1887

Abstract

A novel -like sequence was identified from the dominant human gut bacterium strain A2-162. This sequence was extended to reveal a putative lantibiotic operon with biosynthetic and transport genes, two sets of regulatory genes, immunity genes, three identical copies of a nisin-like gene with an unusual leader peptide, and a fourth putative gene. Comparison with other nisin clusters showed that the closest relationship was to nisin U. A2-162 demonstrated antimicrobial activity against when grown on solid medium in the presence of trypsin. Fusions of predicted structural sequences with the nisin A leader were expressed in containing the nisin A operon without . Expression of the leader sequence fused to the predicted structural produced a growth defect in that was dependent upon the presence of biosynthetic genes, but failed to produce antimicrobial activity. Insertion of the cluster into MG1614 gave an increased immunity to nisin A, but this was not replicated by the expression of . Nisin A induction of containing the cluster and genes allowed detection of the NsoA1 pre-peptide by Western hybridization. When this heterologous producer was grown with nisin induction on solid medium, antimicrobial activity was demonstrated in the presence of trypsin against , and . This research adds to evidence that lantibiotic production may be an important trait of gut bacteria and could lead to the development of novel treatments for intestinal diseases.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000515
2017-09-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/163/9/1292.html?itemId=/content/journal/micro/10.1099/mic.0.000515&mimeType=html&fmt=ahah

References

  1. Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108–160 [View Article][PubMed]
    [Google Scholar]
  2. Cotter PD, Ross RP, Hill C. Bacteriocins – a viable alternative to antibiotics?. Nat Rev Microbiol 2013; 11:95–105 [View Article][PubMed]
    [Google Scholar]
  3. Hegarty JW, Guinane CM, Ross RP, Hill C, Cotter PD. Bacteriocin production: a relatively unharnessed probiotic trait?. F1000Res 2016; 5:2587 [View Article][PubMed]
    [Google Scholar]
  4. Dischinger J, Basi Chipalu S, Bierbaum G. Lantibiotics: promising candidates for future applications in health care. Int J Med Microbiol 2014; 304:51–62 [View Article][PubMed]
    [Google Scholar]
  5. Hammami R, Fernandez B, Lacroix C, Fliss I. Anti-infective properties of bacteriocins: an update. Cell Mol Life Sci 2013; 70:1–21 [View Article][PubMed]
    [Google Scholar]
  6. Malik DK, Bhatia D, Nimbriya A, Kumar S. Lactic acid bacteria and bacteriocin: a review. J Pharm Res 2012; 5:2510–2513
    [Google Scholar]
  7. Chatterjee C, Paul M, Xie L, van der Donk WA. Biosynthesis and mode of action of lantibiotics. Chem Rev 2005; 105:633–684 [View Article][PubMed]
    [Google Scholar]
  8. Field D, Begley M, O'Connor PM, Daly KM, Hugenholtz F et al. Bioengineered nisin A derivatives with enhanced activity against both gram positive and gram negative pathogens. PLoS One 2012; 7:e46884 [View Article][PubMed]
    [Google Scholar]
  9. Montalbán-López M, Van Heel AJ, Kuipers OP. Employing the promiscuity of lantibiotic biosynthetic machineries to produce novel antimicrobials. FEMS Microbiol Rev 2017; 41:5–18 [View Article][PubMed]
    [Google Scholar]
  10. Shin JM, Gwak JW, Kamarajan P, Fenno JC, Rickard AH et al. Biomedical applications of nisin. J Appl Microbiol 2016; 120:1449–1465 [View Article][PubMed]
    [Google Scholar]
