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Afoshin A, Kudryakova I, Tarlachkov S, Leontyevskaya E, Zelenov D, Rudenko P, Leontyevskaya Vasilyeva N. Transcriptomic Analysis Followed by the Isolation of Extracellular Bacteriolytic Proteases from Lysobacter capsici VKM B-2533 T. Int J Mol Sci 2023; 24:11652. [PMID: 37511410 PMCID: PMC10380237 DOI: 10.3390/ijms241411652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The aim of the study was to search for, isolate and characterize new bacteriolytic enzymes that show promising potential for their use in medicine, agriculture and veterinary. Using a transcriptomic analysis, we annotated in Lysobacter capsici VKM B-2533T the genes of known bacteriolytic and antifungal enzymes, as well as of antibiotics, whose expression levels increased when cultivated on media conducive to the production of antimicrobial agents. The genes of the secreted putative bacteriolytic proteases were also annotated. Two new bacteriolytic proteases, Serp and Serp3, were isolated and characterized. The maximum bacteriolytic activities of Serp and Serp3 were exhibited at low ionic strength of 10 mM Tris-HCl, and high temperatures of, respectively, 80 °C and 70 °C. The pH optimum for Serp was 8.0; for Serp3, it was slightly acidic, at 6.0. Both enzymes hydrolyzed autoclaved cells of Micrococcus luteus Ac-2230T, Proteus vulgaris H-19, Pseudomonas aeruginosa and Staphylococcus aureus 209P. Serp also digested cells of Bacillus cereus 217. Both enzymes hydrolyzed casein and azofibrin. The newly discovered enzymes are promising for developing proteolytic antimicrobial drugs on their basis.
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Affiliation(s)
- Alexey Afoshin
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
| | - Irina Kudryakova
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
| | - Sergey Tarlachkov
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
| | - Elena Leontyevskaya
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
| | - Dmitry Zelenov
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
- Pushchino Branch of the Federal State Budgetary Educational Institution of Higher Education «Russian Biotechnological University (BIOTECH University)», 3 Institutskaya Str., Pushchino 142290, Russia
| | - Pavel Rudenko
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
| | - Natalya Leontyevskaya Vasilyeva
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia
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The First Homologous Expression System for the β-Lytic Protease of Lysobacter capsici VKM B-2533 T, a Promising Antimicrobial Agent. Int J Mol Sci 2022; 23:ijms23105722. [PMID: 35628535 PMCID: PMC9145596 DOI: 10.3390/ijms23105722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
A successful homologous expression system based on Lysobacter capsici VKM B-2533T and the plasmid pBBR1-MCS5 was first developed for a promising bacteriolytic enzyme of this bacterium, β-lytic protease (Blp). In the expression strains, blp gene expression under the regulation of the GroEL(A) and T5 promoters increased by 247- and 667-fold, respectively, as compared with the wild-type strain. After the cultivation of the expression strains L. capsici PGroEL(A)-blp and L. capsici PT5-blp, the Blp yield increased by 6.7- and 8.5-fold, respectively, with respect to the wild-type strain. The cultivation of the expression strain L. capsici PT5-blp was successfully scaled up. Under fermentation conditions the yield of the enzyme increased by 1.6-fold. The developed homologous system was used to express the gene of the bacteriolytic serine protease (Serp) of L. capsici VKM B-2533T. The expression of the serp gene in L. capsici PT5-serp increased by 585-fold. The developed homologous system for the gene expression of bacteriolytic Lysobacter enzymes is potentially biotechnologically valuable, and is promising for creating highly efficient expression strains.
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Kudryakova IV, Afoshin AS, Ivashina TV, Suzina NE, Leontyevskaya EA, Leontyevskaya Vasilyeva NV. Deletion of alpB Gene Influences Outer Membrane Vesicles Biogenesis of Lysobacter sp. XL1. Front Microbiol 2021; 12:715802. [PMID: 34484157 PMCID: PMC8415630 DOI: 10.3389/fmicb.2021.715802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
Outer membrane vesicles (OMVs) produced by Gram-negative bacteria constitute important factors in defining interactions with the extracellular milieu. Lysobacter sp. XL1 produces OMVs capable of lysing microbial cells due to the presence in their cargo of bacteriolytic protease L5 (AlpB). Although protein L5 has been functionally and biochemically characterized (including aspects of its packing into OMVs), its role in vesicle biogenesis through genetic deletion of alpB had not been studied previously. Here, we have successfully deleted alpB by allelic replacement and show that the alpB deletion mutant produces a significantly lower amount of OMVs that lack bacteriolytic activity and display altered ultrastructural characteristics in relation to the OMVs produced by the wild-type strain. These results confirm that, as previously proposed, protein L5 participates in OMV production through a mechanism that is not yet fully understood.
