CN115927270B - Staphylococcus aureus phage lyase, variant thereof and application thereof - Google Patents
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
- Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
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Abstract
The invention belongs to the technical fields of microorganism technology and enzyme engineering, and provides staphylococcus aureus phage lyase, a variant thereof and application thereof. The staphylococcus aureus phage DZ25 is separated from milk, a lyase gene is cloned and expressed, the gene is named LysDZ, the property of the gene is researched, the rational design is carried out, a series of staphylococcus aureus phage lyase variants are obtained, and the staphylococcus aureus phage lyase variants which have obvious staphylococcus aureus cleavage performance under high temperature conditions are obtained through experimental verification and screening, so that the method is very beneficial to actual production and living application, lays a foundation for developing a novel effective biological green inhibitor for controlling staphylococcus aureus, and has good practical application value.
Description
Technical Field
The invention belongs to the technical fields of microorganism technology and enzyme engineering, and particularly relates to staphylococcus aureus phage lyase, a variant thereof and application thereof.
Background
The disclosure of this background section is only intended to increase the understanding of the general background of the invention and is not necessarily to be construed as an admission or any form of suggestion that this information forms the prior art already known to those of ordinary skill in the art.
Staphylococcus aureus is a common pathogenic microorganism and important nosocomial infectious bacteria, is a main cause of bacterial infection of blood, lower respiratory tract and the like, and can cause severe infectious diseases such as local suppurative infection, pneumonia, septicemia and the like. The rate of infection with staphylococcus aureus has increased over the past several decades, and in particular the continued emergence and spread of drug-resistant and multi-resistant staphylococcus aureus, traditional antibiotic therapies have gradually been disabled, and development of new and effective bioluminescence inhibitors to control staphylococcus aureus has been urgently needed.
Phage lytic enzymes are enzymes that digest the cell wall of bacteria that are expressed later in the infection of bacteria by double-stranded DNA phage. For gram positive bacteria, the lyase can also destroy bacterial cell wall peptidoglycan from outside to cause bacterial osmotic lysis, thereby achieving the sterilization effect. Many studies have now demonstrated that lytic enzymes have great bactericidal potential. The advantages of lyase over traditional antibiotic treatment are the high efficacy, specificity and safety of the bactericidal action. The cleavage enzymes can be classified into at least 5 classes according to their catalytic domain hydrolysis site on peptidoglycans: muramidase, lytic transglycosidase, N-acetyl-beta-D-glucosaminidase, N-acetyl muramyl-L-alanine amidase and endopeptidase.
Staphylococcus aureus phage lytic enzymes are typically composed of one or two catalytic domains at the N-terminus and a binding domain at the C-terminus. The most common catalytic domains are CHAP (cysteine and histidine dependent amidase), which hydrolyzes the amide bond between peptidoglycan N-acetyl muramic acid and L-alanine. The binding domain at the C end is usually of SH3 type, can target and recognize and bind specific peptidoglycan-related ligands on the cell wall, increases the proximity of the enzyme to the substrate, and ensures high specificity of the enzyme. The combination of the modularized structural domains facilitates the design and transformation of the lyase by using biotechnology such as protein engineering and the like, so that the lyase with higher enzyme activity, wider cleavage spectrum and more stability is obtained.
Disclosure of Invention
The invention provides staphylococcus aureus phage lyase and variants and applications thereof. The invention separates staphylococcus aureus phage DZ25 from milk, clones and expresses lyase gene, named LysDZ25, researches a series of properties and carries out rational design, thus obtaining mutant with obviously improved cleavage activity and thermal stability. Based on the above results, the present invention has been completed.
Specifically, the invention relates to the following technical scheme:
In a first aspect of the invention, a staphylococcus aureus phage lyase is provided, wherein the amino acid sequence of the staphylococcus aureus phage lyase is shown in SEQ ID NO. 1. Experiments prove that the enzyme has bactericidal effect on most staphylococcus aureus, and in order to further improve the bactericidal activity and the thermal stability of the enzyme, the invention carries out rational design on the enzyme to obtain a series of enzyme mutants.
Accordingly, in a second aspect of the invention there is provided a staphylococcus aureus phage lyase variant, said variant being mutated at one or more sites selected from the group consisting of: a220L, S230E, V L, N245R, D299L, N319L, S333V, S333I, S333L, K341P, N342E.
Wherein, the amino acid residue number is shown in SEQ ID NO.1 (amino acid sequence of staphylococcus aureus phage lyase).
The staphylococcus aureus phage lyase variant is mutated based on the wild-type lysostaphin shown above, and the staphylococcus aureus phage lyase variant is selected from the group of mutants consisting of:
Mutant a: S333V;
Mutant B: S333V/N245R;
Mutant C: S333V/N245R/D299L.
In a third aspect of the invention there is provided a polynucleotide encoding a staphylococcus aureus phage lyase according to the first aspect and/or a staphylococcus aureus phage lyase variant according to the second aspect described above.
In a fourth aspect of the present invention, there is provided a recombinant expression vector comprising a polynucleotide according to the third aspect above.
In a fifth aspect of the invention there is provided a cell comprising a recombinant expression vector or chromosome according to the fourth aspect of the invention, integrated with a polynucleotide according to the third aspect of the invention or expressing a staphylococcus aureus phage lyase according to the first aspect of the invention and/or a staphylococcus aureus phage lyase variant according to the second aspect of the invention.
