Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis


Autoři: David Lynch aff001;  Paula M. O’Connor aff002;  Paul D. Cotter aff002;  Colin Hill aff003;  Des Field aff003;  Máire Begley aff001
Působiště autorů: Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland aff001;  Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland aff002;  APC Microbiome Ireland, University College Cork, Cork, Ireland aff003;  School of Microbiology, University College Cork, Cork, Ireland aff004
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223541

Souhrn

One hundred human-derived coagulase negative staphylococci (CoNS) were screened for antimicrobial activity using agar-based deferred antagonism assays with a range of indicator bacteria. Based on the findings of the screen and subsequent well assays with cell free supernatants and whole cell extracts, one strain, designated CIT060, was selected for further investigation. It was identified as Staphylococcus capitis and herein we describe the purification and characterisation of the novel bacteriocin that the strain produces. This bacteriocin which we have named capidermicin was extracted from the cell-free supernatant of S. capitis CIT060 and purified to homogeneity using reversed-phase high performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric (MS) analysis revealed that the capidermicin peptide has a mass of 5,464 Da. Minimal inhibitory concentration (MIC) experiments showed that capidermicin was active in the micro-molar range against all the Gram-positive bacteria that were tested. Antimicrobial activity was retained over a range of pHs (2–11) and temperatures (10–121°C x 15 mins). The draft genome sequence of S. capitis CIT060 was determined and the genes predicted to be involved in the biosynthesis of capidermicin were identified. These genes included the predicted capidermicin precursor gene, and genes that are predicted to encode a membrane transporter, an immunity protein and a transcriptional regulator. Homology searches suggest that capidermicin is a novel member of the family of class II leaderless bacteriocins.

Klíčová slova:

Bacteria – Gene prediction – Matrix-assisted laser desorption ionization time-of-flight mass spectrometry – Proteases – Staphylococcus – Staphylococcus aureus – Staphylococcus epidermidis – Lactococcus lactis


Zdroje

1. Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep. 2013;30(1):108–60. doi: 10.1039/c2np20085f 23165928

2. Perez RH, Zendo T, Sonomoto K. Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications. Microbial Cell Factories. 2014;13(Suppl 1):S3–S. doi: 10.1186/1475-2859-13-S1-S3 25186038

3. Cotter PD, Ross RP, Hill C. Bacteriocins—a viable alternative to antibiotics? Nature Reviews Microbiology. 2013;11(2):95–105. doi: 10.1038/nrmicro2937 23268227

4. Riley MA, Wertz JE. Bacteriocins: Evolution, Ecology, and Application. Annual Review of Microbiology. 2002;56(1):117–37. doi: 10.1146/annurev.micro.56.012302.161024 12142491

5. Dobson A, Cotter PD, Ross RP, Hill C. Bacteriocin Production: a Probiotic Trait? Applied and Environmental Microbiology. 2012;78(1):1–6. doi: 10.1128/AEM.05576-11 22038602

6. Kelly WJ, Asmundson RV, Huang CM. Isolation and characterization of bacteriocin-producing lactic acid bacteria from ready-to-eat food products. International journal of food microbiology. 1996;33(2–3):209–18. doi: 10.1016/0168-1605(96)01157-9 8930706

7. Yanagida F, Chen YS, Shinohara T. Searching for bacteriocin-producing lactic acid bacteria in soil. J Gen Appl Microbiol. 2006;52(1):21–8. Epub 2006/04/07. 16598155.

8. Collins FWJ, O’Connor PM, O'Sullivan O, Rea MC, Hill C, Ross RP. Formicin–a novel broad-spectrum two-component lantibiotic produced by Bacillus paralicheniformis APC 1576. Microbiology. 2016;162(9):1662–71. doi: 10.1099/mic.0.000340 27450592

9. Ringø E, Hoseinifar SH, Ghosh K, Doan HV, Beck BR, Song SK. Lactic Acid Bacteria in Finfish—An Update. Frontiers in Microbiology. 2018;9:1818–. doi: 10.3389/fmicb.2018.01818 30147679

10. Begley M, Cotter PD, Hill C, Ross RP. Identification of a Novel Two-Peptide Lantibiotic, Lichenicidin, following Rational Genome Mining for LanM Proteins. Applied and Environmental Microbiology. 2009;75(17):5451–60. doi: 10.1128/AEM.00730-09 19561184

11. Lakshminarayanan B, Guinane CM, O'Connor PM, Coakley M, Hill C, Stanton C, et al. Isolation and characterization of bacteriocin-producing bacteria from the intestinal microbiota of elderly Irish subjects. Journal of Applied Microbiology. 2013;114(3):886–98. doi: 10.1111/jam.12085 23181509

