Biofilm-associated toxin and extracellular protease cooperatively suppress competitors in Bacillus subtilis biofilms


Autoři: Kazuo Kobayashi aff001;  Yukako Ikemoto aff001
Působiště autorů: Division of Biological Science, Nara Institute of Science & Technology, Ikoma, Nara, Japan aff001
Vyšlo v časopise: Biofilm-associated toxin and extracellular protease cooperatively suppress competitors in Bacillus subtilis biofilms. PLoS Genet 15(10): e32767. doi:10.1371/journal.pgen.1008232
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008232

Souhrn

In nature, most bacteria live in biofilms where they compete with their siblings and other species for space and nutrients. Some bacteria produce antibiotics in biofilms; however, since the diffusion of antibiotics is generally hindered in biofilms by extracellular polymeric substances, i.e., the biofilm matrix, their function remains unclear. The Bacillus subtilis yitPOM operon is a paralog of the sdpABC operon, which produces the secreted peptide toxin SDP. Unlike sdpABC, yitPOM is induced in biofilms by the DegS-DegU two-component regulatory system. High yitPOM expression leads to the production of a secreted toxin called YIT. Expression of yitQ, which lies upstream of yitPOM, confers resistance to the YIT toxin, suggesting that YitQ is an anti-toxin protein for the YIT toxin. The alternative sigma factor SigW also contributes to YIT toxin resistance. In a mutant lacking yitQ and sigW, the YIT toxin specifically inhibits biofilm formation, and the extracellular neutral protease NprB is required for this inhibition. The requirement for NprB is eliminated by Δeps and ΔbslA mutations, either of which impairs production of biofilm matrix polymers. Overexpression of biofilm matrix polymers prevents the action of the SDP toxin but not the YIT toxin. These results indicate that, unlike the SDP toxin and many conventional antibiotics, the YIT toxin can pass through layers of biofilm matrix polymers to attack cells within biofilms with assistance from NprB. When the wild-type strain and the YIT-sensitive mutant were grown together on a solid medium, the wild-type strain formed biofilms that excluded the YIT-sensitive mutant. This observation suggests that the YIT toxin protects B. subtilis biofilms against competitors. Several bacteria are known to produce antibiotics in biofilms. We propose that some bacteria including B. subtilis may have evolved specialized antibiotics that can function within biofilms.

Klíčová slova:

Antibiotics – Bacillus subtilis – Bacterial biofilms – Biofilms – Extracellular matrix – Operons – Polymers – Toxins


Zdroje

1. Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010 Jan;8(1):15–25. doi: 10.1038/nrmicro2259 19946288

2. Raaijmakers JM, Mazzola M. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phytopathol. 2012;50:403–24. doi: 10.1146/annurev-phyto-081211-172908 22681451

3. Liu G, Chater KF, Chandra G, Niu G, Tan H. Molecular regulation of antibiotic biosynthesis in streptomyces. Microbiol Mol Biol Rev. 2013 Mar;77(1):112–43. doi: 10.1128/MMBR.00054-12 23471619

4. Stein T. Bacillus subtilis antibiotics: structures, syntheses and specific functions. Mol Microbiol. 2005 May;56(4):845–57. doi: 10.1111/j.1365-2958.2005.04587.x 15853875

5. Davies D. Understanding biofilm resistance to antibacterial agents. Nat Rev Drug Discov. 2003 Feb;2(2):114–22. doi: 10.1038/nrd1008 12563302

6. Høiby N, Bjarnsholt T, Givskov M, Molin S, Ciofu O. Antibiotic resistance of bacterial biofilms. Int J Antimicrob Agents. 2010 Apr;35(4):322–32. doi: 10.1016/j.ijantimicag.2009.12.011 20149602

7. Ratcliff WC, Denison RF. Alternative actions for antibiotics. Science. 2011 Apr 29;332(6029):547–8. doi: 10.1126/science.1205970 21527704

8. Branda SS, Vik S, Friedman L, Kolter R. Biofilms: the matrix revisited. Trends Microbiol. 2005 Jan;13(1):20–6. 15639628