In a sixth aspect of the invention, there is provided a method of producing a staphylococcus aureus phage lyase and/or variants as described above, comprising the steps of: culturing the cells of the fifth aspect above, thereby expressing the staphylococcus aureus phage lyase and/or variant; separating and purifying to obtain staphylococcus aureus phage lyase and/or variant.
In a seventh aspect of the invention there is provided a staphylococcus aureus inhibitor and/or killer comprising a staphylococcus aureus phage lyase according to the first aspect, a staphylococcus aureus phage lyase variant according to the second aspect and/or a cell according to the fifth aspect described above.
In an eighth aspect of the invention there is provided the use of a staphylococcus aureus bacteriophage lytic enzyme as described in the first aspect, a staphylococcus aureus bacteriophage lytic enzyme variant as described in the second aspect, a polynucleotide molecule as described in the third aspect, a recombinant expression vector as described in the fourth aspect, a cell as described in the fifth aspect, a staphylococcus aureus inhibitor and/or a biocide as described in the seventh aspect in the anti-staphylococcus aureus field.
In a ninth aspect of the present invention, there is provided a method for designing a staphylococcus aureus phage lyase variant according to the second aspect, the method comprising constructing the three-dimensional structure of the staphylococcus aureus phage lyase described above, and predicting the thermal stability of the staphylococcus aureus phage lyase variant based on the MDL method.
The beneficial technical effects of one or more of the technical schemes are as follows:
The technical scheme provides staphylococcus aureus phage lyase and variants and application thereof. The staphylococcus aureus phage DZ25 is separated from milk, a lyase gene is cloned and expressed, the gene is named LysDZ, the property of the gene is researched, the rational design is carried out, a series of staphylococcus aureus phage lyase variants are obtained, and the staphylococcus aureus phage lyase variants which have obvious staphylococcus aureus cleavage performance under high temperature conditions are obtained through experimental verification and screening, so that the method is very beneficial to actual production and living application, lays a foundation for developing a novel effective biological green inhibitor for controlling staphylococcus aureus, and has good practical application value.
Drawings
The accompanying drawings, which are included to provide a further understanding of the invention and are incorporated in and constitute a part of this specification, illustrate embodiments of the invention and together with the description serve to explain the invention.
FIG. 1 shows the cloning of the DZ25 gene and the expression and purification of DZ25 protein in the examples of the present invention. (a) is a DZ25 gene expression profile; (b) is a DZ25 protein expression profile.
FIG. 2 is a schematic diagram of a mutant design strategy in an embodiment of the present invention.
FIG. 3 is a diagram showing the predicted LysDZ three-dimensional structure and domain resolution of RoseTTAFold in an embodiment of the invention. (a) is a predicted LysDZ three-dimensional block diagram; (b) is a LysDZ domain split map.
FIG. 4 shows the activity of LyzDZ25 and its mutants as measured by OD 600nm nephelometry in examples of the invention. (a) is a single-point mutant, (b) is a double-point mutant, and (c) is a triple-point mutant.
FIG. 5 shows the stability of LyzDZ and its mutants at various temperatures as measured by OD600nm turbidity in examples of the invention. (a) Single and double point mutants, and (b) three point mutants.
FIG. 6 is a graph showing the evaluation of thermostability and cleavage activity of LysDZ and its optimal single-, double-, and triple-point mutants in the examples of the present invention. (a) is a thermal stability assessment (half-life assessment), (b) is a lytic activity assessment, (c) is a lytic activity assessment in milk.
FIG. 7 shows the lytic effect of LysDZ and its mutants on Staphylococcus aureus in the examples of the present invention. (a) is a blank, (b) is wild-type LysDZ, (c) is a single-point mutant S333V, (D) is a double-point mutant S333V/N245R, and (e) is a three-point mutant S333V/N245R/D299L.
Detailed Description
It should be noted that the following detailed description is illustrative and is intended to provide further explanation of the application. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs.
It is noted that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of exemplary embodiments according to the present application. As used herein, the singular is also intended to include the plural unless the context clearly indicates otherwise, and furthermore, it is to be understood that the terms "comprises" and/or "comprising" when used in this specification are taken to specify the presence of stated features, steps, operations, devices, components, and/or combinations thereof. Experimental methods in the following embodiments, unless specific conditions are noted, are generally in accordance with conventional methods and conditions of molecular biology within the skill of the art, and are fully explained in the literature. See, e.g., sambrook et al, molecular cloning: the techniques and conditions described in the handbook, or as recommended by the manufacturer.
In an exemplary embodiment of the present invention, a staphylococcus aureus phage lyase is provided, the amino acid sequence of which is shown in SEQ ID NO. 1. Experiments prove that the enzyme has bactericidal effect on most staphylococcus aureus, and in order to further improve the bactericidal activity and the thermal stability of the enzyme, the invention carries out rational design on the enzyme to obtain a series of enzyme mutants.
Accordingly, in one or more embodiments of the present invention, there is provided a staphylococcus aureus phage lyase variant, said variant being mutated at one or more sites selected from the group consisting of: a220L, S230E, V L, N245R, D299L, N319L, S333V, S333I, S333L, K341P, N342E.