  11. Horn N, Swindell S, Dodd H, Gasson M. Nisin biosynthesis genes are encoded by a novel conjugative transposon. Mol Gen Genet 1991; 228:129–135 [View Article][PubMed]
    [Google Scholar]
  12. O'Connor PM, O'Shea EF, Guinane CM, O'Sullivan O, Cotter PD et al. Nisin H is a new Nisin variant produced by the gut-derived strain Streptococcus hyointestinalis DPC6484. Appl Environ Microbiol 2015; 81:3953–3960 [View Article][PubMed]
    [Google Scholar]
  13. Garg N, Tang W, Goto Y, Nair SK, Van der Donk WA. Lantibiotics from Geobacillus thermodenitrificans. Proc Natl Acad Sci USA 2012; 109:5241–5246 [View Article][PubMed]
    [Google Scholar]
  14. Field D, Connor PM, Cotter PD, Hill C, Ross RP. The generation of nisin variants with enhanced activity against specific gram-positive pathogens. Mol Microbiol 2008; 69:218–230 [View Article][PubMed]
    [Google Scholar]
  15. Field D, Quigley L, O'Connor PM, Rea MC, Daly K et al. Studies with bioengineered Nisin peptides highlight the broad-spectrum potency of Nisin V. Microb Biotechnol 2010; 3:473–486 [View Article][PubMed]
    [Google Scholar]
  16. Yuan J, Zhang ZZ, Chen XZ, Yang W, Huan LD. Site-directed mutagenesis of the hinge region of nisinZ and properties of nisinZ mutants. Appl Microbiol Biotechnol 2004; 64:806–815 [View Article][PubMed]
    [Google Scholar]
  17. Karakas Sen A, Narbad A, Horn N, Dodd HM, Parr AJ et al. Post-translational modification of nisin. The involvement of NisB in the dehydration process. Eur J Biochem 1999; 261:524–532 [View Article][PubMed]
    [Google Scholar]
  18. Ra R, Beerthuyzen MM, de Vos WM, Saris PE, Kuipers OP. Effects of gene disruptions in the nisin gene cluster of Lactococcus lactis on nisin production and producer immunity. Microbiology 1999; 145:1227–1233 [View Article][PubMed]
    [Google Scholar]
  19. Wirawan RE, Klesse NA, Jack RW, Tagg JR. Molecular and genetic characterization of a novel Nisin variant produced by Streptococcus uberis. Appl Environ Microbiol 2006; 72:1148–1156 [View Article][PubMed]
    [Google Scholar]
  20. De Vos WM, Mulders JW, Siezen RJ, Hugenholtz J, Kuipers OP. Properties of nisin Z and distribution of its gene, nisZ, in Lactococcus lactis. Appl Environ Microbiol 1993; 59:213–218[PubMed]
    [Google Scholar]
  21. Heidrich C, Pag U, Josten M, Metzger J, Jack RW et al. Isolation, characterization, and heterologous expression of the novel lantibiotic epicidin 280 and analysis of its biosynthetic gene cluster. Appl Environ Microbiol 1998; 64:3140–3146[PubMed]
    [Google Scholar]
  22. O'Keeffe T, Hill C, Ross RP. Characterization and heterologous expression of the genes encoding enterocin a production, immunity, and regulation in Enterococcus faecium DPC1146. Appl Environ Microbiol 1999; 65:1506–1515[PubMed]
    [Google Scholar]
  23. Aso Y, Nagao J, Koga H, Okuda K, Kanemasa Y et al. Heterologous expression and functional analysis of the gene cluster for the biosynthesis of and immunity to the lantibiotic, nukacin ISK-1. J Biosci Bioeng 2004; 98:429–436 [View Article][PubMed]
    [Google Scholar]
  24. Li H, O'Sullivan DJ. Heterologous expression of the Lactococcus lactis bacteriocin, nisin, in a dairy Enterococcus strain. Appl Environ Microbiol 2002; 68:3392–3400 [View Article][PubMed]
    [Google Scholar]
  25. Rink R, Kuipers A, de Boef E, Leenhouts KJ, Driessen AJ et al. Lantibiotic structures as guidelines for the design of peptides that can be modified by lantibiotic enzymes. Biochemistry 2005; 44:88738882 [View Article][PubMed]
    [Google Scholar]