12. O'Connor PM, O'Shea EF, Guinane CM, O'Sullivan O, Cotter PD, Ross RP, et al. Nisin H Is a New Nisin Variant Produced by the Gut-Derived Strain Streptococcus hyointestinalis DPC6484. Applied and Environmental Microbiology. 2015;81(12):3953–60. doi: 10.1128/AEM.00212-15 25841003

13. O’Sullivan O, Begley M, Ross RP, Cotter PD, Hill C. Further Identification of Novel Lantibiotic Operons Using LanM-Based Genome Mining. Probiotics and Antimicrobial Proteins. 2011;3(1):27–40. doi: 10.1007/s12602-011-9062-y 26781497

14. Collins FWJ, O’Connor PM, O’Sullivan O, Gómez-Sala B, Rea MC, Hill C, et al. Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome. Scientific Reports. 2017;7(1):3481–. doi: 10.1038/s41598-017-03339-y 28615683

15. Walsh CJ, Guinane CM, Hill C, Ross RP, O’Toole PW, Cotter PD. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database. BMC Microbiology. 2015;15(1):183. doi: 10.1186/s12866-015-0515-4 26377179

16. Cameron DR, Jiang J-H, Hassan KA, Elbourne LDH, Tuck KL, Paulsen IT, et al. Insights on virulence from the complete genome of Staphylococcus capitis. Frontiers in microbiology. 2015;6:980–. doi: 10.3389/fmicb.2015.00980 26441910

17. Zipperer A, Konnerth MC, Laux C, Berscheid A, Janek D, Weidenmaier C, et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature. 2016;535(7613):511–6. doi: 10.1038/nature18634 27466123

18. Janek D, Zipperer A, Kulik A, Krismer B, Peschel A, Bertram R. High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors. PLOS Pathogens. 2016;12(8):e1005812–e. doi: 10.1371/journal.ppat.1005812 27490492

19. O'Sullivan JN, Rea MC, O'Connor PM, Hill C, Ross RP. Human skin microbiota is a rich source of bacteriocin-producing staphylococci that kill human pathogens. FEMS Microbiology Ecology. 2019;95(2). doi: 10.1093/femsec/fiy241 30590567

20. Cogen AL, Nizet V, Gallo RL. Skin microbiota: a source of disease or defence? British Journal of Dermatology. 2008;158(3):442–55. doi: 10.1111/j.1365-2133.2008.08437.x 18275522

21. Kumar R, Jangir PK, Das J, Taneja B, Sharma R. Genome Analysis of Staphylococcus capitis TE8 Reveals Repertoire of Antimicrobial Peptides and Adaptation Strategies for Growth on Human Skin. Scientific reports. 2017;7(1):10447–. doi: 10.1038/s41598-017-11020-7 28874737

22. Christensen GJ, Bruggemann H. Bacterial skin commensals and their role as host guardians. Benef Microbes. 2014;5(2):201–15. Epub 2013/12/11. doi: 10.3920/BM2012.0062 24322878.

23. Nakatsuji T, Chen TH, Narala S, Chun KA, Two AM, Yun T, et al. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Science translational medicine. 2017;9(378):eaah4680–eaah. doi: 10.1126/scitranslmed.aah4680 28228596

24. Götz F, Perconti S, Popella P, Werner R, Schlag M. Epidermin and gallidermin: Staphylococcal lantibiotics. International Journal of Medical Microbiology. 2014;304(1):63–71. doi: 10.1016/j.ijmm.2013.08.012 24119540

25. Field D, Gaudin N, Lyons F, O'Connor PM, Cotter PD, Hill C, et al. A Bioengineered Nisin Derivative to Control Biofilms of Staphylococcus pseudintermedius. PLOS ONE. 2015;10(3):e0119684–e. doi: 10.1371/journal.pone.0119684 25789988

26. Cotter PD, Draper LA, Lawton EM, McAuliffe O, Hill C, Ross RP. Overproduction of wild-type and bioengineered derivatives of the lantibiotic lacticin 3147. Applied and environmental microbiology. 2006;72(6):4492–6. doi: 10.1128/AEM.02543-05 16751576

27. Field D, Begley M, O’Connor PM, Daly KM, Hugenholtz F, Cotter PD, et al. Bioengineered Nisin A Derivatives with Enhanced Activity against Both Gram Positive and Gram Negative Pathogens. PLoS ONE. 2012;7(10):e46884–e. doi: 10.1371/journal.pone.0046884 23056510

28. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology. 2012;19(5):455–77. doi: 10.1089/cmb.2012.0021 22506599

29. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11(1):119–. doi: 10.1186/1471-2105-11-119 20211023

30. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research. 2016;44(D1):D279–D85. doi: 10.1093/nar/gkv1344 26673716

31. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols. 2015;10(6):845–58. doi: 10.1038/nprot.2015.053 25950237

32. Cheung GY, Joo HS, Chatterjee SS, Otto M. Phenol-soluble modulins—critical determinants of staphylococcal virulence. FEMS microbiology reviews. 2014;38(4):698–719. Epub 2014/01/01. doi: 10.1111/1574-6976.12057 24372362; PubMed Central PMCID: PMC4072763.