Wherein, the amino acid residue number adopts SEQ ID NO.1 (amino acid sequence of staphylococcus aureus phage lyase), and the specific amino acid sequence information is as follows:
MLMTRNQAEKWFDNSLGKQFNPDGWYGFQCYDYANMFFMLATGERLQGLYAYNIPFDNKAKIEKYGQIIKNYDSFLPQKLDIVVFPSKYGGGAGHVEIVESANLNTFISFGQNWNGKGWTNGVAQPGWGPETVTRHVHYYDNPMYFIRLNFPDSISVKDKAKGIIKQATAKKEAVIKPKRIMLVAGHGYNDPGAVGNGTNERDFIRKYITPNIAKYLRHAGHEVALYGGSSQSQDMYQDTAYGVNVGNKKDYGLYWVKSQGYDIVLEIHLDAAGESASGGHVIISSQFNADTIDKSIQDVIKNNLGQIRGITPRNDLLNVNVSAEININYRLSELGFITNKNDMDWIKKNYDLYSKLIAGAIHGKPIGGLVASEVKAPVKNEKNPPVPAGYTLDSKGVPYKKEQGNYTVANVKGNNVRDGYSTNSRITGVLPNNTTITYDGAYCINGYRWITYIANSGQRRYIATGEVDKAGNRISSFGKFSTI. It consists of 484 amino acid residues.
In one or more embodiments of the invention, the number of mutation sites in the staphylococcus aureus phage lyase variant is 1-9, preferably 1-6, more preferably 1-3, such as 1,2, or 3.
In one or more specific embodiments of the invention, the staphylococcus aureus phage lyase variant is mutated on the basis of the wild-type lysostaphin shown in SEQ ID No.1, and the staphylococcus aureus phage lyase variant is selected from the group of mutants consisting of:
Mutant a: S333V;
Mutant B: S333V/N245R;
Mutant C: S333V/N245R/D299L.
Experiments prove that the three staphylococcus aureus phage lyase variants are optimal single-point, double-point and three-point mutants with improved bactericidal activity and thermal stability. The cleavage activity of the optimal three-point mutant S333V/N245R/D299L was increased by 17.28, 26.65, 20.24 and 50.09 times, respectively, compared with that of the wild type LysDZ under the conditions of 37 ℃, 40 ℃, 45 ℃ and 50 ℃. The cleavage activity half-life of the three-point mutant S333V/N245R/D299L was 4 times that of the wild-type LysDZ at 37 ℃. Under laboratory or practical (milk) conditions, the optimal three-point mutant S333V/N245R/D299L can reduce the OD 600 of the host bacterium (Staphylococcus aureus) by 4log10 and 3log10 respectively.
In one or more embodiments of the invention, a polynucleotide encoding a staphylococcus aureus phage lyase and/or a staphylococcus aureus phage lyase variant described above is provided.
The polynucleotide sequence for encoding the staphylococcus aureus phage lyase is shown as SEQ ID NO.2, and the specific nucleotide sequence information is as follows:
ATGTTAATGACAAGAAATCAAGCAGAAAAATGGTTTGATAACTCATTAGGAAAACAATTTAATCCAGATGGTTGGTATGGGTTTCAATGTTACGATTATGCAAATATGTTCTTTATGTTAGCAACAGGAGAAAGGCTACAAGGTTTATACGCTTATAATATCCCATTTGATAATAAAGCGAAAATTGAAAAATATGGTCAAATAATTAAAAACTATGACAGCTTTTTACCACAAAAGTTGGACATTGTCGTCTTCCCATCGAAGTATGGTGGTGGAGCGGGTCATGTTGAAATTGTTGAGAGTGCAAATTTAAACACTTTCATATCATTTGGTCAAAACTGGAATGGGAAAGGATGGACTAATGGCGTTGCGCAACCTGGCTGGGGTCCTGAAACTGTTACAAGACATGTCCATTATTATGACAATCCAATGTATTTTATTAGATTAAATTTCCCTGATAGCATAAGTGTTAAGGATAAGGCTAAAGGTATTATTAAGCAAGCAACTGCAAAAAAAGAGGCAGTAATTAAACCTAAAAGGATTATGCTTGTGGCTGGTCATGGATATAATGATCCAGGCGCAGTTGGTAATGGAACAAACGAACGTGATTTCATCCGTAAATATATAACGCCCAATATCGCTAAGTATCTAAGACATGCGGGACATGAAGTTGCTTTATATGGCGGCTCCAGTCAATCACAAGACATGTATCAAGATACTGCATACGGTGTTAATGTAGGAAATAAAAAAGACTATGGCTTATATTGGGTTAAATCACAGGGGTATGACATTGTTTTAGAGATACATTTAGATGCAGCAGGAGAAAGCGCAAGTGGCGGTCATGTTATTATCTCAAGTCAATTCAATGCAGATACTATTGATAAAAGTATACAAGATGTTATTAAAAATAACTTGGGACAAATAAGAGGTATAACACCTCGTAATGATTTGCTAAATGTTAATGTATCAGCTGAAATAAATATTAATTACCGCTTATCTGAATTAGGTTTTATTACTAATAAAAATGATATGGATTGGATTAAGAAAAATTACGACTTGTACTCTAAACTAATAGCTGGTGCGATTCATGGTAAGCCTATAGGTGGTTTGGTAGCTAGTGAGGTTAAAGCGCCAGTTAAAAACGAAAAGAATCCACCAGTACCAGCAGGTTATACCTTAGATAGTAAAGGGGTACCCTATAAAAAAGAACAAGGCAATTACACAGTAGCTAATGTTAAAGGTAATAATGTAAGAGACGGTTATTCAACTAATTCAAGAATCACTGGGGTGTTACCTAACAACACAACAATCACGTATGACGGCGCCTATTGTATCAATGGCTATAGATGGATTACTTATATTGCTAATAGTGGACAACGTCGTTATATCGCGACAGGAGAGGTAGACAAGGCAGGTAATAGAATAAGTAGTTTTGGTAAGTTTAGCACGATTTAG. It consists of 1455 nucleotides, of which nucleotides 1 to 1452 are the coding sequence and nucleotides 1453 to 1455 are transcribed to terminate codon termination peptide chain synthesis.