9. Flemming HC, Wingender J. The biofilm matrix. Nat Rev Microbiol. 2010 Sep;8(9):623–33. doi: 10.1038/nrmicro2415 20676145

10. Rendueles O, Ghigo JM. Multi-species biofilms: how to avoid unfriendly neighbors. FEMS Microbiol Rev. 2012 Sep;36(5):972–89. doi: 10.1111/j.1574-6976.2012.00328.x 22273363

11. Mulcahy H, Charron-Mazenod L, Lewenza S. Extracellular DNA chelates cations and induces antibiotic resistance in Pseudomonas aeruginosa biofilms. PLoS Pathog. 2008 Nov;4(11):e1000213. doi: 10.1371/journal.ppat.1000213 19023416

12. Billings N, Millan M, Caldara M, Rusconi R, Tarasova Y, Stocker R, Ribbeck K. The extracellular matrix Component Psl provides fast-acting antibiotic defense in Pseudomonas aeruginosa biofilms. PLoS Pathog. 2013;9(8):e1003526 doi: 10.1371/journal.ppat.1003526 23950711

13. Tseng BS, Zhang W, Harrison JJ, Quach TP, Song JL, Penterman J, Singh PK, Chopp DL, Packman AI, Parsek MR. The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin. Environ Microbiol. 2013 Oct;15(10):2865–78. doi: 10.1111/1462-2920.12155 23751003

14. Toska J, Ho BT, Mekalanos JJ. Exopolysaccharide protects Vibrio cholerae from exogenous attacks by the type 6 secretion system. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):7997–8002. doi: 10.1073/pnas.1808469115 30021850

15. Doroshenko N, Tseng BS, Howlin RP, Deacon J, Wharton JA, Thurner PJ, Gilmore BF, Parsek MR, Stoodley P. Extracellular DNA impedes the transport of vancomycin in Staphylococcus epidermidis biofilms preexposed to subinhibitory concentrations of vancomycin. Antimicrob Agents Chemother. 2014 Dec;58(12):7273–82. doi: 10.1128/AAC.03132-14 25267673

16. Singh R, Sahore S, Kaur P, Rani A, Ray P. Penetration barrier contributes to bacterial biofilm-associated resistance against only select antibiotics, and exhibits genus-, strain- and antibiotic-specific differences. Pathog Dis. 2016 Aug;74(6). pii: ftw056. doi: 10.1093/femspd/ftw056 27402781

17. Yan L, Boyd KG, Adams DR, Burgess JG. Biofilm-specific cross-species induction of antimicrobial compounds in bacilli. Appl Environ Microbiol. 2003 Jul;69(7):3719–27. doi: 10.1128/AEM.69.7.3719-3727.2003 12839737

18. Kreth J, Merritt J, Bordador C, Shi W, Qi F. Transcriptional analysis of mutacin I (mutA) gene expression in planktonic and biofilm cells of Streptococcus mutans using fluorescent protein and glucuronidase reporters. Oral Microbiol Immunol. 2004 Aug;19(4):252–6. 15209996

19. Nandi M, Berry C, Brassinga AK, Belmonte MF, Fernando WG, Loewen PC, de Kievit TR. Pseudomonas brassicacearum strain DF41 kills Caenorhabditis elegans through biofilm-dependent and biofilm-independent mechanisms. Appl Environ Microbiol. 2016 Dec;82(23):6889–6898. doi: 10.1128/AEM.02199-16 27637885

20. Rendueles O, Beloin C, Latour-Lambert P, Ghigo JM. A new biofilm-associated colicin with increased efficiency against biofilm bacteria. ISME J. 2014 Jun;8(6):1275–88. doi: 10.1038/ismej.2013.238 24451204

21. Waite RD, Curtis MA. Pseudomonas aeruginosa PAO1 pyocin production affects population dynamics within mixed-culture biofilms. J Bacteriol. 2009 Feb;191(4):1349–54. doi: 10.1128/JB.01458-08 19060137