33. Netz DJA, Pohl R, Beck-Sickinger AG, Selmer T, Pierik AJ, Bastos MdCdF, et al. Biochemical Characterisation and Genetic Analysis of Aureocin A53, a New, Atypical Bacteriocin from Staphylococcus aureus. Journal of Molecular Biology. 2002;319(3):745–56. doi: 10.1016/S0022-2836(02)00368-6 12054867

34. Zheng J, Gänzle MG, Lin XB, Ruan L, Sun M. Diversity and dynamics of bacteriocins from human microbiome. Environmental Microbiology. 2015;17(6):2133–43. doi: 10.1111/1462-2920.12662 25346017

35. Carson DA, Barkema HW, Naushad S, De Buck J. Bacteriocins of non-aureus staphylococci isolated from bovine milk. Applied and environmental microbiology. 2017:AEM.01015-17. doi: 10.1128/AEM.01015-17 28667105

36. Sugai M, Fujiwara T, Akiyama T, Ohara M, Komatsuzawa H, Inoue S, et al. Purification and molecular characterization of glycylglycine endopeptidase produced by Staphylococcus capitis EPK1. Journal of bacteriology. 1997;179(4):1193–202. doi: 10.1128/jb.179.4.1193-1202.1997 9023202

37. Miljkovic M, Uzelac G, Mirkovic N, Devescovi G, Diep DB, Venturi V, et al. LsbB Bacteriocin Interacts with the Third Transmembrane Domain of the YvjB Receptor. Applied and Environmental Microbiology. 2016;82(17):5364–74. doi: 10.1128/AEM.01293-16 27342562

38. Kojic M, Strahinic I, Fira D, Jovcic B, Topisirovic L. Plasmid content and bacteriocin production by five strains of Lactococcus lactis isolated from semi-hard homemade cheese. Can J Microbiol. 2006;52(11):1110–20. Epub 2007/01/12. doi: 10.1139/w06-072 17215903.

39. Ceotto H, Brede D, Salehian Z, Nascimento Jdos S, Fagundes PC, Nes IF, et al. Aureocins 4185, bacteriocins produced by Staphylococcus aureus 4185: potential application in food preservation. Foodborne pathogens and disease. 2010;7(10):1255–62. Epub 2010/07/14. doi: 10.1089/fpd.2010.0578 20618078.

40. Iwatani S, Zendo T, Yoneyama F, Nakayama J, Sonomoto K. Characterization and Structure Analysis of a Novel Bacteriocin, Lacticin Z, Produced by Lactococcus lactis QU 14. Bioscience, Biotechnology, and Biochemistry. 2007;71(8):1984–92. doi: 10.1271/bbb.70169 17690480

41. Fujita K, Ichimasa S, Zendo T, Koga S, Yoneyama F, Nakayama J, et al. Structural analysis and characterization of lacticin Q, a novel bacteriocin belonging to a new family of unmodified bacteriocins of gram-positive bacteria. Applied and environmental microbiology. 2007;73(9):2871–7. doi: 10.1128/AEM.02286-06 17351096

42. Sandiford S, Upton M. Identification, characterization, and recombinant expression of epidermicin NI01, a novel unmodified bacteriocin produced by Staphylococcus epidermidis that displays potent activity against Staphylococci. Antimicrobial agents and chemotherapy. 2012;56(3):1539–47. doi: 10.1128/AAC.05397-11 22155816

43. Perez RH, Zendo T, Sonomoto K. Circular and Leaderless Bacteriocins: Biosynthesis, Mode of Action, Applications, and Prospects. Frontiers in microbiology. 2018;9:2085–. doi: 10.3389/fmicb.2018.02085 30233551

44. Iwatani S, Yoneyama F, Miyashita S, Zendo T, Nakayama J, Sonomoto K. Identification of the genes involved in the secretion and self-immunity of lacticin Q, an unmodified leaderless bacteriocin from Lactococcus lactis QU 5. Microbiology. 2012;158(Pt_12):2927–35. doi: 10.1099/mic.0.062943-0 23103973

45. Iwatani S, Horikiri Y, Zendo T, Nakayama J, Sonomoto K. Bifunctional Gene Cluster lnqBCDEF Mediates Bacteriocin Production and Immunity with Differential Genetic Requirements. Applied and Environmental Microbiology. 2013;79(7):2446–9. doi: 10.1128/AEM.03783-12 23335763