In one or more embodiments of the present invention, there is provided a recombinant expression vector comprising the polynucleotide of the present invention described above. The recombinant expression vector is obtained by effectively connecting the polynucleotide molecules to an expression vector, wherein the expression vector is a viral vector, a plasmid, a phage or an artificial chromosome; preferably, the expression vector is a plasmid, and in one embodiment of the present invention, the plasmid may be pET29b.
In one or more embodiments of the present invention, a cell is provided comprising the recombinant expression vector or chromosome integrated with the polynucleotide or the cell expresses the staphylococcus aureus phage lyase and/or staphylococcus aureus phage lyase variant described above.
The cells may be prokaryotic or eukaryotic.
In one or more embodiments of the invention, the host cell is any one or more of a bacterial cell, a fungal cell;
wherein the bacterial cell is any of the genera escherichia, agrobacterium, bacillus, streptomyces, pseudomonas, or staphylococcus;
The bacterial cells are E.coli (such as E.coli DH5 alpha, BL21 (DE 3), etc.), agrobacterium tumefaciens, agrobacterium rhizogenes, lactococcus lactis, bacillus subtilis, bacillus cereus or Pseudomonas fluorescens.
The fungal cells include yeast.
In one or more embodiments of the present invention, there is provided a method for producing the above-described staphylococcus aureus phage lyase and/or variants, comprising the steps of: culturing the cells to express the staphylococcus aureus phage lyase and/or variant; separating and purifying to obtain staphylococcus aureus phage lyase and/or variant.
In one or more embodiments of the present invention, there is provided a staphylococcus aureus inhibitor and/or killer comprising the above-described staphylococcus aureus phage lyase, staphylococcus aureus phage lyase variant and/or cells.
In one or more embodiments of the invention, the staphylococcus aureus inhibitor and/or killer further comprises an adjunct ingredient acceptable for general enzyme preparations or biological cell preparations, including, but not limited to, one or more of a dispersant, a wetting agent, a disintegrant, a binder, an antifoaming agent, an anti-freeze agent, a thickener, a filler, and a solvent. The source of acceptable auxiliary materials and the like are not particularly limited.
In one or more embodiments of the present invention, there is provided the use of a staphylococcus aureus phage lyase, a staphylococcus aureus phage lyase variant, a polynucleotide molecule, a recombinant expression vector, a cell, a staphylococcus aureus inhibitor and/or a biocide as described above in the field of anti-staphylococcus aureus.
Wherein, the staphylococcus aureus resistant field comprises but is not limited to various fields of food, medicine, medical treatment, environment, environmental protection, materials and the like, and can relate to research and work related to the inhibition or killing of staphylococcus aureus, and the staphylococcus aureus phage lyase variant of the invention remarkably improves the bactericidal activity, the thermal stability and the like, so that the application range of the staphylococcus aureus phage lyase variant is effectively widened, and the application environment can be high temperature (such as 40-50 ℃ inclusive, such as 40, 45 and 55 ℃) in the application field. Experiments prove that the staphylococcus aureus phage lyase variant shows better lytic activity on staphylococcus aureus than the staphylococcus aureus phage lyase in the high-temperature environment.
In one or more embodiments of the present invention, there is provided a method of designing the above-described staphylococcus aureus phage lyase variant, the method comprising constructing the three-dimensional structure of the above-described staphylococcus aureus phage lyase and predicting the thermal stability of the staphylococcus aureus phage lyase variant based on the MDL method;
Specifically, roseTTAFold is selected for constructing the three-dimensional structure LysDZ; in addition, the heat stability is an important factor for limiting the industrial application of the staphylococcus aureus phage lyase, and in order to improve the heat stability of the staphylococcus aureus phage lyase, the MDL method developed in the laboratory is used for predicting mutants with improved heat stability of the staphylococcus aureus phage lyase. Given the important role of conserved sites in protein structure and function, CD-search was used to identify these conserved key residue sites and was excluded from mutant design.
The invention is further illustrated by the following examples, which are not to be construed as limiting the invention. It is to be understood that these examples are illustrative of the present invention and are not intended to limit the scope of the present invention.