  26. Arora T, Wegmann U, Bobhate A, Lee YS, Greiner TU et al. Microbially produced glucagon-like peptide 1 improves glucose tolerance in mice. Mol Metab 2016; 5:725–730 [View Article][PubMed]
    [Google Scholar]
  27. Mierau I, Kleerebezem M. 10 years of the nisin-controlled gene expression system (NICE) in Lactococcus lactis. Appl Microbiol Biotechnol 2005; 68:705–717 [View Article][PubMed]
    [Google Scholar]
  28. Majchrzykiewicz JA, Lubelski J, Moll GN, Kuipers A, Bijlsma JJ et al. Production of a class II two-component lantibiotic of Streptococcus pneumoniae using the class I nisin synthetic machinery and leader sequence. Antimicrob Agents Chemother 2010; 54:1498–1505 [View Article][PubMed]
    [Google Scholar]
  29. Kluskens LD, Kuipers A, Rink R, De Boef E, Fekken S et al. Post-translational modification of therapeutic peptides by NisB, the dehydratase of the lantibiotic nisin. Biochemistry 2005; 44:12827–12834 [View Article][PubMed]
    [Google Scholar]
  30. Rink R, Kluskens LD, Kuipers A, Driessen AJ, Kuipers OP et al. NisC, the cyclase of the lantibiotic Nisin, can catalyze cyclization of designed nonlantibiotic peptides. Biochemistry 2007; 46:13179–13189 [View Article][PubMed]
    [Google Scholar]
  31. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012; 3:289–306 [View Article][PubMed]
    [Google Scholar]
  32. Birri DJ, Brede DA, Tessema GT, Nes IF. Bacteriocin production, antibiotic susceptibility and prevalence of haemolytic and gelatinase activity in faecal lactic acid bacteria isolated from healthy ethiopian infants. Microb Ecol 2013; 65:504–516 [View Article][PubMed]
    [Google Scholar]
  33. Walsh CJ, Guinane CM, Hill C, Ross RP, O'Toole PW et al. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the human microbiome project's reference genome database. BMC Microbiol 2015; 15:183 [View Article][PubMed]
    [Google Scholar]
  34. Barcenilla A. Diversity of the Butyrate-Producing Microflora of the Human Gut Aberdeen, UK, Robert Gordon University, PhD Thesis 1999
    [Google Scholar]
  35. Dabek M, Mccrae SI, Stevens VJ, Duncan SH, Louis P. Distribution of beta-glucosidase and β-glucuronidase activity and of β-glucuronidase gene gus in human colonic bacteria. FEMS Microbiol Ecol 2008; 66:487–495 [View Article][PubMed]
    [Google Scholar]
  36. Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol 2007; 9:1101–1111 [View Article][PubMed]
    [Google Scholar]
  37. Lawson PA, Finegold SM. Reclassification of Ruminococcus obeum as Blautia obeum comb. nov. Int J Syst Evol Microbiol 2015; 65:789–793 [View Article][PubMed]
    [Google Scholar]
  38. Mayer M, Dodd H, Narbad A, Gasson M. Identifying lantibiotic gene clusters and novel lantibiotic genes. PCT/GB2006/001429 2006
  39. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual Plainview, NY: Cold Spring Harbor lab Press; 1989
    [Google Scholar]
  40. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944–945 [View Article][PubMed]
    [Google Scholar]
  41. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article][PubMed]
    [Google Scholar]
  42. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  43. Mayer MJ, Narbad A, Gasson MJ. Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin. J Bacteriol 2008; 190:6734–6740 [View Article][PubMed]
    [Google Scholar]
  44. Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 1989; 77:61–68 [View Article][PubMed]
    [Google Scholar]
  45. Fernandez A, Horn N, Wegmann U, Nicoletti C, Gasson MJ et al. Enhanced secretion of biologically active murine interleukin-12 by Lactococcus lactis. Appl Environ Microbiol 2009; 75:869–871 [View Article][PubMed]