46. Nascimento JdS Coelho MLV, Ceotto H, Potter A, Fleming LR, Salehian Z, et al. Genes Involved in Immunity to and Secretion of Aureocin A53, an Atypical Class II Bacteriocin Produced by Staphylococcus aureus A53. Journal of Bacteriology. 2012;194(4):875–83. doi: 10.1128/JB.06203-11 22155775

47. Netz DJA, Sahl H-G, Marcolino R, dos Santos Nascimento Jn, de Oliveira SS, Soares MB, et al. Molecular characterisation of aureocin A70, a multi-peptide bacteriocin isolated from Staphylococcus aureus 11 Edited by M. Yaniv. Journal of Molecular Biology. 2001;311(5):939–49. doi: 10.1006/jmbi.2001.4885 11531330

48. Coelho MLV, Coutinho BG, Cabral da Silva Santos O, Nes IF, Bastos MdCdF. Immunity to the Staphylococcus aureus leaderless four-peptide bacteriocin aureocin A70 is conferred by AurI, an integral membrane protein. Research in Microbiology. 2014;165(1):50–9. doi: 10.1016/j.resmic.2013.11.001 24239961

49. Acedo JZ, van Belkum MJ, Lohans CT, Towle KM, Miskolzie M, Vederas JC. Nuclear Magnetic Resonance Solution Structures of Lacticin Q and Aureocin A53 Reveal a Structural Motif Conserved among Leaderless Bacteriocins with Broad-Spectrum Activity. Biochemistry. 2016;55(4):733–42. Epub 2016/01/16. doi: 10.1021/acs.biochem.5b01306 26771761.

50. Wladyka B, Wielebska K, Wloka M, Bochenska O, Dubin G, Dubin A, et al. Isolation, biochemical characterization, and cloning of a bacteriocin from the poultry-associated Staphylococcus aureus strain CH-91. Applied Microbiology and Biotechnology. 2013;97(16):7229–39. doi: 10.1007/s00253-012-4578-y 23196985

51. Towle KM, Vederas JC. Structural features of many circular and leaderless bacteriocins are similar to those in saposins and saposin-like peptides. MedChemComm. 2017;8:276–85. doi: 10.1039/c6md00607h 30108744.

52. Yoneyama F, Imura Y, Ohno K, Zendo T, Nakayama J, Matsuzaki K, et al. Peptide-lipid huge toroidal pore, a new antimicrobial mechanism mediated by a lactococcal bacteriocin, lacticin Q. Antimicrobial agents and chemotherapy. 2009;53:3211–7. doi: 10.1128/AAC.00209-09 19470516

53. Li M, Yoneyama F, Toshimitsu N, Zendo T, Nakayama J, Sonomoto K. Lethal hydroxyl radical accumulation by a lactococcal bacteriocin, lacticin Q. Antimicrobial agents and chemotherapy. 2013;57(8):3897–902. Epub 2013/06/05. doi: 10.1128/AAC.00638-13 23733459; PubMed Central PMCID: PMC3719721.

54. Netz DJ, Bastos Mdo C, Sahl HG. Mode of action of the antimicrobial peptide aureocin A53 from Staphylococcus aureus. Appl Environ Microbiol. 2002;68(11):5274–80. Epub 2002/10/31. doi: 10.1128/AEM.68.11.5274-5280.2002 12406714; PubMed Central PMCID: PMC129900.

55. Ovchinnikov KV, Chi H, Mehmeti I, Holo H, Nes IF, Diep DB. Novel group of leaderless multipeptide bacteriocins from Gram-positive bacteria. Applied and Environmental Microbiology. 2016;82:5216–24. doi: 10.1128/AEM.01094-16 27316965

56. Iwatani S, Horikiri Y, Zendo T, Nakayama J, Sonomoto K. Bifunctional Gene Cluster lnqBCDEF Mediates Bacteriocin Production and Immunity with Differential Genetic Requirements. Applied and Environmental Microbiology. 2013;79:2446–9. doi: 10.1128/AEM.03783-12 23335763.

57. Gibreel TM, Upton M. Synthetic epidermicin NI01 can protect Galleria mellonella larvae from infection with Staphylococcus aureus. Journal of Antimicrobial Chemotherapy. 2013;68:2269–73. doi: 10.1093/jac/dkt195 23711896

58. Halliwell S, Warn P, Sattar A, Derrick JP, Upton M. A single dose of epidermicin NI01 is sufficient to eradicate MRSA from the nares of cotton rats. The Journal of antimicrobial chemotherapy. 2017;72:778–81. doi: 10.1093/jac/dkw457 27999015.


Článek vyšel v časopise

PLOS One


2019 Číslo 10