Examples
1. Materials and methods
1.1 Strains, plasmids and primers
TABLE 1 strains, plasmids and primers used in this study
1.2 Medium, buffer and culture conditions
LB liquid medium: 10g/L of sodium chloride, 5g/L of yeast powder and 10g/L of tryptone. The LB solid culture medium is prepared by adding 1% of agar powder on the basis of the LB liquid culture medium. The final concentration of kanamycin was 50. Mu.g/mL when used. Isopropyl- β -D-thiogalactoside (IPTG) was used at a final concentration of 1mM. Sodium phosphate buffer ：50mM Na2HPO4·12H2O,50mM NaH2PO4·2H2O,300mM NaCl,pH 7.0.Tris-HCl buffer: 50mM Tris-HCl, pH 10.0. E.coli was grown at 37℃at 220r/min until OD 600 = 0.6-0.8 and induced at 1.0mM IPTG final concentration at 16℃at 100r/min for 20h.
1.3 Construction of LysDZ25 expression vector and protein purification
The whole genome of staphylococcus aureus phage DZ25 obtained by separating and purifying from milk by Shandong agricultural academy of sciences is used as a template, a DZ25-FP/DZ25-RP primer pair (Table 1) is used for PCR amplification of a target gene, underlined parts are HindIII and XhoI restriction enzyme sites respectively, and the target gene and pET29b plasmid are subjected to double restriction enzyme digestion by using restriction enzymes HindIII and XhoI after being recovered. And (3) connecting the fragment obtained after the digestion and recovery with a carrier by using a ligase Solution I, transferring the connected product into escherichia coli DH5 alpha through heat shock conversion, transferring the plasmid with correct sequencing into escherichia coli BL21 (DE 3) through heat shock conversion, and preserving strains and performing expansion culture.
Inoculating in 300mL LB with 50 mug/mL final concentration of kanamycin at 1%, culturing at 37 ℃ at 220r/min to OD 600 = 0.6-0.8, adding IPTG with final concentration of 1.0mM, inducing at 16 ℃ at 100r/min for 20h, collecting thalli, suspending the precipitate with 30mL sodium phosphate buffer solution, ultrasonically crushing, centrifuging at 4 ℃ at 12000r/min for 20min, collecting supernatant, performing sterile filtration, purifying with Ni-NTA column, and performing SDS-PAGE verification to obtain purified protein LysDZ25.
1.4 Construction of LysDZ25 three-dimensional Structure and design of mutant with improved thermal stability
In order to obtain the three-dimensional structure of LysDZ, homology modeling was used to construct the three-dimensional structure of LysDZ25, but no suitable template was searched for, with sequence identity (coverage) and coverage (identity) of only 16% and 37.04% for the optimal template (PDB id:5 UDN), respectively. To obtain a suitable three-dimensional structure RoseTTAFold is ultimately used to construct the three-dimensional structure of LysDZ 25. Thermal stability is an important factor limiting the commercial application of LysDZ and in order to improve the thermal stability of LysDZ, the MDL method developed in this laboratory was used for mutant predictions of LysDZ with improved thermal stability. Given the important role of conserved sites in protein structure and function, CD-search was used to identify these conserved key residue sites and was excluded from mutant design.
1.5 Construction and expression of mutants
Based on the different mutants, we designed the corresponding primers. Then, the pET29b-DZ25 plasmid was amplified by linearization, 1. Mu.L of DpnI was added to the PCR product, the reaction was carried out at 37℃for 2 hours for template digestion, and after recovery, seamless cloning reagent 2x MultiF Seamless Assembly Mix was added and incubated at 50℃for 30 minutes in a PCR instrument. And then transferring the heat shock transformation into escherichia coli DH5 alpha, transferring the plasmid with correct sequencing into escherichia coli BL21 (DE 3), preserving strains and performing expansion culture.
1.6LysDZ25 and enzyme Activity determination of mutants thereof
Turbidity assay: phage Staphylococcus aureus DZ (sa.dz25) were incubated at 37 ℃ at 220r/min to OD 600 =1.2, the pellet was harvested by centrifugation, washed twice with 50mM Tris-HCl (ph=10.0) buffer and its OD 600 =1.0 was adjusted with Tris-HCl buffer. LysDZ25 with final concentration of 0.025mg/mL was mixed with Sa.DZ25 suspension, the temperature of the microplate reader was set to 37℃for reaction, the change in OD 600 value was measured, and 20. Mu.L of sodium phosphate buffer was used as a control instead of LysDZ. All experiments were set up in triplicate.
Bacterial colony Count (CFU): sa.DZ25 was treated in the same manner as above, lysDZ at a final concentration of 0.020mg/mL was mixed with the Sa.DZ25 suspension, and 100. Mu.L was immediately removed for dilution plating after 0min, 5min, 10min, 20min in a shaker at 37℃and placed in a incubator at 37℃overnight to calculate the total bacterial colony count.
1.7 Measurement of the thermal stability of LysDZ25 and its mutants
Packaging LysDZ and its mutant, standing at 4deg.C, 25deg.C, 30deg.C, 37deg.C, 40deg.C, 45deg.C, 50deg.C for 20min, and ice-bathing on ice for 30min. Subsequently, the corresponding Δod 600 value was determined within 15 min. Finally, the thermostability of LysDZ and its mutants was determined.
Packaging LysDZ and its mutant, and standing at 37deg.C for 0min, 5min, 10min, 15min, 20min, 25min, 30min, 35min, 40min, 45min, 50min, 55min, and longer. Subsequently, the corresponding Δod 600 values were determined within 30 min. Finally, the half-life of LysDZ and its mutants in enzyme activity was determined to evaluate their thermostability.
