Method of obtaining a polyepitopic protein and polyepitopic DNA vector
10874735 ยท 2020-12-29
Assignee
Inventors
- Piotr SKOWRON (Gdansk, PL)
- Agnieszka ZYLICZ-STACHULA (Gdansk, PL)
- Olga ZOLNIERKIEWICZ (Gdansk, PL)
- Malgorzata SKOWRON (Gdynia, PL)
- Lukasz Janus (Poznan, PL)
- Joanna JEZEWSKA-FRACKOWIAK (Gdansk, PL)
- Daria KREFFT (Reda, PL)
- Dawid NIDZWORSKI (Gdansk, PL)
- Kasjan SZEMIAKO (Gdansk, PL)
- Natalia MACIEJEWSKA (Plosnica, PL)
- Marta NOWAK (Reda, PL)
- Aneta SZYMANSKA (Gdansk, PL)
Cpc classification
C12N2730/10122
CHEMISTRY; METALLURGY
C12N2730/10134
CHEMISTRY; METALLURGY
C12N2730/10151
CHEMISTRY; METALLURGY
C12N15/64
CHEMISTRY; METALLURGY
C12N15/70
CHEMISTRY; METALLURGY
C12N2800/80
CHEMISTRY; METALLURGY
A61K39/292
HUMAN NECESSITIES
C12N15/66
CHEMISTRY; METALLURGY
International classification
C12N15/66
CHEMISTRY; METALLURGY
C12N15/10
CHEMISTRY; METALLURGY
C12N15/70
CHEMISTRY; METALLURGY
Abstract
The present invention is directed to a method of manufacturing a polyepitopic protein comprising the steps of cloning a blunt-ended DNA sequence by encoding the epitope that is to be cloned into a DNA vector recognized by the endonuclease SmaI or the endonuclease SapI and isolating the polyepitopic protein by transforming a bacterial host cell with such vector.
Claims
1. A method of manufacturing polyepitopic protein, comprising the steps of: a) cloning a blunt-ended DNA sequence encoding an epitope into a DNA vector comprising two convergent DNA sequences recognized by Sap I endonuclease and a DNA sequence found between them containing a site for cloning in an insert recognised by Sma I endonuclease having a sequence selected from the group consisting of SEQ ID No: 1, 2, 3, 4, 5, 6, 7 or 11, b) amplifying the vector in a bacterial host, isolating the vector, digesting the vector with Sap I endonuclease, isolating a fragment containing the DNA sequence encoding the epitope, c) autoligating the isolated fragment of step (b), d) inserting the isolated fragment of step (c) into said DNA vector at a site recognised by Sap I endonuclease, e) transforming a bacterial host with the vector, expressing and isolating a polyepitopic protein.
2. The method according to claim 1, wherein the epitope is an HBV epitope.
3. The method according to claim 1, wherein said two convergent DNA sequences recognized by Sap I endonuclease and a DNA sequence found between them containing a site for cloning in an insert recognised by Sma I endonuclease form a monomeric unit capable of coding at least two epitopes originating from different proteins or different regions of the same protein.
4. The method according to claim 1, wherein the polyepitopic protein additionally comprise a sequence as a part thereof comprising a fusion tag containing a sequence of 6 histidine residues, and further wherein the polyepitopic protein is isolated with a metalloaffinity chromatography.
5. The method according to claim 1, wherein the step e) comprises immobilizing the polyepitopic protein on a macromolecular carrier.
6. The method according to claim 1, wherein Steps (b) to (d) are repeated to increase the size of the polyepitopic protein prior to Step (e).
7. The method according to claim 2, wherein the HBV epitope is encoded by SEQ ID NO: 9.
8. The method according to claim 3, wherein the different proteins or different regions of the same protein are encoded by a synthetic sequence.
9. The method according to claim 4, wherein the metalloaffinity chromatography comprises immobilized nickel.
10. The method according to claim 4, further comprising an additional purification step selected from the group consisting of heating the polyepitopic protein, fractionation using polyethylenimine, salting out with ammonium sulphate, and molecular sieving gel chromatography.
11. The method according to claim 5, wherein the macromolecular carrier is selected from the group consisting of microorganisms, cells, bacteria, bacteriophages, viruses, defective virions, autoaggregating proteins, and nanoparticles.
12. The method according to claim 11, wherein the macromolecular carrier is a T7 bacteriophage.
13. The method of claim 1, wherein the DNA sequence is SEQ ID NO: 7.
14. The method of claim 1, wherein the DNA vector is a protein expression vector, and additionally comprises an origin of replication, an antibiotic resistance gene, a transcription promoter, a repressor gene, and a translation initiation signal.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION OF THE INVENTION
(13) The following examples contain a detailed description of one possible embodiment variant of the method according to the present invention. An alternative method of cloning in the insert is the use of a Sapl-digested vector with sticky ends filled in using DNA polymerase in the presence of deoxyribonucleotide triphosphates. Following the present invention a person skilled in the art can propose subsequent embodiment variants.
