying the ligation product obtained from the solid support.

(82) It will be understood that not all vectors, expression control sequences and hosts will function equally well to express the DNA sequences of this invention. Neither will all hosts function equally well with the same expression system. However, one skilled in the art will be able to select the proper vectors, expression control sequences, and hosts without undue experimentation to accomplish the desired expression without departing from the scope of the invention.

(83) In the present invention, characterizing and identifying a polypeptide obtainable by the methods of the present invention as a lytic polypeptide includes, but is not limited to, testing selected clones for their lytic activity against several bacterial strains, i.e., for example, against different Listeria serovars. Thus, a lytic polypeptide obtainable by the methods of the present invention can be characterized for its lytic activity against one or more bacterial strains.

(84) In the present invention, characterizing and identifying a polypeptide obtainable by the methods of the present invention as a lytic polypeptide also includes, but is not limited to, sequencing of the clones showing lytic activity against bacterial strains, i.e. identifying the sequence of the lytic polypeptide encoded by the plasmid carrying the ligation product obtained in the methods of the present invention.

(85) In the present invention, characterizing and identifying a polypeptide obtainable by the methods of the present invention as a lytic polypeptide furthermore includes, but is not limited to, performing tests on expression of the lytic polypeptide encoded by the plasmid carrying the ligation product obtained in the methods of the present invention.

(86) In the present invention, removing non-ligated domain sequences after performing the steps of ligating domains to the solid support phase includes, but is not limited to, washing the solid support phase using an appropriate washing buffer for washing away non-ligated domain sequences. Thus, in the present invention the step of removing non-ligated domain sequences after a ligation step is preferably a washing step. The same holds for the step of removing unbound domain sequences after binding first domain sequences and/or ligation constructs according to the present invention to a solid support.

(87) In general, the methods according to the present invention may comprise one or more washing steps after each step of binding of a first domain sequence or a ligation construct of two or more domain sequences selected from CBD and EAD sequences to a solid support. The same applies to each step of ligating domain sequences to a first domain sequence and/or to a ligation construct of two or more domain sequences selected from CBD and EAD sequences, which are originally bound to the solid support in order to form ligation products by repeatedly performing ligation steps on said first domain sequence(s) and/or said ligation construct(s). As used herein, the washing steps provide for changing buffers, which may become necessary due to, for example, different restriction enzymes to be used when performing the ligation steps of the methods of the present invention. Similarly, a washing step may become necessary between the steps of binding of a first domain sequence or a ligation construct of two or more domain sequences selected from CBD and EAD sequences to a solid support and the subsequent ligation steps. In addition, one or more washing steps may become necessary after performing a restriction digest on the solid support phase as described herein above, i.e., a restriction digest performed on the growing ligation product. Such washing steps may not only become necessary for changing buffers, in particular restriction enzyme buffers, but may also be performed in order to remove, i.e. washing away, undesired products resulting from the restriction digest. Accordingly, such washing steps as described before may be performed after any step of performing a restriction digest in the present invention.

(88) As will be understood by the one of skilled in the art, the method of generating a chimeric polypeptide having at least one CBD and at least one EAD according to the present invention (cf. item [2] under Summary of the Invention) may furthermore comprise a step of cloning the ligation product obtained in step (l) into a cloning vector prior to characterizing the obtained ligation products. The characterization of a polypeptide obtainable by said method as a chimeric polypeptide in accordance with the present invention includes, but is not limited to, sequencing of the ligation products obtained and thus elucidating the CBD and EAD domain structures. Furthermore, characterization of a polypeptide obtainable by said method as a chimeric polypeptide in accordance with the present invention may be done by testing the polypeptide for its cell wall binding and lytic activity against several bacterial strains, for example, against different Listeria serovars.

(89) In the present invention, the terms protein and peptide may be used interchangeably with the term enzyme. In other words, a lytic chimeric polypeptide obtainable by the methods of the present invention is a polypeptide, which comprises one or more heterologous domains exhibiting lytic activity on pathogenic bacterial cells.

(90) In various embodiments of the present invention, the methods further comprise a step of selecting expression hosts carrying the expression vector with the ligation product cloned therein prior to culturing the expression host under conditions suitable to allow expression of a lytic polypeptide encoded by the domain sequences of the cloned ligation product.

(91) In various embodiments of the present invention, the domain sequences are joined (linked) by a linker sequence, which is a native or a synthetic linker sequence. In various embodiments of the present invention, the linker sequence refers to an amino acid sequence that joins two domain sequences of a lytic chimeric polypeptide of the present invention or fragments or variants thereof. In general, as used herein, a linker includes, but is not limited to, an amino acid sequence that covalently links the domains of the lytic chimeric polypeptide obtainable by the present invention. More specifically, the linker comprises at least one peptide bond. As appreciated by one of skill in the art, the linker can comprise additional amino acids. In general, a linker sequence or domain linker as used in the present invention denotes an amino acid sequence functioning to connect single domain sequences with each other. Properties of linker sequences or domain linkers in accordance with the present invention as well as methods to detect those are known to the person skilled in the art. In the present invention, a linker sequence may be incorporated into a chimeric polypeptide obtainable by the methods of the present invention if it is part of a cloning vector as exemplarily shown in FIG. 1. While FIG. 1 shows exemplarily a synthetic linker, the linker of the cloning vector may also be a native linker cloned into the cloning vector. Alternatively, a native linker may be incorporated into a chimeric polypeptide obtainable by the methods of the present invention if a selected domain sequence is isolated together with its native linker sequence. Furthermore, a linker sequence may be incorporated into a chimeric polypeptide obtainable by the methods of the present invention by means of PCR applied in various steps of the methods of the present invention.

(92) The methods for generating a chimeric polypeptide having at least one CBD and at least one EAD according to the present invention provide for a plurality of chimeric polypeptides.

(93) The present invention also provides a DNA library comprising the clones carrying the ligation products obtained in the methods according to the present invention.

(94) Based on comparative test methods available in the art (see, for example, Kusuma and Kokai-Kun 2005), the person skilled in the art can easily determine whether a lytic chimeric polypeptide obtained by the methods of the present invention shows improved biological properties over lytic polypeptides known in the art. Improved biological properties means an improvement with respect to lower working concentration, higher stability, altered specificity and/or hydrolyzing activity on bacterial cell walls.

(95) In various preferred embodiments, the methods of the present invention comprise amplifying the 1.sup.st, 2.sup.nd and 3.sup.rd domain sequences, and optionally amplifying one or more further domain sequences.