1.8LysDZ25 and detection of cleavage spectra of mutants thereof
Staphylococcus aureus TA22, DZ02, DZ04, LY05, LY53, sa.2-3, sa.2hun, WF107, standard staphylococcus aureus ATCC6538 from the strain room total of 9 gram positive and five gram negative bacteria dh5α, BL21 (DE 3), JM109, MG1655, min O157 were cultivated to OD 600 =1.2 at 37 ℃,220r/Min, harvested by centrifugation, pellet washed twice with 50mM Tris-HCl (ph 10.0) buffer and its OD 600 =1.0 was adjusted with Tris-HCl buffer. LysDZ25 with final concentration of 0.025mg/mL was mixed with staphylococcus aureus suspension, the temperature of the enzyme-labeled instrument was set to 37 ℃ for reaction, three strains were arranged in parallel, and sodium phosphate buffer was used as a control instead of LysDZ. Finally, the corresponding DeltaOD 600 values for the respective strains were determined.
1.9 Scanning Electron microscope observation experiments
After reacting Sa.DZ25 with enzyme at 37 ℃ for 5min, centrifuging, washing with 1 XPBS, fixing with 2.5% glutaraldehyde, dehydrating with ethanol water solutions with different concentrations, drying with a platform critical point dryer, observing and photographing the sample with a field emission scanning electron microscope after metal spraying, and observing the change of the staphylococcus aureus morphology by taking Sa.DZ25 which is not reacted with enzyme as a control.
2. Results and analysis
2.1 Expression purification of LysDZ25 and determination of its cleavage Spectrum
Gene DZ25 was cloned from the whole genome of Staphylococcus aureus phage DZ25 using primer pairs DZ25-FP and DZ25-RP with a fragment length of 1452bp (FIG. 1 a). DH5 alpha is transformed after connection of pET29b vector, transformant is picked and sequenced, plasmid which is sequenced correctly is transferred into expression strain BL21 (DE 3), ni-NTA purification is carried out after expansion culture, and the protein size is 54kDa (figure 1 b).
To evaluate the lysis profile of LysDZ, we examined the bactericidal effect of LysDZ on staphylococcus aureus (ATCC 6538) and 5 gram-negative bacteria (dh5α, BL21 (DE 3), JM109, MG1655, min O157) isolated from 9 environmental staphylococcus aureus (sa.dz25, sa.dz04, sa.dz02, sa.ta22, sa.2-3, sa.2hun, sa.wf107, sa.LY05, sa.ly53). As shown in Table 2, lysDZ had bactericidal effect on most Staphylococcus aureus, and no lytic effect on 5 gram-negative bacteria detected, except Sa.LY05.
TABLE 2 lytic Effect of LysDZ25 on Staphylococcus aureus and gram-negative bacteria
| Numbering device | Strain name | Strain numbering | LysDZ25 cleavage Effect of |
| 1 | Staphylococcus aureus | ATCC 6528 | +++ |
| 2 | Staphylococcus aureus | DZ25 | ++++ |
| 3 | Staphylococcus aureus | TA22 | ++++ |
| 4 | Staphylococcus aureus | DZ04 | ++++ |
| 5 | Staphylococcus aureus | DZ02 | ++++ |
| 6 | Staphylococcus aureus | 2-3 | +++ |
| 7 | Staphylococcus aureus | 2HUN | +++ |
| 8 | Staphylococcus aureus | WF107 | ++++ |
| 9 | Staphylococcus aureus | LY53 | +++ |
| 10 | Staphylococcus aureus | LY05 | - |
| 11 | E.coli | DH5α | - |
| 12 | E.coli | BL21(DE3) | - |
| 13 | E.coli | JM109 | - |
| 14 | E.coli | MG1655 | - |
| 15 | E.coli | Min O157 | - |
The cracking activity is 10% -30%, "+"; the cracking activity is 31% -50%, "++"; the cracking activity is between 51 and 70 percent, "+". Plus "; the cracking activity is 71% -100%, "+ ++ + plus"; the cleavage activity was less than 10%, "-".
2.2 Construction of the three-dimensional Structure of LysDZ25 and prediction of mutants with improved thermostability
To improve the thermal stability of LysDZ, we devised a rational engineering strategy for improving the thermal stability of LysDZ. As shown in fig. 2, this strategy is divided into three parts: protein structure prediction, protein conformational sampling, and mutant design with improved thermostability. To obtain the three-dimensional structure of LysDZ, roseTTAFold is used for the construction of the three-dimensional structure. As a result, as shown in FIG. 3, the domains CHAP and AmiC, and the domains AmiC and SH3b were linked by linker, respectively. Considering the complexity of dynamic changes in protein conformation, we performed molecular dynamics simulations and conformational sampling (10 frames) of the three domains of LysDZ, respectively, using NAMD. Based on the 10-frame conformation of the conformation collection, we designed and experimentally verified mutants with improved thermostability for LysDZ using the MDL method developed in this laboratory.