(14) Preferably, the epitope is a HBV epitope, particularly that encoded by the synthetic sequence 9 (see also
(15) Preferably, the amplified monomer segment may contain different epitopes, from different proteins or different regions of the same protein, preferably encoded by a synthetic sequence (see schematic in
(16) We also disclose a method of constructing as well as using artificial genes that do not occur in nature using genetic engineering methods as well as chemical synthesis, containing multiple DNA copies encoding repeating segments, containing multiple monomer units of one or more peptides. The amplification of a gene, encoding a peptide (epitope) with a particular biological or chemical function leads to the amplification of the desirable interaction of the resulting (poly)peptide with a specific ligand. In particular such polyepitopic proteins are useful as: (i) artificial antigensa new generation of vaccines with a magnified potential stimulation of the immune system; (ii) polyproteins containing modules for rare metal chelation for their industrial production or environmental remediation; (iii) a binding module for enzyme cofactors (such as cations, anions, organic molecules) such as proteases acting within a wound in order to stop deleterious activities; (iv) protective multiepitopic proteins, multiplex modules containing peptides with activators or inhibitors of biological functions for the treatment of molecular, viral and bacterial diseases; (V) multiepitopic proteins containing multimers of peptide hormones or biologically active fragments of signalling proteins and those that stimulate tissue regeneration. Such proteins, placed in a wound, would gradually release biologically active peptides under the influence of proteinases, stimulating the regeneration of tissue; (vi) the polyepitopic protein is immobilized on macromolecular carriers, such as microorganisms, cells, bacteria, bacteriophages, viruses, defective virions, autoaggregating proteins, or nanoparticles. The immobilization may be performed using genetic or chemical means. Immobilized polyepitopic proteins, may magnify the effect of the envisaged uses (i)-(vi).
(17) In particular, we designed a vector-enzymatic system for the amplification of a DNA segment. The amplified DNA segment may be natural origin or the result of a chemical synthesis.
Example 1. General Schematic of the Embodiment of the Method According to the Present Invention
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(19) The amplifying vector contains 2 convergent DNA sequences recognised by the sub-type IIS restriction endonuclease, that preferentially recognises a relatively long DNA sequence, which cuts DNA and generates 3-nt (or multiples of 3 nt) sticky ends. We used the Saplendonuclease, whose particular characteristic is that it recognises a relatively long sequence of 7 base pairs (unique in the vector and amplified DNA segment) which cuts DNA at a distance of 1 nt in the upper chain and 4 nt in the lower chain, thereby generating 3-nt sticky ends, or the equivalent of a single codon. The Sapl sites are adjacent in the vector to the sequence of the classic Type II endonuclease, which is designed for cloning in the inserted DNA. We used the Smal endonuclease, which cuts DNA within the recognition sequence, generating the so-called blunt ends. A vector cut with Smal may be cloned with any arbitrary DNA segment, synthetic or natural, which is then to be amplified. In a preferable embodiment, the amplified DNA segment encodes an antigen or amino-acid sequence encompassing several identical or differing antigens. The only limit is the length of the amplified fragment, as dictated by the length of the insert DNA accepted by a given class of DNA vector. The amplifying module may be transferred to different classes of vectors using cloning.
Example 2. A Series of 6 Designed pAMP1 Vectors
(20) In the example embodiment shown in
(21) Vectors contain the origin of replication p15A, an antibiotic resistance gene against chloramphenicol, the strong transcription promoter PR from the lambda bacteriophage, a repressor gene, c1857ts, translation initiation signals, a sequence of 6 histidine residues with an affinity for nickel ions, a restriction site system for fusing to the translation start codon ATG as well as a module for the directional amplification of a DNA fragment maintaining the ORF, containing convergent restriction sites for a IIS subtype endonuclease, preferably Sapl, separated by a short DNA segment, which can contain ancillary restriction sites for cloning in the insert DNA, preferably Smal. The variants differ in terms of the possibility of manipulating three reading frames (which may be significant when amplifying natural, non-synthetic DNA sequences) as well as the presence or absence of a His6 tag (excellent for easing the subsequent isolation of the expressed polyepitopic protein, regardless of its charge, solubility and other biochemical parameters). Variant 4 was used for the following example of the amplification of the epitope from the surface antigen of HBV. The amplifying module may be introduced by way of cloning in various classes of vector, containing, for example, alternative origins of replication, antibiotic resistance genes, transcriptional promoters and translation signals. For example, we transferred the amplifying module to the vector pBAD/Myc-HisA as well as pET21d21d(+), possessing ampicillin resistance, a colE1 origin of replication as well as araBAD or T7 transcription promoters, respectively. Synthetic modules with sticky ends for the enzymes Ncol and Sacl, in versions containing and not containing the His6 residue affinity tag, were cloned into a vector cut with these enzymes, thereby enabling the expression of the polyepitopic proteins using the araBAD or T7 promoters (respectively). We obtained the vectors: pBADAMP1-A, pBADAMP1-HisA, pETAMP1-A, pETAMP1-HisA possessing the inserted amplifying module at the standard MCS (multiple cloning site).