(96) In various embodiments of the method for generating a chimeric polypeptide according to the first aspect of the invention, step (m), i.e. characterizing the ligation product obtained in step (l), comprises the steps of:

(97) (m) cloning the ligation product obtained in step (l) into an expression vector;

(98) (n) introducing the vector obtained in step (m) into an expression host, preferably into a bacterial expression host;

(99) (o) culturing the expression host of step (n) carrying the vector obtained in step (m) under conditions suitable to allow expression of a lytic polypeptide encoded by the domain sequences of the cloned ligation product;

(100) (p) selecting and isolating an expression clone expressing a lytic polypeptide according to step (o) using the lytic activity of the polypeptide; and

(101) (q) characterizing the lytic polypeptide expressed by the isolated expression clone of step (p) and identifying a lytic chimeric polypeptide having at least one CBD and at least one EAD.

(102) In various embodiments of the method of screening for a lytic chimeric polypeptide and the method of generating a chimeric polypeptide according to the second aspect of the invention, steps (h) and (j) and steps (k) and (l) may be combined, as reflected in corresponding steps (h) and (j) of the following embodiments of the claimed methods according to the second aspect of the invention: 1. A method of screening for a lytic chimeric polypeptide comprising the steps of:

(103) (a) providing one or more DNA sequences each encoding at least one cell binding domain (CBD) and one or more DNA sequences each encoding at least one enzymatic active domain (EAD) and optionally one or more DNA sequences each encoding at least one CBD and at least one EAD, wherein the EAD is selected from the group consisting of

(104) (i) the lytic domain of a bacteriophage lysin,

(105) (ii) the lytic domain of a bacteriocin,

(106) (iii) the lytic domain of a bacterial autolysin; and

(107) (iv) a bacteriophage tail-associated protein having lytic activity;

(108) (b) amplifying a first (1.sup.st) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce different restriction sites at the 5-end and at the 3-end, and a tag labeling at the 5-end or at the 3-end;

(109) (c) amplifying a second (2.sup.nd) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce:

(110) (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the 1.sup.st domain, and at the 3-end a restriction site different from the restriction sites introduced into the 1.sup.st domain sequence,

(111) (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the 1.sup.st domain, and at the 5-end a restriction site different from the restriction sites introduced into the 1.sup.st domain sequence;

(112) (d) optionally amplifying a third (3.sup.rd) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce:

(113) (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the preceding 2.sup.nd domain, and at the 3-end a restriction site that is different from that at the 5-end of the 1.sup.st domain,

(114) (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the preceding 2.sup.nd domain, and at the 5-end a restriction site that is different from that at the 3-end of the 1.sup.st domain;

(115) wherein the pair of primers is further designed such that the restriction sites are different at the 5-end and the 3-end of the 3.sup.rd domain sequence;

(116) (e) optionally amplifying one or more further domain sequences selected from the domain sequences of (a) for extending the series of domain sequences according to steps (b) to (d), using for each of said one or more further domain sequences a pair of primers designed following the principle of steps (c) and (d) so as to introduce:

(117) (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the preceding domain, and at the 3-end a restriction site that is different from that at the 5-end of the 1.sup.st domain,

(118) (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the preceding domain, and at the 5-end a restriction site that is different from that at the 3-end of the 1.sup.st domain;

(119) wherein the pair of primers is further designed such that the restriction sites are different at the 5-end and the 3-end of each of said one or more further domain sequences;

(120) (f) performing a restriction digest of the domain sequences of any of steps (b) to (e):

(121) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the domain sequence of step (b) with a restriction enzyme targeting the restriction site at the 3-end and performing a restriction digest of the domain sequences of any of steps (c) to (e) with restriction enzymes targeting the restriction sites at the 5-ends,

(122) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the domain sequence of step (b) with a restriction enzyme targeting the restriction site at the 5-end and performing a restriction digest of the domain sequences of any of steps (c) to (e) with restriction enzymes targeting the restriction sites at the 3-ends;

(123) (g) ligating the digested 1.sup.st and 2.sup.nd domain sequence obtained in step (f) to obtain a ligation product comprising the 1.sup.st and 2.sup.nd domain sequence;

(124) (h) binding the ligation product of step (g) to a solid support using the tag labeling of the 1.sup.st domain sequence to obtain a bound ligation product comprising the 1.sup.st and 2.sup.nd domain sequence, and performing a restriction digest of said bound ligation product:

(125) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the 2.sup.nd domain, (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5 end of the 2.sup.nd domain;

(126) (j) optionally ligating the digested 3.sup.rd domain sequence of step (d) obtained in step (f) to the bound ligation product of step (h) to obtain a bound ligation product comprising the 1.sup.st, 2.sup.nd and 3.sup.rd domain sequence, and performing a restriction digest of said bound ligation product:

(127) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the 3.sup.rd domain.

(128) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5-end of the 3.sup.rd domain.

(129) (k) optionally ligating one or more digested domain sequences of (e) obtained in step (f) to the bound ligation product of step (j) to obtain a bound ligation product comprising one or more further domain sequences of step (e), thereby performing after each ligation step a restriction digest of the bound ligation product as follows:

(130) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the said further domain sequence that was ligated to the bound ligation product,

(131) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5-end of the said further domain sequence that was ligated to the bound ligation product;

(132) (l) releasing the ligation product obtained in any of steps (h) to (k) from the solid support;

(133) (m) cloning the ligation product obtained in step (l) into an expression vector;

(134) (n) introducing the vector obtained in step (m) into an expression host, preferably into a bacterial expression host;

(135) (o) culturing the expression host of step (n) carrying the vector obtained in step (m) under conditions suitable to allow expression of a lytic polypeptide encoded by the domain sequences of the cloned ligation product;

(136) (p) selecting and isolating an expression clone expressing a lytic polypeptide according to step (o) using the lytic activity of the polypeptide; and

(137) (q) characterizing the lytic polypeptide expressed by the isolated expression clone of step (p) and identifying a lytic chimeric polypeptide.

(138) 2. A method of generating a chimeric polypeptide having at least one cell binding domain (CBD) and at least one enzymatic active domain (EAD), the method comprising the steps of:

(139) (a) providing one or more DNA sequences each encoding at least one CBD and one or more DNA sequences each encoding at least one EAD, and optionally one or more DNA sequences each encoding at least one CBD and at least one EAD, wherein the EAD is selected from the group consisting of

(140) (i) the lytic domain of a bacteriophage lysin;

(141) (ii) the lytic domain of a bacteriocin;

(142) (iii) the lytic domain of a bacterial autolysin; and

(143) (iv) a bacteriophage tail-associated protein having lytic activity.