22. Oluyombo O, Penfold CN, Diggle SP. Competition in biofilms between cystic fibrosis isolates of Pseudomonas aeruginosa is shaped by R-pyocins. MBio. 2019 Jan 29;10(1). pii: e01828–18. doi: 10.1128/mBio.01828-18 30696740

23. Anderson MS, Garcia EC, Cotter PA. Kind discrimination and competitive exclusion mediated by contact-dependent growth inhibition systems shape biofilm community structure. PLoS Pathog. 2014 Apr 17;10(4):e1004076. doi: 10.1371/journal.ppat.1004076 24743836

24. Branda SS, González-Pastor JE, Ben-Yehuda S, Losick R, Kolter R. Fruiting body formation by Bacillus subtilis. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11621–6. 11572999

25. Branda SS, González-Pastor JE, Dervyn E, Ehrlich SD, Losick R, Kolter R. 2004. Genes involved in formation of structured multicellular communities by Bacillus subtilis. J Bacteriol. 2004 Jun;186(12):3970–9. doi: 10.1128/JB.186.12.3970-3979.2004 15175311

26. Branda SS, Chu F, Kearns DB, Losick R, Kolter R. A major protein component of the Bacillus subtilis biofilm matrix. Mol Microbiol. 2006 Feb;59(4):1229–38. doi: 10.1111/j.1365-2958.2005.05020.x 16430696

27. Romero D, Aguilar C, Losick R, Kolter R. Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2230–4 doi: 10.1073/pnas.0910560107 20080671

28. Kobayashi K, Iwano M. BslA(YuaB) forms a hydrophobic layer on the surface of Bacillus subtilis biofilms. Mol Microbiol. 2012 Jul;85(1):51–66 doi: 10.1111/j.1365-2958.2012.08094.x 22571672

29. Hobley L, Ostrowski A, Rao FV, Bromley KM, Porter M, Prescott AR, MacPhee CE, van Aalten DM, Stanley-Wall NR. BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm. Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13600–5. doi: 10.1073/pnas.1306390110 23904481

30. Hamon MA, Stanley NR, Britton RA, Grossman AD, Lazazzera BA. Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis. Mol Microbiol. 2004 May;52(3):847–60. doi: 10.1111/j.1365-2958.2004.04023.x 15101989

31. Kearns DB, Chu F, Branda SS, Kolter R, Losick R. A master regulator for biofilm formation by Bacillus subtilis. Mol Microbiol. 2005 Feb;55(3):739–49. doi: 10.1111/j.1365-2958.2004.04440.x 15661000

32. Chu F, Kearns DB, Branda SS, Kolter R, Losick R. Targets of the master regulator of biofilm formation in Bacillus subtilis. Mol Microbiol. 2006 Feb;59(4):1216–28. doi: 10.1111/j.1365-2958.2005.05019.x 16430695

33. Verhamme DT, Murray EJ, Stanley-Wall NR. DegU and Spo0A jointly control transcription of two loci required for complex colony development by Bacillus subtilis. J Bacteriol. 2009 Jan;191(1):100–8. doi: 10.1128/JB.01236-08 18978066

34. López D, Fischbach MA, Chu F, Losick R, Kolter R. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):280–5. doi: 10.1073/pnas.0810940106 19114652

35. Mielich-Süss B, Lopez D. Molecular mechanisms involved in Bacillus subtilis biofilm formation. Environ Microbiol. 2015 Mar;17(3):555–65. 24909922

36. Straight PD, Fischbach MA, Walsh CT, Rudner DZ, Kolter R. A singular enzymatic megacomplex from Bacillus subtilis. Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):305–10. doi: 10.1073/pnas.0609073103 17190806

37. Abriouel H, Franz CM, Ben Omar N, Gálvez A. Diversity and applications of Bacillus bacteriocins. FEMS Microbiol Rev. 2011 Jan;35(1):201–32. doi: 10.1111/j.1574-6976.2010.00244.x 20695901

38. Koskiniemi S, Lamoureux JG, Nikolakakis KC, t'Kint de Roodenbeke C, Kaplan MD, Low DA, Hayes CS. Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7032–7. doi: 10.1073/pnas.1300627110 23572593