In view of the functional differences between the different domains, we selected a mutant design with an increased thermostability of AmiC domain with amidase domain (FIG. 3 b). Based on the rational strategy described above, we performed two rounds of mutant design, as shown in table 3: (1) Single point mutant design on wild type LysDZ protein resulted in 25 mutants with possibly improved thermostability; (2) The single-point mutant obtained by one round of mutation is subjected to combined mutation to obtain an optimal double-point mutant (S333V/N245R) with improved heat stability/activity, and 20 mutants with possibly improved heat stability are designed by two rounds of mutant design based on the mutant.
TABLE 3 two rounds of mutant design based on rational design strategy
# Mutated residues are evolutionarily conserved amino acid residues.
2.3 Activity determination of LysDZ25 and mutants thereof
To obtain mutants with improved thermostability without significant reduction in enzyme activity, we constructed single/double/triple point mutants and evaluated the enzyme activity of the mutants using nephelometry at 37 ℃. As shown in Table 3, based on 25 single-point mutants of one round design, we obtained 5 single-point mutants with significantly improved activity, S333V, S333I, S333L, N R and N319L, respectively (FIG. 4 a). Wherein, the activity of S333V is improved most significantly, which is 7.51 times higher than that of LysDZ. Based on the single point mutant S333V, we performed double site combinatorial mutations on 5 single point mutants with increased activity. The results are shown in FIG. 4b, wherein the optimal double point mutant is S333V/N245R, which is 1.36 times as active as S333V, 11.57 times as active as wild type LysDZ.
In order to further improve the activity of the mutant, we performed two rounds of rational design of mutants based on the optimal double-point mutant S333V/N245R, and constructed 20 mutants (Table 3) in total. As a result, we finally obtained 5 mutants with further improved activity, as shown in FIG. 4 c: S333V/N245R/A220L, S333V/N245R/K341P, S V/N245R/N342E, S V/N245R/S230E and S333V/N245R/V244L. The activity of the mutant is respectively improved by 50%, 66%, 58%, 63% and 50% compared with that of the mutant S333V/N245R, and is respectively improved by 16.3, 18.2, 17.2, 17.8 and 16.3 times compared with that of the wild type LysDZ.
2.4 Measurement of the thermal stability of LysDZ25 and its mutants
Based on the above mutants with improved activity, we performed further thermal stability evaluations (4 ℃, 25 ℃,30 ℃,37 ℃, 40 ℃, 45 ℃ and 50 ℃). Considering that the double-point mutant and the triple-point mutant are constructed on the basis of the single-point mutant S333V, only LysDZ and S333V and the double-point mutant and the triple-point mutant thereof are evaluated in the follow-up process. As a result, as shown in FIG. 5, the activity of S333V was 56% higher than that of LysDZ by 20min at 37℃and the activity of S333V/N245R was 5.36-fold higher than that of LysDZ by 20min (FIG. 5 a). Based on the double point mutant S333V/N245R, the two rounds of mutation gave 6 triple point mutants with further improved thermostability (S333V/N245R/A220L, S V/N245R/D299L, S V/N245R/S230E, S V/N245R/S230P, S333V/N245R/V244L and S333V/N245R/N304F), which were treated at 37℃for 20min, the activities were improved 11.57, 17.28, 15.75, 17.69, 10.15 and 8.22 fold respectively compared with the wild type LysDZ 25. In addition, the activity of 5 mutants (S333V/N245R/D299L, S V/N245R/S230E, S V/N245R/S230P, S V/N245R/V244L and S333V/N245R/N304F) was significantly better than LysDZ and S333V/N245R, when treated at 40 ℃, 45 ℃ and 50 ℃ for 20 min.
2.5LysDZ25 and determination of cleavage Property of 3 optimal mutants
Considering that the mutants S333V/N245R/D299L had optimal enzymatic activity at 40, 45 and 50 ℃, we selected one single, two and three point mutants (S333V, S V/N245R and S333V/N245R/D299L) for cleavage property determination. We first further evaluated their thermostability (fig. 6 a), and the results show that the half-life of the wild type LysDZ enzyme activity is only 15 minutes at 37 ℃; the half-life of the enzyme activities of the mutants S333V and S333V/N245R is between 20 and 25 minutes; the relative enzyme activity of the optimal three-point mutant S333V/N245R/D299L is still maintained above 80% after 55 minutes of treatment.
Subsequently, cell counts were used to evaluate the lytic activity of the mutants, and the results are shown in FIG. 6b, in which the bactericidal effect of the mutants was significantly improved compared to that of wild-type LysDZ, wherein the optimal mutant S333V/N245R/D299L treated host bacteria had a reduction in OD 600 of about 4log10 compared to the control and about 2log10 compared to the OD 600 of the wild-type LysDZ25 treated host bacteria. To further evaluate the lytic activity of the mutants in practice, we measured its lytic activity in milk and as shown in FIG. 6c, the OD 600 of LysDZ 25-treated host bacteria was reduced by about 1log10, the OD 600 of S333V and S333V/N245R-treated host bacteria was reduced by about 1.5log10, and the OD 600 of S333V/N245R/D299L-treated host bacteria was reduced by about 3log10 in milk at 37 ℃.