    [Google Scholar]
  46. Dertli E, Colquhoun IJ, Gunning AP, Bongaerts RJ, Le Gall G et al. Structure and biosynthesis of two exopolysaccharides produced by Lactobacillus johnsonii FI9785. J Biol Chem 2013; 288:31938–31951 [View Article][PubMed]
    [Google Scholar]
  47. Pitino I, Randazzo CL, Cross KL, Parker ML, Bisignano C et al. Survival of Lactobacillus rhamnosus strains inoculated in cheese matrix during simulated human digestion. Food Microbiol 2012; 31:57–63 [View Article][PubMed]
    [Google Scholar]
  48. Ryan MP, Rea MC, Hill C, Ross RP. An application in cheddar cheese manufacture for a strain of Lactococcus lactis producing a novel broad-spectrum bacteriocin, lacticin 3147. Appl Environ Microbiol 1996; 62:612–619[PubMed]
    [Google Scholar]
  49. Cheng F, Takala TM, Saris PE. Nisin biosynthesis in vitro. J Mol Microbiol Biotechnol 2007; 13:248–254 [View Article][PubMed]
    [Google Scholar]
  50. Sahl HG, Jack RW, Bierbaum G. Biosynthesis and biological activities of lantibiotics with unique post-translational modifications. Eur J Biochem 1995; 230:827–853 [View Article][PubMed]
    [Google Scholar]
  51. Richards VP, Lang P, Bitar PD, Lefébure T, Schukken YH et al. Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infect Genet Evol 2011; 11:1263–1275 [View Article][PubMed]
    [Google Scholar]
  52. Plat A, Kluskens LD, Kuipers A, Rink R, Moll GN. Requirements of the engineered leader peptide of nisin for inducing modification, export, and cleavage. Appl Environ Microbiol 2011; 77:604–611 [View Article][PubMed]
    [Google Scholar]
  53. Jenq RR, Taur Y, Devlin SM, Ponce DM, Goldberg JD et al. Intestinal Blautia is associated with reduced death from graft-versus-host disease. Biol Blood Marrow Transplant 2015; 21:1373–1383 [View Article][PubMed]
    [Google Scholar]
  54. Bajaj JS, Hylemon PB, Ridlon JM, Heuman DM, Daita K et al. Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation. Am J Physiol Gastrointest Liver Physiol 2012; 303:G675–G685 [View Article][PubMed]
    [Google Scholar]
  55. Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F et al. Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. BMC Med 2013; 11:46 [View Article][PubMed]
    [Google Scholar]
  56. Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 2012; 7:e39743 [View Article][PubMed]
    [Google Scholar]
  57. Chen J, Stevenson DM, Weimer PJ. Albusin B, a bacteriocin from the ruminal bacterium Ruminococcus albus 7 that inhibits growth of Ruminococcus flavefaciens. Appl Environ Microbiol 2004; 70:3167–3170 [View Article][PubMed]
    [Google Scholar]
  58. Crost EH, Ajandouz EH, Villard C, Geraert PA, Puigserver A et al. Ruminococcin C, a new anti-Clostridium perfringens bacteriocin produced in the gut by the commensal bacterium Ruminococcus gnavus E1. Biochimie 2011; 93:1487–1494 [View Article][PubMed]
    [Google Scholar]
  59. Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D et al. Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces. Appl Environ Microbiol 2001; 67:4111–4118 [View Article][PubMed]
    [Google Scholar]
  60. Marcille F, Gomez A, Joubert P, Ladiré M, Veau G et al. Distribution of genes encoding the trypsin-dependent lantibiotic Ruminococcin A among bacteria isolated from human fecal microbiota. Appl Environ Microbiol 2002; 68:3424–3431 [View Article][PubMed]
    [Google Scholar]
  61. Lawton EM, Ross RP, Hill C, Cotter PD. Two-peptide lantibiotics: a medical perspective. Mini Rev Med Chem 2007; 7:1236–1247 [View Article][PubMed]
    [Google Scholar]