39. Liu WT, Yang YL, Xu Y, Lamsa A, Haste NM, Yang JY, Ng J, Gonzalez D, Ellermeier CD, Straight PD, Pevzner PA, Pogliano J, Nizet V, Pogliano K, Dorrestein PC. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16286–90. doi: 10.1073/pnas.1008368107 20805502

40. González-Pastor JE, Hobbs EC, Losick R. Cannibalism by sporulating bacteria. Science. 2003 Jul 25;301(5632):510–3 doi: 10.1126/science.1086462 12817086

41. Pérez Morales TG, Ho TD, Liu WT, Dorrestein PC, Ellermeier CD. Production of the cannibalism toxin SDP is a multistep process that requires SdpA and SdpB. J Bacteriol. 2013 Jul;195(14):3244–51. doi: 10.1128/JB.00407-13 23687264

42. Lamsa A, Liu WT, Dorrestein PC, Pogliano K. The Bacillus subtilis cannibalism toxin SDP collapses the proton motive force and induces autolysis. Mol Microbiol. 2012 May;84(3):486–500. doi: 10.1111/j.1365-2958.2012.08038.x 22469514

43. Ellermeier CD, Hobbs EC, Gonzalez-Pastor JE, Losick R. A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Cell. 2006 Feb 10;124(3):549–59. doi: 10.1016/j.cell.2005.11.041 16469701

44. Fujita M, Losick R. Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A. Genes Dev. 2005 Sep 15;19(18):2236–44. doi: 10.1101/gad.1335705 16166384

45. López D, Vlamakis H, Losick R, Kolter R. Cannibalism enhances biofilm development in Bacillus subtilis. Mol Microbiol. 2009 Nov;74(3):609–18. doi: 10.1111/j.1365-2958.2009.06882.x 19775247

46. Lyons NA, Kraigher B, Stefanic P, Mandic-Mulec I, Kolter R. A Combinatorial Kin Discrimination System in Bacillus subtilis. Curr Biol. 2016 Mar 21;26(6):733–42. doi: 10.1016/j.cub.2016.01.032 26923784

47. Kobayashi K. Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis. Mol Microbiol. 2007 Oct;66(2):395–409. doi: 10.1111/j.1365-2958.2007.05923.x 17850253

48. Verhamme DT, Kiley TB, Stanley-Wall NR. DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis. Mol Microbiol. 2007 Jul;65(2):554–68. doi: 10.1111/j.1365-2958.2007.05810.x 17590234

49. Quisel JD, Burkholder WF, Grossman AD. In vivo effects of sporulation kinases on mutant Spo0A proteins in Bacillus subtilis. J Bacteriol. 2001 Nov;183(22):6573–8. doi: 10.1128/JB.183.22.6573-6578.2001 11673427

50. Leighton TJ, Doi RH. The stability of messenger ribonucleic acid during sporulation in Bacillus subtilis. J Biol Chem. 1971 May 25;246(10):3189–95. 4995746

51. Butcher BG, Helmann JD. Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. Mol Microbiol. 2006 May;60(3):765–82. doi: 10.1111/j.1365-2958.2006.05131.x 16629676

52. Cao M, Bernat BA, Wang Z, Armstrong RN, Helmann JD. FosB, a cysteine-dependent fosfomycin resistance protein under the control of sigma(W), an extracytoplasmic-function sigma factor in Bacillus subtilis. J Bacteriol. 2001 Apr;183(7):2380–3. doi: 10.1128/JB.183.7.2380-2383.2001 11244082

53. Yamada Y, Tikhonova EB, Zgurskaya HI. YknWXYZ is an unusual four-component transporter with a role in protection against sporulation-delaying-protein-induced killing of Bacillus subtilis. J Bacteriol. 2012 Aug;194(16):4386–94. doi: 10.1128/JB.00223-12 22707703

54. Huang X, Gaballa A, Cao M, Helmann JD. Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W. Mol Microbiol. 1999 Jan;31(1):361–71. doi: 10.1046/j.1365-2958.1999.01180.x 9987136