(144) (b) amplifying a first (1.sup.st) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce different restriction sites at the 5-end and at the 3-end, and a tag labeling at the 5-end or at the 3-end;

(145) (c) amplifying a second (2.sup.nd) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce:

(146) (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the first domain, and at the 3-end a restriction site different from the restriction sites introduced into the 1.sup.st domain sequence,

(147) (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the 1.sup.st domain, and at the 5-end a restriction site different from the restriction sites introduced into the 1.sup.st domain sequence;

(148) (d) optionally amplifying a third (3.sup.rd) domain sequence selected from the domain sequences of (a) using a pair of primers designed to introduce:

(149) (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the preceding 2.sup.nd domain, and at the 3-end a restriction site that is different from that at the 5-end of the 1.sup.st domain,

(150) (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the preceding 2.sup.nd domain, and at the 5-end a restriction site that is different from that at the 3-end of the 1.sup.st domain;

(151) wherein the pair of primers is further designed such that the restriction sites are different at the 5-end and the 3-end of the 3.sup.rd domain sequence;

(152) (e) optionally amplifying one or more further domain sequences selected from the domain sequences of (a) for extending the series of domain sequences according to steps (b) to (d), using for each of said one or more further domain sequences a pair of primers designed following the principle of steps (c) and (d) so as to introduce:

(153) (i) in case of 5-end labelling of the 1.sup.st domain: at the 5-end the same restriction site as at the 3-end of the preceding domain, and at the 3-end a restriction site that is different from that at the 5-end of the 1.sup.st domain,

(154) (ii) in case of 3-end labelling of the 1.sup.st domain: at the 3-end the same restriction site as at the 5-end of the preceding domain, and at the 5-end a restriction site that is different from that at the 3-end of the 1.sup.st domain;

(155) wherein the pair of primers is further designed such that the restriction sites are different at the 5-end and the 3-end of each of said one or more further domain sequences;

(156) (f) performing a restriction digest of the domain sequences of any of steps (b) to (e):

(157) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the domain sequence of step (b) with a restriction enzyme targeting the restriction site at the 3-end and performing a restriction digest of the domain sequences of any of steps (c) to (e) with restriction enzymes targeting the restriction sites at the 5-ends,

(158) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the domain sequence of step (b) with a restriction enzyme targeting the restriction site at the 5-end and performing a restriction digest of the domain sequences of any of steps (c) to (e) with restriction enzymes targeting the restriction sites at the 3-ends;

(159) (g) ligating the digested 1.sup.st and 2.sup.nd domain sequence obtained in step (f) to obtain a ligation product comprising the 1.sup.st and 2.sup.nd domain sequence;

(160) (h) binding the ligation product of step (g) to a solid support using the tag labeling of the 1.sup.st domain sequence to obtain a bound ligation product comprising the 1.sup.st and 2.sup.nd domain sequence, and performing a restriction digest of said bound ligation product:

(161) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the 2.sup.nd domain, (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5 end of the 2.sup.nd domain;

(162) (j) optionally ligating the digested 3.sup.rd domain sequence of step (d) obtained in step (f) to the bound ligation product of step (h) to obtain a bound ligation product comprising the 1.sup.st, 2.sup.nd and 3.sup.rd domain sequence, and performing a restriction digest of said bound ligation product:

(163) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the 3.sup.rd domain.

(164) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5-end of the 3.sup.rd domain.

(165) (k) optionally ligating one or more digested domain sequences of (e) obtained in step (f) to the bound ligation product of step (j) to obtain a bound ligation product comprising one or more further domain sequences of step (e), thereby performing after each ligation step a restriction digest of the bound ligation product as follows:

(166) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the said further domain sequence that was ligated to the bound ligation product,

(167) (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5-end of the said further domain sequence that was ligated to the bound ligation product;

(168) (l) releasing the ligation product obtained in any of steps (h) to (k) from the solid support;

(169) (m) characterizing the ligation product obtained in step (l) and identifying chimeric polypeptides having at least one CBD and at least one EAD.

(170) 3. The method of item 1 or 2, further comprising a washing step after binding the first ligation product to the solid support in step (h) to remove unbound ligation products and/or non-ligated domain sequences.

(171) 4. The method of any one of items 1 to 3, wherein steps (g) and (h) are replaced by a step of binding the digested 1.sup.st domain sequence to a solid support using the tag labeling at the 5-end or 3-end, respectively, and a subsequent step of ligating the digested 2.sup.nd domain sequence of step (c) obtained in step (f) to the bound 1.sup.st domain sequence to obtain a bound ligation product comprising the 1.sup.st and 2.sup.nd domain sequence, followed by performing a restriction digest of said bound ligation product:

(172) (i) in case of 5-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 3-end of the 2.sup.nd domain, (ii) in case of 3-end labelling of the 1.sup.st domain: performing a restriction digest of the bound ligation product with a restriction enzyme targeting the 5 end of the 2.sup.nd domain.

(173) 5. The method of item 4, further comprising a step of removing unbound domain sequences after binding the first ligation product to the solid support, and optionally a further step of removing non-ligated domain sequences after ligating the second domain sequence to the bound first domain sequence.

(174) 6. The method for screening a lytic chimeric polypeptide of any one of items 1 and 3 to 5, further comprising a step of removing non-ligated domain sequences and/or undesired products resulting from the restriction digest after each ligation and restriction step performed in any of steps (h) to (k).

(175) 7. The method for generating chimeric polypeptides having at least one CBD and at least one EAD of any one of items 2 to 5, further comprising a step of removing non-ligated domain sequences and/or undesired products resulting from the restriction digest after each ligation and restriction step performed in steps (h) to (k).

(176) 8. The method of any one of items 2 to 5, wherein step (m) comprises the steps of:

(177) (m) cloning the ligation product obtained in step (l) into an expression vector;

(178) (n) introducing the vector obtained in step (m) into an expression host, preferably into a bacterial expression host;

(179) (o) culturing the expression host of step (n) carrying the vector obtained in step (m) under conditions suitable to allow expression of a lytic polypeptide encoded by the domain sequences of the cloned ligation product;

(180) (p) selecting and isolating an expression clone expressing a lytic polypeptide according to step (o) using the lytic activity of the polypeptide; and

(181) (q) characterizing the lytic polypeptide expressed by the isolated expression clone of step (p) and identifying a lytic chimeric polypeptide having at least one CBD and at least one EAD.

(182) 9. The method of any one of items 1 to 8, wherein the domain sequences of (a) are cloned into a vector prior to amplification.

(183) 10. The method of any one of items 1 to 9, wherein the step of releasing the ligation product or ligation products from the solid support is carried out using a restriction enzyme targeting the restriction site at that end of the 1.sup.st domain, which is carrying the tag labelling.

(184) 11. The method of any one of items 1 to 10, wherein in case of repeated ligation steps optionally after any repeated ligation step part of the obtained bound ligation product is separated from the method prior to performing a subsequent ligation step.