2.6LysDZ25 and 3 optimal mutant lysis experiment electron microscope observations thereof
To further evaluate the lytic activity of LysDZ and its mutants, we observed the lytic effect of LysDZ and its mutants on staphylococcus aureus using electron microscopy experiments. The results are shown in FIG. 7, where the non-lyase treated Staphylococcus aureus is full and the cell membrane is intact without outflow of cell content (FIG. 7 a); the LysDZ treated staphylococcus aureus cells began to become wrinkled (fig. 7 b); the single point mutant S333V treated staphylococcus aureus cells showed a significant increase in folds (fig. 7 c); the cell folds of staphylococcus aureus treated with the double point mutant S333V/N245R continued to increase and cell content outflow was clearly visible (fig. 7 d); staphylococcus aureus cells treated with the three-point mutant S333V/N245R/D299L were wrinkled over a large area and the cell contents flowed out in large amounts (FIG. 7 e).
In this study, we identified and rationally engineered a phage lyase LysDZ that was capable of cleaving staphylococcus aureus: (1) The protein three-dimensional structure of LysDZ was constructed using RoseTTAFold; (2) Performing structural optimization and conformational acquisition on three domains of LysDZ through molecular dynamics simulation; (3) Two rounds of mutant predictions of increased thermostability were made for the conformational set of domains LysDZ using the MDL strategy. Finally, the optimal single-point, double-point and three-point mutants (S333V, S V/N245R and S333V/N245R/D299L) with improved activity and thermal stability are obtained through experimental verification. The cleavage activity of the optimal three-point mutant S333V/N245R/D299L was increased by 17.28, 26.65, 20.24 and 50.09 times, respectively, compared with that of the wild type LysDZ under the conditions of 37 ℃,40 ℃, 45 ℃ and 50 ℃. The cleavage activity half-life of the three-point mutant S333V/N245R/D299L was 4 times that of the wild-type LysDZ at 37 ℃. Under laboratory or practical (milk) conditions, the optimal three-point mutant S333V/N245R/D299L can reduce the OD 600 of the host bacterium (Staphylococcus aureus) by 4log10 and 3log10 respectively.
Finally, it should be noted that: the foregoing description is only a preferred embodiment of the present invention, and the present invention is not limited thereto, but it is to be understood that modifications and equivalents of some of the technical features described in the foregoing embodiments may be made by those skilled in the art, although the present invention has been described in detail with reference to the foregoing embodiments. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present invention should be included in the protection scope of the present invention.
Claims (8)
1. A staphylococcus aureus phage lyase variant, characterized in that the variant is a sequence with amino acid as shown in SEQ ID No.1, wherein the following site mutations are performed: S333V; or S333V/N245R; or S333V/N245R/D299L.
2. A polynucleotide encoding the staphylococcus aureus phage lyase variant of claim 1.
3. A recombinant expression vector comprising the polynucleotide of claim 2.
4. A cell comprising the recombinant expression vector of claim 3 or a chromosome incorporating the polynucleotide of claim 2; the cells are non-animal cells and plant cells.
5. A method of producing the variant of claim 1, comprising the steps of: culturing the cell of claim 4, thereby expressing the staphylococcus aureus phage lyase variant; separating and purifying to obtain staphylococcus aureus phage lyase variant.
6. A staphylococcus aureus inhibitor and/or killer comprising the staphylococcus aureus phage lyase variant of claim 1 and/or the cell of claim 4.
7. Use of a staphylococcus aureus phage lyase variant according to claim 1, a polynucleotide according to claim 2, a recombinant expression vector according to claim 3, a cell according to claim 4, a staphylococcus aureus inhibitor and/or a biocide according to claim 6 in the field of anti-staphylococcus aureus; the uses are methods of treatment and diagnosis of non-disease.
8. The use according to claim 7, wherein the application environment is a high temperature environment of 37 ℃, 40 ℃, 45 ℃ or 50 ℃.
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Citations (3)
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| CN102676490A (en) * | 2012-05-21 | 2012-09-19 | 江苏省农业科学院 | Lywallzyme of phage of staphylococcus aureus as well as preparation method and application thereof |
| CN104862297A (en) * | 2015-06-10 | 2015-08-26 | 江苏省农业科学院 | Genetic engineering-modified staphylococcus aureus staphylophage lyase as well as preparation method and application thereof |
| CN111808837A (en) * | 2020-07-17 | 2020-10-23 | 青岛诺安百特生物技术有限公司 | Staphylococcus aureus bacteriophage lyase and preparation method and application thereof |
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Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102676490A (en) * | 2012-05-21 | 2012-09-19 | 江苏省农业科学院 | Lywallzyme of phage of staphylococcus aureus as well as preparation method and application thereof |
| CN104862297A (en) * | 2015-06-10 | 2015-08-26 | 江苏省农业科学院 | Genetic engineering-modified staphylococcus aureus staphylophage lyase as well as preparation method and application thereof |
| CN111808837A (en) * | 2020-07-17 | 2020-10-23 | 青岛诺安百特生物技术有限公司 | Staphylococcus aureus bacteriophage lyase and preparation method and application thereof |
Non-Patent Citations (2)
| Title |
|---|
| N-acetylmuramoyl-L-alanine amidase [Staphylococcus aureus];WP_031887119.1;NCBI;20220517;ORIGIN * |
| 奶牛***炎金黄色葡萄球菌裂解性噬菌体裂解酶LysIMEP5基因的克隆及序列分析;张倩;张湘莉兰;孙耀强;于会举;张培生;刘鸽;屈勇刚;童贻刚;李岩;;中国兽药杂志;20161020;第50卷(第10期);第15-21页 * |
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