  62. Mcauliffe O, Hill C, Ross RP. Identification and overexpression of ltnl, a novel gene which confers immunity to the two-component lantibiotic lacticin 3147. Microbiology 2000; 146:129–138 [View Article][PubMed]
    [Google Scholar]
  63. Piper C, Hill C, Cotter PD, Ross RP. Bioengineering of a Nisin A-producing Lactococcus lactis to create isogenic strains producing the natural variants Nisin F, Q and Z. Microb Biotechnol 2011; 4:375–382 [View Article][PubMed]
    [Google Scholar]
  64. Corvey C, Stein T, Düsterhus S, Karas M, Entian KD. Activation of subtilin precursors by Bacillus subtilis extracellular serine proteases subtilisin (AprE), WprA, and Vpr. Biochem Biophys Res Commun 2003; 304:48–54 [View Article][PubMed]
    [Google Scholar]
  65. Stein T, Entian KD. Maturation of the lantibiotic subtilin: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to monitor precursors and their proteolytic processing in crude bacterial cultures. Rapid Commun Mass Spectrom 2002; 16:103–110 [View Article][PubMed]
    [Google Scholar]
  66. Qi F, Chen P, Caufield PW. The group I strain of Streptococcus mutans, UA140, produces both the lantibiotic mutacin I and a nonlantibiotic bacteriocin, mutacin IV. Appl Environ Microbiol 2001; 67:15–21 [View Article][PubMed]
    [Google Scholar]
  67. Gomez A, Ladiré M, Marcille F, Fons M. Trypsin mediates growth phase-dependent transcriptional regulation of genes involved in biosynthesis of Ruminococcin A, a lantibiotic produced by a Ruminococcus gnavus strain from a human intestinal Microbiota. J Bacteriol 2002; 184:18–28 [View Article][PubMed]
    [Google Scholar]
  68. Lee JH, Li X, O'Sullivan DJ. Transcription analysis of a lantibiotic gene cluster from Bifidobacterium longum DJO10A. Appl Environ Microbiol 2011; 77:5879–5887 [View Article][PubMed]
    [Google Scholar]
  69. Mcclerren AL, Cooper LE, Quan C, Thomas PM, Kelleher NL et al. Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic. Proc Natl Acad Sci USA 2006; 103:17243–17248 [View Article][PubMed]
    [Google Scholar]
  70. Hoover SE, Perez AJ, Tsui HC, Sinha D, Smiley DL et al. A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthesis gene cluster. Mol Microbiol 2015; 97:229–243 [View Article][PubMed]
    [Google Scholar]
  71. Gasson MJ. Transfer of sucrose fermenting ability, nisin resistance and nisin production into Streptococcus lactis 712. FEMS Microbiol Lett 1984; 21:7–10 [View Article]
    [Google Scholar]
  72. Dodd HM, Horn N, Gasson MJ. Analysis of the genetic determinant for production of the peptide antibiotic nisin. J Gen Microbiol 1990; 136:555–556 [View Article][PubMed]
    [Google Scholar]
  73. Dodd HM, Horn N, Giffard CJ, Gasson MJ. A gene replacement strategy for engineering nisin. Microbiology 1996; 142:47–55 [View Article][PubMed]
    [Google Scholar]
  74. Wegmann U, Klein JR, Drumm I, Kuipers OP, Henrich B. Introduction of peptidase genes from Lactobacillus delbrueckii subsp. lactis into Lactococcus lactis and controlled expression. Appl Environ Microbiol 1999; 65:4729–4733[PubMed]
    [Google Scholar]
  75. Casadaban MJ, Cohen SN. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol 1980; 138:179–207 [View Article][PubMed]
    [Google Scholar]
  76. Simon D, Chopin A. Construction of a vector plasmid family and its use for molecular cloning in Streptococcus lactis. Biochimie 1988; 70:559–566 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000515
Loading
/content/journal/micro/10.1099/mic.0.000515
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error