(185) 12. The method of any one of items 1 to 11, wherein the solid support is a particle, a surface of a device, a foil or a fleece.

(186) 13. The method of item 12, wherein the particle is a silica bead or an organic polymer bead being magnetic.

(187) 14. A lytic chimeric polypeptide obtainable by the method for screening a lytic chimeric polypeptide of any one of items 1 and 3 to 13.

(188) 15. A chimeric polypeptide or a plurality of chimeric polypeptides obtainable by the method of generating chimeric polypeptides having at least one CBD and at least one EAD of any one of items 2 to 13.

(189) 16. A library of chimeric polypeptides obtainable by the method of any one of items 2 to 13.

EXAMPLES

Example 1: Cloning of Selected Domains

(190) Table 1 shows selected domains used for library construction.

(191) TABLE-US-00002 TABLE1 Selecteddomainswithdescriptionofproteinsource,domainborders oftheaminoacidsequenceandenzymaticspecificityofEADs. Proteinsource SEQIDNO: Domain Domainborders Specificity Endolysin,Ply511 1 EAD511 1-195 Amidase2 Endolysin,Ply511 1 CBD511 194-141+ Linsyn Endolysin,Ply500 2 EAD500 1-154 VanY Endolysin,Ply500 2 CBD500 148-189+ Linsyn Endolysin,PlyP40 3 EADP40 1-225 Chalaropsis Lysozyme Endolysin,PlyP40 3 CBDP40 A:226-344+ Linsyn B:192-344+ Linsyn C:192-344 Endolysin,PlyP35 4 EADP35 1-150 VanY Endolysin,PlyP35 4 CBDP35 140-291+ Linsyn Endolysin,PlyB054 5 EADB054 1-194 Amidase3 Endolysin,PlyPSA 6 EADPSA 1-182 Amidase3 Endolysin,Ply006 7 CBD006 157-235+ Linsyn Endolysin,PlyB025 8 CBDB025 127-276+ Linsyn LyticTailprotein, 9 EADgp29 641-795+ Linsyn NlpC/p60 gp29ofP100 (CHAP) Autolysin, 10 MurA A:52-327 Lysozym L.monocytogenes B:142-327 type2 Autolysin, 11 IspC 1-226 Lysozym L.monocytogenes type2 Bacteriocin, 12 Mutanolysin 79-294+ Linsyn Chalaropsis S.coelicolorMilner Lysozyme Autolysin, 13 Slel 201-334+ Linsyn NlpC/p60 S.aureusUSA300 (CHAP) Linsyn: synthetic linker sequence, amino acid sequence: GGSKPGGTKPGGSKP.

(192) The domains were amplified via PCR primers with the following design:

(193) TABLE-US-00003 Forwardprimer (SEQIDNO:15) CACACACCATGGCG(begindomain) ReverseprimerSpeI (SEQIDNO:16) TGTGTGACTAGT(enddomainwithoutSTOPcodon) ReverseprimerBamHI (SEQIDNO:17) TGTGTGGGATCC (enddomainwithoutSTOPcodon)

(194) Forward primer contain a NcoI-site, and reverse primer for attachment of a synthetic linker sequence have a SpeI-site, reverse primer for cloning without synthetic linker sequence have a BamHI-site. Restriction sites are shown in bold and underlined.

(195) The purified PCR products were digested with NcoI and SpeI or NcoI and BamHI and ligated in a modified plasmid vector pET14b as shown in FIG. 1. This pET14b holds the sequence for the 3 synthetic linker region. The synthetic linker sequence is positioned between the SpeI site and the pET14b-BamHI site.

(196) After transformation of E. coli HMS174 (DE3) using common procedures, positive clones were selected with ampicillin resistance. Clones that expressed the right sized protein were sequenced.

Example 2: Generation of Ligatable, Position Specific PCR Fragments

(197) For introduction of the position specific restriction sites, the domains were amplified via PCR by position specific primer combinations (see FIG. 2 and Table 1). As PCR templates served the domains cloned in pET14b. FIG. 3 shows exemplarily the PCR products for position 1, 2 and 3 of EAD500.

(198) TABLE-US-00004 TABLE2 Positionspecificprimerpairs. Pos.1 forward: B-5-GTTTAACTTTAAGAAGGAGATATACCATGGCG-3 (SEQIDNO:18) reverse: 5-CCTTTCGGGCTTTGTTACTGCAGGGATCC-3 (SEQIDNO:19) Pos.2 forward: 5-GTTTAACTTTAAGAAGGAGACTGCAGATGGCG-3 (SEQIDNO:20) reverse: 5-CCTTTCGGGCTTTGTTAGTCGACGGATCC-3 (SEQIDNO:21) Pos.3 forward: 5-GTTTAACTTTAAGAAGGAGAGTCGACATGGCG-3 (SEQIDNO:22) reverse: 5-CCTTTCGGGCTTTGTTAGATATCGGATCC-3 (SEQIDNO:23) B: 5-attached Biotin-tag CCATGG: NcoI-site CTGCAG: PstI-site GTCGAC: SalI-site GATATC: EcoRV-site

(199) PCR for domain position 3 was performed twice: with non-biotinylated forward primer and with biotinylated forward primer. PCR products for position 1 and without biotin-tag are to be purified using common purification kits. PCR products with biotin-tag (all except for position 1) can be purified per streptavidin coated magnetic particles: binding to beads, washing and removing of beads by restriction digest.

Example 3: Test for Activity of Cloned Domains

(200) All cloned domains were tested for domain activity. EADs were tested for Listeria lytic activity, CBDs were tested for Listeria binding activity.

(201) 3-1. Testing Listeria Lytic Activity of EADs

(202) E. coli HMS (174) clones containing the pET14bEAD constructs were spotted on LB Top Agar plates containing IPTG for the induction of protein expression, ampicillin for the plasmid selection pressure and 120 l heat inactivated Listeria cells of Listeria monocytogenes EGDe (J.Kreft), serotype 1/2a. Each domain was spotted and incubated at 30 C. and afterwards at room temperature. In case of Listeria lysis, the spotted E. coli clone is surrounded by a clearing in the agar. As a result, all tested EADs show lysis on Listeria monocytogenes EGDe.

(203) Generation of heat inactivated Listeria cells: Listeria were grown in Tryptose Broth (TB), 30 C., shaking until OD=1. After harvesting, the cells were resuspended in 1/200 volume PBST (1PBS+0.1% Tween) pH 8. The cells were heat inactivated for 20 minutes at 80 C. and stored at 20 C.