55. Marlow VL, Cianfanelli FR, Porter M, Cairns LS, Dale JK, Stanley-Wall NR. The prevalence and origin of exoprotease-producing cells in the Bacillus subtilis biofilm. Microbiology. 2014 Jan;160(Pt 1):56–66. doi: 10.1099/mic.0.072389-0 24149708

56. Spizizen J. Transformation of Biochemically Deficient Strains of Bacillus subtilis by Deoxyribonucleate. Proc Natl Acad Sci U S A. 1958 Oct 15;44(10):1072–8. doi: 10.1073/pnas.44.10.1072 16590310

57. West SA, Diggle SP, Buckling A, Gardner A, Griffin AS. The Social lives of microbes. Ann Rev Ecol Evol Syst. 2007;38:53–77.

58. Lyons NA, Kraigher B, Stefanic P, Mandic-Mulec I, Kolter R. A Combinatorial Kin Discrimination System in Bacillus subtilis. Curr Biol. 2016 Mar 21;26(6):733–42. doi: 10.1016/j.cub.2016.01.032 26923784

59. Tsuge K, Ano T, Hirai M, Nakamura Y, Shoda M. The genes degQ, pps, and lpa-8 (sfp) are responsible for conversion of Bacillus subtilis 168 to plipastatin production. Antimicrob Agents Chemother. 1999 Sep;43(9):2183–92. 10471562

60. Koumoutsi A, Chen XH, Vater J, Borriss R. DegU and YczE positively regulate the synthesis of bacillomycin D by Bacillus amyloliquefaciens strain FZB42. Appl Environ Microbiol. 2007 Nov;73(21):6953–64. doi: 10.1128/AEM.00565-07 17827323

61. Chen XH, Scholz R, Borriss M, Junge H, Mögel G, Kunz S, Borriss R. Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefaciens are efficient in controlling fire blight disease. J Biotechnol. 2009 Mar 10;140(1–2):38–44. doi: 10.1016/j.jbiotec.2008.10.015 19061923

62. Kobayashi K. Plant methyl salicylate induces defense responses in the rhizobacterium Bacillus subtilis. Environ Microbiol. 2015 Apr;17(4):1365–76. doi: 10.1111/1462-2920.12613 25181478

63. Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, Mizunoe Y. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature. 2010 May 20;465(7296):346–9. doi: 10.1038/nature09074 20485435

64. Baidamshina DR, Trizna EY, Holyavka MG, Bogachev MI, Artyukhov VG, Akhatova FS, Rozhina EV, Fakhrullin RF, Kayumov AR. Targeting microbial biofilms using Ficin, a nonspecific plant protease. Sci Rep. 2017 Apr 7;7:46068. doi: 10.1038/srep46068 28387349

65. Mitrofanova O, Mardanova A, Evtugyn V, Bogomolnaya L, Sharipova M. Effects of Bacillus serine proteases on the bacterial biofilms. Biomed Res Int. 2017;2017:8525912. doi: 10.1155/2017/8525912 28904973

66. Kumar L, Cox CR, Sarkar SK. Matrix metalloprotease-1 inhibits and disrupts Enterococcus faecalis biofilms. PLoS One. 2019 Jan 11;14(1):e0210218. doi: 10.1371/journal.pone.0210218 30633757

67. Kobayashi K. Bacillus subtilis pellicle formation proceeds through genetically defined morphological changes. J Bacteriol. 2007 Jul;189(13):4920–31. doi: 10.1128/JB.00157-07 17468240

68. Uchiyama I, Mihara M, Nishide H, Chiba H. MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. Nucleic Acids Res. 2015 Jan;43(Database issue):D270–6. doi: 10.1093/nar/gku1152 25398900

69. Vlamakis H, Aguilar C, Losick R, Kolter R. Control of cell fate by the formation of an architecturally complex bacterial community. Genes Dev. 2008 Apr 1;22(7):945–53. 18381896

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Genetika Reprodukční medicína

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