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Affiliation(s)
- Irina V Kudryakova
- Laboratory of Microbial Cell Surface Biochemistry, Pushchino Center for Biological Research, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Alexey S Afoshin
- Laboratory of Microbial Cell Surface Biochemistry, Pushchino Center for Biological Research, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Tanya V Ivashina
- Laboratory of Molecular Microbiology, Pushchino Center for Biological Research, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Natalia E Suzina
- Laboratory of Microbial Cytology, Pushchino Center for Biological Research, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Elena A Leontyevskaya
- Laboratory of Microbial Cell Surface Biochemistry, Pushchino Center for Biological Research, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Natalia V Leontyevskaya Vasilyeva
- Laboratory of Microbial Cell Surface Biochemistry, Pushchino Center for Biological Research, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
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β-Lytic Protease of Lysobacter capsici VKM B-2533 T. Antibiotics (Basel) 2020; 9:antibiotics9110744. [PMID: 33126447 PMCID: PMC7693508 DOI: 10.3390/antibiotics9110744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022] Open
Abstract
Bacteriolytic enzymes are promising antimicrobial agents for developing new-generation drugs. Recently, we have isolated a β-lytic protease (BlpLc) from the culture liquid of Lysobacter capsici VKM B-2533T. This BlpLc possesses a valuable property, not described for β-lytic proteases (Blps) earlier, of hydrolyzing living cells of Staphylococcus aureus 55 MRSA clinical isolate. This work phylogenetically characterized the BlpLc and investigated its properties. Analysis revealed a variability of pre-/pro-parts of Blp precursors. The mature BlpLc is the closest to the earlier annotated but not isolated Blp from Lysobacter sp. Root690. The biochemical characterization found conditions for the BlpLc general bacteriolytic activity relative to autoclaved S. aureus 209P cells to differ from that of earlier isolated Blp. Unexpected was the effect of serine (phenylmethylsulfonyl fluoride (PMSF)) and cysteine (p-chloromercuribenzoate (p-CMB)) protease inhibitors on BlpLc bacteriolytic and proteolytic activities. The specificity of BlpLc proteolytic action relative to hemoglobin, elastin, gelatin, collagen, azofibrin, myoglobin, ovalbumin, and ovamucoid was found. New types of peptide bonds—Gly-X, Ser-X, Lys-X, Ala-X, Val-X, Glu-X, and Phe-X—hydrolyzed by the enzyme in protein substrates were first revealed using MALDI-TOF. Turbidimetrically, the BlpLc was found to lyze living cells of S. aureus 209P, Micrococcus luteus B1819, and M. roseus B1236, which is important for expanding the enzyme’s applied properties.
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Afoshin AS, Kudryakova IV, Borovikova AO, Suzina NE, Toropygin IY, Shishkova NA, Vasilyeva NV. Lytic potential of Lysobacter capsici VKM B-2533 T: bacteriolytic enzymes and outer membrane vesicles. Sci Rep 2020; 10:9944. [PMID: 32561806 PMCID: PMC7305183 DOI: 10.1038/s41598-020-67122-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/03/2020] [Indexed: 11/10/2022] Open
Abstract
Recent recurrent outbreaks of bacterial resistance to antibiotics have shown the critical need to identify new lytic agents to combat them. The species Lysobacter capsici VKM B-2533T possesses a potent antimicrobial action against a number of bacteria, fungi and yeasts. Its activity can be due to the impact of bacteriolytic enzymes, antibiotics and peptides. This work isolated four homogeneous bacteriolytic enzymes and a mixture of two proteins, which also had a bacteriolytic activity. The isolates included proteins identical to L. enzymogenes α- and β-lytic proteases and lysine-specific protease. The proteases of 26 kDa and 29 kDa and a protein identified as N-acetylglycosaminidase had not been isolated in Lysobacter earlier. The isolated β-lytic protease digested live methicillin-resistant staphylococcal cells with high efficiency (minimal inhibitory concentration, 2.85 μg/mL). This property makes the enzyme deserving special attention. A recombinant β-lytic protease was produced. The antimicrobial potential of the bacterium was contributed to by outer membrane vesicles (OMVs). L. capsici cells were found to form a group of OMVs responsible for antifungal activity. The data are indicative of a significant antimicrobial potential of this bacterium that requires thorough research.
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Affiliation(s)
- A S Afoshin
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - I V Kudryakova
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - A O Borovikova
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - N E Suzina
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - I Yu Toropygin
- Department of Proteomics, V.N. Orekhovich Research Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaja Str., Moscow, 119832, Russia
| | - N A Shishkova
- Laboratory of Anthrax Microbiology, FBIS State Research Center for Applied Microbiology and Biotechnology, Obolensk, Serpukhov District, Moscow Region, 142279, Russia
| | - N V Vasilyeva
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia.
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