(204) 3-2. Testing Listeria Binding Activity of CBDs

(205) Protein purification of C-His tagged proteins: The CBDs were subcloned in pQE60 NcoI and BamHI-sites. After transformation of E. Coli M15, CBDs were expressed with C-terminal His-tag.

(206) Cell disruption was performed by sonication of the cell pellet in wash buffer (50 mM sodiumchloride buffer (NaPi) pH 7.5, 1 M NaCl, 20 mM Imidazole, 0.05% Tween). After centrifugation the supernatant was used for common affinity chromatography with Ni-sepharose. Washing steps were performed with wash buffer; elution was performed with elution buffer (50 mM NaPi pH 7.5, 1 M NaCl, 250 mM Imidazole, 0.05% Tween). The purified proteins were dialyzed against 25 mM Tris pH 8, 250 mM NaCl, 2.5 mM EDTA.

(207) ELISA for cell binding test: Cell ELISA

(208) Tested Listeria strains:

(209) WSLC 2011: Listeria innocua, serotype 6a

(210) WSLC 1485: Listeria monocytogenes, serotype 3a

(211) EGDe (J.Kreft): Listeria monocytogenes, serotype 1/2a

(212) Scott A 1685: Listeria monocytogenes, serotype 4b

(213) Listeria strains were cultivated in TB until OD600=1. After washing the cells twice in 1PBS pH 7.2, 96 well plates (MaxiSorp, Nunc) were coated with 10{circumflex over ()}8 cfu in 1PBS for 1 h at room temperature. Anti-His-pUD-conjugate in PBST (0.05% Tween) pH 7.2 with 0.5% BSA was added for 1 h at room temperature after 3 washing steps with PBST. Before the substrate ABTS was added, the wells were washed twice with PBST and once with PBS.

(214) The absorption was measured at 405/600 nm per ELISA reader. Result of binding is shown in Table 3.

(215) TABLE-US-00005 TABLE 3 Qualification of cell binding. Shown is the minimal amount of signal to conclude strong cell binding. CBD-C His Cell-ELISA CBD006 CBD025 CBD511 30 fold background signal CBD500 37 fold background signal CBDP40-A, -B, -C CBDP35 75 fold background signal

Example 4: Specific Capture of Biotinylated DNA with Streptavidin Magnetic Particles (No Binding of Non-Biotinylated DNA) and Release by Restriction Digest

(216) 75 g of streptavidin coated Beads (Microcoat) were washed with 500 l 1SSC (0.3 M sodiumcitrate, 3 M NaCl pH 7) and incubated with 3.76 pmol biotinylated DNA of 600 bp, 3.76 pmol biotinylated DNA of 1.4 kb and 3.76 pmol non-biotinylated DNA of 800 bp. After incubation at room temperature for 1 h the supernatant was removed (=S1) for agarose gel analysis. After two washing steps with 200 l SSC the beads were washed with restriction buffer 1NEB P3. The beads were resuspended in 20 l 1NEB P3 containing 10 U NcoI (NEB). The digest was performed for 2 h at 37 C. The supernatant (=S2) was removed for agarose gel analysis. S1, S2 and the beads were prepared for agarose gel analysis with gel buffer.

(217) FIG. 4 shows that S1 still contains biotinylated DNA (600 bp and 1.4 kbp). This means, that the binding capacity of the beads was exceeded. The entire non-biotinylated DNA (800 bp) is also found in S1, thus showing that the beads do not bind unspecific to DNA. Captured biotinylated DNA could be removed completely of the beads by restriction digest.

Example 5: Random Ligation of 4 N-Terminal EADs and 4 C-Terminal CBDs

(218) Four EADs for position 1 and four CBDs for position 2 were selected to be ligated randomly to 16 possible variants (see FIG. 5). For CBDP40 the variant A was chosen (see Table 1).

(219) 5-1. Generation of Position Specific PCR-Fragments of Domains

(220) The EADs were amplified via specific PCR for position 1, the CBDs were amplified via specific PCR for position 2 (see Example 2). The PCR products were analyzed per agarose gel electrophoresis as shown in FIG. 6 and purified by common gel purification kits. All PCR products were digested with PstI and purified by common PCR purification kits.

(221) 5-2. Ligation of PstI-Digested Fragments and Capture by Streptavidin Coated Magnetic Particles

(222) Ligation was performed with a pool of 0.2 pmol of each digested fragment, T4 Ligase (NEB) and T4 Ligase buffer for 3 h at 16 C.

(223) One third of the ligation was removed for gel analysis (L). The rest of ligated DNA was incubated with 750 g magnetic streptavidin beads (MyOne Dynal-Beads Ti) which were washed twice with 500 l 1BW buffer (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl) before usage. After 30 minutes of shaking at room temperature the supernatant was removed. Three washing steps with 1NEB4 buffer equilibrated the beads for digest in 1NEB4 with SalI (NEB) for 2 h. The supernatant was removed (S-SalI) and the beads were washed with 1NEB4. For cutting the DNA off the beads, NcoI-HF digest was performed in 1NEB4 buffer for 2 h. The half of the supernatant (NS) was analyzed by agarose gel analysis (see FIG. 7). After heat inactivating the NcoI-HF enzyme (20 min., 80 C.) the remaining DNA was used for cloning (D).

(224) 5-3. Cloning in Expression Vector and Transformation of E. coli, Plating on Selection Plates

(225) The remaining DNA was ligated via NcoI and SalI in pQE60-lib, a pQE60 with a modified multiple cloning site (see FIG. 8).

(226) Ultracompetent E. coli cells M15 were transformed with the ligated DNA and plated on lysis selection plates containing LB Top Agar, 120 l heat inactivated Listeria cells of WSLC 2011 (see Example 3-1), IPTG and Amp. Colonies that express a functionable and soluble Listeria lytic protein show lysis (see FIG. 9).

(227) 5-4. Confirmation of 16 Possible Variants and Test for Functionability

(228) To show that all possible domain combinations out of 4 N-terminal EADs and 4 C-terminal CBDs were generated, Colony PCR was performed on 88 clones with pQE forward and reverse primer. The PCR product was digested by PstI and analyzed on agarose gels. The result was confirmed by domain specific PCR. All but one construct was found using this procedure. The last construct (B in FIG. 10) was identified by Colony PCR on further 93 clones using cloning primer of EADP40-forward and CBD500-reverse, B was found two times. In conclusion all variants existed (see FIG. 10).

(229) Expression was tested of all 16 variants for affirmation of the correct assembly of the two domains. As FIG. 11 shows, all 16 proteins have the right molecular weight.