(22) The full sequence of the pAMP1-HisA vector used in example 3 is shown as sequence 7. Furthermore, in
(23) The sequences of the synthetic oligodeoxyribonucleotides, encoding the amplifying module transferred into pBAD and pET vectors, used in example 2 are shown as sequences 12, 13, 14 and 15.
Example 3. Production of a Polyepitopic Protein Containing a Model 7 Amino-Acid Epitope of the HBV Surface Antigen
(24) A model 7 amino-acid epitope of the HBV surface antigen subjected to the amplification reaction is shown in
(25) The synthetic DNA fragment encoding the epitope of the HBV surface antigen was subjected to a pilot amplification experiment in the vector pAMP1-HisA. We obtained >60 copies of the epitope in the DNA concatemer in vitro as well as 13 copies IN THE HYBRID polyepitopic protein cloned in vivo.
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(27) We analysed the amplification reaction using PAGE. We cloned a synthetic DNA fragment of 21 bp into the amplifying vector pAMP1-HisA, encoding the 7 amino-acid epitope of HBV. A plasmid containing the monomer HBV epitope digested with the Sapl endonuclease, excising the modified epitope gene from the plasmid construct. The modification consisted of adding to it 3-nt, single-stranded 5 sticky ends. Aside from the amplification function, in the final polymeric hybrid protein, these ends are responsible for the addition of a proline residue, the so-called helical breaker, which separate the epitope monomers and facilitate the independent folding of the epitope into tertiary structures, thereby help to maintain their natural spatial structure. The number of added helical breakers can be regulated arbitrarily by incorporating amino-acids encoding them to the end of the synthetic epitope (at the level of its encoding DNA). The excised modified DNA encoding the epitope was subjected to autoligation in vitro. Lanes from 5 to 160 minutes show the autoligation kinetics. Reaction products were analysed electrophoretically, yielding a series of DNA segments of increasing length, that are directional concatemers (polymers) of the epitope gene in relation to the control reaction without the DNA ligase (K). The resulting in vitro concatemers were re-cloned into pAMP1-HisA, where they could be subjected to another amplification cycle or expression of the encoded multimeric protein.
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(29) The mixture of in vitro polymerised synthetic HBV epitope genes (
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(31) The DNA fragment was excised using the Sapl endonuclease from a pAMP1-HisA construct containing a concatemer of 5 epitope copies, obtained during the 1st round of amplification and subjected to amplification again. The largest concatemer, visible at the edge of agarose gel resolution, contains 12 copies of the pentamer, constituting a 60-fold directionally polymerised HBV epitope. Larger concatemers are evidently visible, although not separated into distinct bands. The resulting 2nd round products were recloned into pAMP-HisA and may be subjected to a third round of round of amplification, leading to the production of hundreds or thousands of HBV epitope copies, set out in a single recombinant polypeptide (protein) with a continuous ORF. These clones were also subjected to analytical expression in order to obtain variants of epitope multiplication within the polyepitopic protein.
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(34) Because none of the recombinant host's own proteins contain the sequence of 6 histidines, the positive reaction indisputably confirms that the isolated protein is the polyepitope 13-mer of HBV. An additional confirmation is the expected size of the isolated protein in comparison to mass markers as well as specific binding to the HiTrap IMAC HP gel. The procedure is universal, successfully confirmed in the isolation of other variants of polyepitopic proteins, fused with 6 histidine residue tags, and contains varying amounts of polymerised HBV epitope.
Example 4. Production of Higher Order Multimeric Structures Containing Several Hundred Immobilised Copies of the Polyepitopic Protein, Containing the Model 7 Amino-Acid Epitope of the HBV Surface Antigen on the Capsid Surface of T7 Bacteriophage
(35) The construction of polyepitopic proteins facilitates a multiple increase in the concentration of the epitope in a single protein molecule, and a subsequent amplification stage is based on the combination of many polyepitopic protein molecules in one higher order structure. This may be achieved: (i) biologically, through the fusion of the gene encoding the polyepitopic protein with the genetic material of a higher order structural carrier such as a chromosome, nucleoid, microorgamal plasmid, a bacterium, bacteriophage or virus or (ii) by chemical means, through the use of factors that conjoin macromolecules.
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(37) The sequence of the PCR product being the substrate for producing the insert for the Phage Display System (encoding a variant of the pentamer HBV epitope) used in Example 4 is shown as sequence 16, and the sequences of the PCR primers used to amplify the variant of 5 HBV epitopes are shown as sequences 17 and 18.
Example 5. Immunological Activity of the Polyepitope HBV Protein
(38) The 25-mer polyepitope HBV protein of Example 2 was isolated from recombinant bacteria using the procedure shown in Example 4. Representative groups of mice (6 individuals each) were inoculated with 20 ug/mouse with a purified 25-mer in PBS buffer mixed with Freund's incomplete adjuvant. In parallel, we inoculated a control group with PBS and Freund's incomplete adjuvant. The vaccination cycle encompassed 3 injections at 3-week intervals.
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