(230) The Listeria lytic activity was tested on LB Top agar plates with heat inactivated Listeria cells (see Example 3-1). The proteins behaved as expected along the corresponding CBDs, an exception were the constructs with CBDP40-A, that showed no serovar specific lytic activity (see FIG. 12). This result implies that CBDP40-A is inactive.

Example 6: Random Ligation of 19 Domains to 2-Domain Proteins and 3-Domain Proteins

(231) For the generation of 2- and 3-domain proteins every domain from Table 1 except for CBDP40-A was chosen, altogether this means the random combination of 19 different domains. That is, every domain can appear at every position. For 2 domain proteins, there are 361 possible domain combinations. For 3 domain proteins there are 6859 possible domain combinations.

(232) 6-1. 2-Domain Proteins

(233) For every domain position specific PCR for position 1 and 2 was performed. Both fragments were digested with PstI. 0.06 pmol of each fragment were ligated by T4 Ligase in T4 buffer (NEB) and captured with 120 l streptavidin beads (Microcoat) (twice washed with 1BW) in 1BW (2BW=10 mM Tris pH 7.5, 1 mM EDTA, 2 M NaCl). The supernatant with unbound DNA was removed and the beads were washed with 1NEB4. After 2 h digest with SalI-HF in 1NEB4 (NEB) the beads were washed again. For release of DNA of beads NcoI-HF digest was performed in 1NEB4 buffer for 2 h. After heat inactivating the NcoI-HF enzyme (20 min, 80 C.) the DNA was used for cloning.

(234) The DNA was ligated via NcoI and SalI in pQE60-lib, ultracompetent E. coli cells M15 were transformed and plated on lysis selection plates containing LB Top Agar, 120 l heat inactivated Listeria cells of WSLC 2011 (see Example 3-1), IPTG and ampicillin. Colonies that expressed a functionable and soluble Listeria lytic protein showed lysis and were collected.

(235) The collected E. coli clones were tested for lysis on several strains:

(236) WSLC 2011: Listeria innocua, serotype 6a

(237) WSLC 1485: Listeria monocytogenes, serotype 3a

(238) EGDe (J.Kreft): Listeria monocytogenes, serotype 1/2a

(239) Scott A 1685: Listeria monocytogenes, serotype 4b

(240) 1057 clones were analyzed, i.e. nearly 3-fold more clones than possible variants. 49 clones showed lysis on L. innocua WSLC 2011 and were picked and sequenced. Sequencing showed that the 49 clones contained 21 different combinations, and 11 of the 21 different combinations lysed all of the 4 tested serovars. For validation 20 clones independent of lytic behaviour were sequenced. As a result, there were 18 different domain combinations and one clone with a domain foreign fragment. All domains were found except for CBDP35.

(241) 6-2. 3-Domain Proteins

(242) The construction of 3-domain proteins follows the same protocol as for 2-domain proteins but after the SalI-HF digest the DNA is not released of the beads but ligated with a 10 fold amount of SalI digested fragment for position 3 (0.6 pmol of each domain) in 1NEB4 buffer with T4 Ligase and 1 mM ATP. Afterwards the DNA is digested by EcoRV-HF in NEB4 for 2 hours and released of the beads by NcoI digest in 1NEB4 buffer for 2 h. After heat inactivating the NcoI-HF enzyme (20 min., 80 C.) the DNA was used for cloning.

(243) The DNA was ligated via NcoI and EcoRV in pQE60-lib, ultracompetent E. coli cells M15 were transformed with the ligation and plated on lysis selection plates containing LB Top Agar, 120 l heat inactivated Listeria monocytogenes cells of EGDe (see Example 3-1), IPTG and ampicillin. Colonies that expressed a functionable and soluble Listeria lytic protein showed lysis and were collected.

(244) The collected E. coli clones were tested for lysis on several strains:

(245) WSLC 2011: Listeria innocua, serotype 6a

(246) WSLC 1485: Listeria monocytogenes, serotype 3a

(247) EGDe (J.Kreft): Listeria monocytogenes, serotype 1/2a

(248) Scott A 1685: Listeria monocytogenes, serotype 4b

(249) 13482 clones were analyzed, i.e. means nearly 2-fold more clones than possible variants. About 940 clones showed lysis on L. monocytogenes EGDe and were picked. 240 clones showed lysis on at least 3 of the 4 tested serovars. Sequencing has revealed 132 different 3-domain proteins with at least one CBD and at least one EAD. In the 240 sequence clones all domains were found in almost every possible position.

REFERENCES

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(251) TABLE-US-00006 SEQUENCELISTING SEQIDNO:1:aminoacidsequenceofendolysinPly511(341aminoacidresidues; origin:bacteriophageA511) 1MVKYTVENKIIAGLPKGKLKGANFVIAHETANSKSTIDNEVSYMTRNWKN 51AFVTHFVGGGGRVVQVANVNYVSWGAGQYANSYSYAQVELCRTSNATTFK 101KDYEVYCQLLVDLAKKAGIPITLDSGSKTSDKGIKSHKWVADKLGGTTHQ 151DPYAYLSSWGISKAQFASDLAKVSGGGNTGTAPAKPSTPAPKPSTPSTNL 201DKLGLVDYMNAKKMDSSYSNRDKLAKQYGIANYSGTASQNTTLLSKIKGG 251APKPSTPAPKPSTSTAKKIYFPPNKGNWSVYPTNKAPVKANAIGAINPTK 301FGGLTYTIQKDRGNGVYEIQTDQFGRVQVYGAPSTGAVIKK SEQIDNO:2:aminoacidsequenceofendolysinPly500(289aminoacidresidues; origin:bacteriophageA500) 1MALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYR 51STAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIW 101ESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAATQ 151NTNTNSNRYEGKVIDSAPLLPKMDFKSSPFRMYKVGTEFLVYDHNQYWYK 201TYIDDKLYYMYKSFCDVVAKKDAKGRIKVRIKSAKDLRIPVWNNIKLNSG 251KIKWYAPNVKLAWYNYRRGYLELWYPNDGWYYTAEYFLK SEQIDNO:3:aminoacidsequenceofendolysinPlyP40(344aminoacidresidues; origin:bacteriophageP40) 1MVLVLDISKWQPTVNYSGLKEDVGFVVIRSSNGTQKYDERLEQHAKGLDK 51VGMPFGLYHYALFEGGQDTINEANMLVSAYKKCRQLGAEPTFLFLDYEEV 101KLKSGNVVNECQRFIDHVKGQTGVKVGLYAGDSFWKTHDLDKVKHDLRWV 151ARYGVDNGKPSTKPSIPYDLWQYTSKGRIKAIASPVDMNTCSSDILNKLK 201GSKAPVKPAPKPTPSKPAPAKPAPKTTTKYVNTAHLNIREKASADSKVLG 251VLDLNDSVQVISESGGWSKLKSGNKQVYVSSKYLSKSKTTPKAKPSSKQY 301YTIKSGDNLSYIAKKYKTTVKQIQNWNGIKDANKIYAGQKIRVK SEQIDNO:4:aminoacidsequenceofendolysinPlyP35(291aminoacidresidues; origin:bacteriophageP35) 1MARKFTKAELVAKAEKKVGGLKPDVKKAVLSAVKEAYDRYGIGIIVSQGY 51RSIAEQNGLYAQGRTKPGNIVTNAKGGQSNHNFGVAVDFAIDLIDDGKID 101SWQPSATIVNMMKRRGFKWGGDWKSFTDLPHFEACDWYRGERKYKVDTSE 151WKKKENINIVIKDVGYFQDKPQFLNSKSVRQWKHGTKVKLTKHNSHWYTG 201VVKDGNKSVRGYIYHSMAKVTSKNSDGSVNATINAHAFCWDNKKLNGGDF 251INLKRGFKGITHPASDGFYPLYFASRKKTFYIPRYMFDIKK SEQIDNO:5:aminoacidsequenceofendolysinPlyB054(321aminoacidresidues; origin:bacteriophageB054) 1MAKKLKLAIYAGHGGVDSGATGEGYREDDLTLDIAKRTTKVLRGAGHTVI 51NNRTTDVNRNISADAKLANREKVDAVIEFHFDAAGASAEGTTGFYCEGSS 101SSKKLAQCVNDKLDDVFKDRNVKPDTSTRHGRLGILRETNAVATLQEVAF 151ITNKNDMIKYNQRADEIAKKAAEGILSYFNEKLPEQNPNRHDGAVVDSIP 201ALPKPDFKTVPSKMYKAGSELLVYDHNKYWYKTYINDKLCYIYKSFCISN 251GKKDSKGRIPIKIKSVKDLRIPVWDNTKLSSGKIKWYAPNTKLSWYNNKK 301GYLELYYPNQGWYYTANYFLK SEQIDNO:6:aminoacidsequenceofendolysinPlyPSA(314aminoacidresidues; origin:bacteriophagePSA) 1MSNYSMSRGHSDKCVGAEDILSEIKEAEKVLNAASDELKREGHNVKTFID 51RTSTTQSANLNKIVNWHNANPADVHISVHLNAGKGTGVEVWYYAGDEKGR 101KLAVEISAKMAKALGLPNRGAKATKDLRFLNSTKGTAVLLEVCFVDRKED 151ANAIHKSGMYDKLGIAIAEGLTGKTVAAKNPNRHSGAVVDSVPMLSKMDF 201KSSPIKMYKAGSSLLVYEHNKYWYKAYINDKLCYIYKSFCISNGKKDAKG 251RIKVRIKSAKDLRIPVWNNTKLNSGKIKWYSPGTKLSWYDNKKGYLELWY 301EKDGWYYTANYFLK SEQIDNO:7:aminoacidsequenceofendolysinPly006(235aminoacidresidues; origin:bacteriophageA006) 1MALTEAWLIEKANRKLNVSGMNKSVADKTRNVIKKMAKKGIYLCVAQGYR 51SSAEQNALYAQGRTKPGAVVTNAKGGQSNHNYGVAVDLCLYTSDGKNVIW 101ESTTSRWKTVVSAMKAEGFEWGGDWKSFKDYPHFELYDAAGGEKAPSTSA 151SKPATSTSSNKNVYYTENPRKVKTLVQCDLYNSVDFTEKHKTGGTYPAGT 201VFTISGMGKTKGGTPRLKTKSGYYLTANKKFVKKI SEQIDNO:8:aminoacidsequenceofendolysinPlyB025(276aminoacidresidues; origin:bacteriophageB025) 1MTMYYEERSRNNIAKLAANTRAKALEWFNWCCKNGIEVLVYETIRTKEQQ 51AANVANGKSQTMRSYHIVGQAFDFVMAKGKTVDWGGYKTAKAKKVIAKAK 101ALGFSWGGDWSGFVDCPHMQYEYKGYGTDKFTADKLVANNKTGKQGVYAR 151DFLNIRTKATWDSPVAFKVPIYYYAQILWDTKNGDWVQIEFQGKKGWYKP 201SFKEYWYEKDPCTSYICVADVNFRKSSKWDSPVAQKKKKGETVRMVKKAK 251NGWLEFGLTNGVIGYIPNSAKYVKKK SEQIDNO:9:aminoacidsequenceoflytictailproteingp29(795aminoacid residues;origin:bacteriophageP100) 1MTTVKRMPEFDLKFVTEKNDYLIRYDARNPSSDTLAEKVISVTTKNAMSD 51DSAVFSIVVAGDMEWDKILDSNDVVILKIYPNLRVMMPDNVVVLVGLISE 101VRREGDYSNNSIIYRITGQSFAKSFMQFQLGVIQEVSVVITDIGWLPDSK 151ADGVEFTGKTAAEIGKSITDRFKKYMKYNFNREYTMENFLDYSFSSWKDY 201EKLADPTPFINYEGSLKQLLDDVTAKPFNELFFESTSDEKCKMIMRRTPF 251NKEDWDKLPSYKISTEAVISDSLAKGDTEAYSIFNVTSGNMAGATSVDLN 301SFPQYHQALVDKYGYKKLEVDNRYLFESSTDGSSTTEKADVGSKEKTKTV 351ITYSKFNSFMRSYTSDQVRMNQSSIAKSLVDSYDKLTTSQANQLLAKYSA 401VGAISEADFKKIVGDIAEGDNTGTATLDFDSVNSWFSLNYSSLSEVSTNR 451DATIKAFVKNFANTDEDQATKIVALYISSQGVMTKEKFDAIIKESTSSST 501KDPDNTTGNSSSALQYFSKTIYNWYSENANFYAGDIKVIGSPVYRLGSKL 551LVEDKQQGDEWEFYIESVSHEYSYTAGYTTTLGVTRGLNNKGKDRFTHLW 601GKSSDFKGGLLGEKTSAELIQEAGSTSSGSDGSGDVSAPDVQGSDVAVAA 651LRYGLAHKKPEKKSVYSFGGGRGSSNPMEGKEPYAMDCSSFVWWCYKACG 701VTLAGAQTQAILGDDRFNTVSSRGSKSKEIFKKMQVGDLVYFYDNNTHIG 751MYAGEGKFLGCNGDGSWDTNGGVQLKPMDSGYWWTQFQGHVIRFV SEQIDNO:10:aminoacidsequenceofautolysinMurAfromListeriamonocytogenes residues,origin:ListeriamonocytogenesEGDe(J.Kreft),serotype1/2a) 1MQKTRKERILEALQEEKKNKKSKKFKTGATIAGVTAIATSITVPGIEVIV 51SADETAPADEASKSAEANTTKEASATATPENTAKQTVGPQQTETKEQTKT 101PEEKQAATNQVEKAPAEPATVSNPDNATSSSTPATYNLLQKSALRSGATV 151QSFIQTIQASSSQIAAENDLYASVMIAQAILESAYGTSELGSAPNYNLFG 201IKGAYNGQSYTKQTLEDDGKGNYYTITAKFRKYPSYHQSLEDYAQVIRKG 251PSWNPNYYSKAWKSNTTSYKDATKALTGTYATDTAYATKLNDLISRYNLT 301QYDSGKTTGGNSGSTGNSSNTGNTNTSNAKIYTVVKGDSLWRIANNHKVT 351VANLKAWNNLKSDFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGT 401STNAKVYTVVKGDSLWRIANNNKVTIANLKAWNNLKSDFIYPGQKLKVSA 451GSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTI 501ANLKAWNNLKSDFIYPGQKLKVSAGSTTNTNTAKPSTNNPSNSTVKTYTV 551KKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK SEQIDNO:11:aminoacidsequenceofautolysinIspCfromListeriamonocytogenes (774aminoacidresidues;origin:ListeriamonocytogenesLI0521,serotype4b) 1MINKKWMKIVMIPMLVVPMYGLTTVGGQLQDSLTGENSFVKEVEAATTAS 51QQAFIDKIAPAAQASQEKYHLLSSITLAQAILESGWGKSGLATQGYNLFG 101IKGKYNGQSVIMTTSEYVNGEWIKIDAEFRKYPSWNESVTDHTLLLVNGT 151SWNKDLYKKVVDATDYKVTAMEPQKAGYATSPTYGASLIQVIENYDLAKY 201DVLYDKILTQKSTSGKATVTSPTGNGVWTLPYKVKGVQSVSPASTYANKD 251IDLVSVATTKRGTYYQFKYNGKVVGWVDGKALTIYDSVNYDKVNVGRAKI 301TSPVSNGIWSKPYNVYGREFVTNATTYAQQEIKLLREAQTAKGTYYQFSI 351NNKTIGWIDKRALTIYPYDSIISSKNVNLDGQITNPTGNGIWTKAYKLEG 401TTSVAQATKYANKDVKISQQIETQHGTYYNISIDGKAIGWLDRNAITLYD 451QEEYNKTVAIDAVVKNVKGNAVWTEPYRTVGTKLIGPAETYLNKEVEVVR 501EAKTPKGTYYQFKSGGKVIGWLDKKAFDVYDNINYNKAVNLDAVVENVTG 551NAVWTAPYKSKGVKLVTSAATYKGKATKITREAQTSRGTYYEFSVDGKVI 601GWLDKKAFDVYDNINYNKAVNLDAVVENVTGNAVWTAPYKSKGVKLVTSA 651ATYKDKATKITREAQTSRGTYYEFSVNGKVIGWLDKKAFDVYDSIEYNKA 701INMTGLLSNAPGNGIWTEPYRVIGTKNVGQATAYANKTVQLIREAKTTRA 751TYYQMSVNGKIVGWVDKRAFTNVK SEQIDNO:12:aminoacidsequenceofbacteriocinfromStreptomycescoelicolor Wier(294aminoacidresidues;origin:StreptomycescoelicolorWier) 1MPAYSSLARRGRRPAVVLLGGLVSASLALTLAPTAAAAPLAPPPGKDVGP 51GEAYMGVGTRIEQGLGAGPDERTIGPADTSGVQGIDVSHWQGSINWSSVK 101SAGMSFAYIKATEGTNYKDDRFSANYTNAYNAGIIRGAYHFARPNASSGT 151AQADYFASNGGGWSRDNRTLPGVLDIEHNPSGAMCYGLSTTQMRTWINDF 201HARYKARTTRDVVIYTTASWWNTCTGSWNGMAAKSPFWVAHWGVSAPTVP 251SGFPTWTFWQYSATGRVGGVSGDVDRNKFNGSAARLLALANNTA SEQIDNO:13:aminoacidsequenceofautolysinfromStaphylococcusaureus USA300(334aminoacidresidues;origin:StaphylococcusaureusUSA300) 1MQKKVIAAIIGTSAISAVAATQANAATTHTVKPGESVWAISNKYGISIAK 51LKSLNNLTSNLIFPNQVLKVSGSSNSTSNSSRPSTNSGGGSYYTVQAGDS 101LSLIASKYGTTYQNIMRLNGLNNFFIYPGQKLKVSGTASSSNAASNSSRP 151STNSGGGSYYTVQAGDSLSLIASKYGTTYQKIMSLNGLNNFFIYPGQKLK 201VTGNASTNSGSATTTNRGYNTPVFSHQNLYTWGQCTYHVFNRRAEIGKGI 251STYWWNANNWDNAAAADGYTIDNRPTVGSIAQTDVGYYGHVMFVERVNND 301GSILVSEMNYSAAPGILTYRTVPAYQVNNYRYIH SEQIDNO:14:artificialsequence(aminoacidsequencedesignedtoactasalinker) GGSKPGGTKPGGSKP SEQIDNO:15:artificialsequence(nucleotidesequencedesignedtoactasaprimer) CACACACCATGGCG SEQIDNO:16:artificialsequence(nucleotidesequencedesignedtoactasaprimer) TGTGTGACTAGT SEQIDNO:17:artificialsequence(nucleotidesequencedesignedtoactasaprimer) TGTGTGGGATCC SEQIDNO:18:artificialsequence(nucleotidesequencedesignedtoactasaprimer) GTTTAACTTTAAGAAGGAGATATACCATGGCG SEQIDNO:19:artificialsequence(nucleotidesequencedesignedtoactasaprimer) CCTTTCGGGCTTTGTTACTGCAGGGATCC SEQIDNO:20:artificialsequence(nucleotidesequencedesignedtoactasaprimer) GTTTAACTTTAAGAAGGAGACTGCAGATGGCG SEQIDNO:21:artificialsequence(nucleotidesequencedesignedtoactasaprimer) CCTTTCGGGCTTTGTTAGTCGACGGATCC SEQIDNO:22:artificialsequence(nucleotidesequencedesignedtoactasaprimer) GTTTAACTTTAAGAAGGAGAGTCGACATGGCG SEQIDNO:23:artificialsequence(nucleotidesequencedesignedtoactasaprimer) CCTTTCGGGCTTTGTTAGATATCGGATCC