Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Bacteriocin Mining in Metagenomes

  • Orla O’Sullivan
  • Colin Hill
  • Paul Ross
  • Paul Cotter
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_689-3

Definition

Bacteriocins are heat-stable ribosomally synthesized peptides produced by one bacterium which are active against other bacteria and against which the producer has a specific immunity mechanism.

Introduction

Bacteriocins are ribosomally synthesized antimicrobial peptides that are produced by many bacteria and which kill or inhibit the growth of other bacteria. Bacteriocin producers are protected as a consequence of dedicated immunity (self-protective) systems (Cotter et al. 2005). Bacteriocins are of both academic and commercial interest, with several in use as food preservatives or as the active agent in clinical or veterinary antimicrobials. It is not surprising that there is significant interest in the identification and characterization of new bacteriocin gene clusters. The growing volume of metagenomic sequence data is an important resource which can be mined for the in silico discovery of novel bacteriocins.

A Background to Bacteriocins

Bacteriocins were first described...

Keywords

Cysteine Serine Dehydration Microbe Arena 
This is a preview of subscription content, log in to check access

References

  1. Abriouel H, Franz CMAP, Omar NB, Gálvez A. Diversity and applications of Bacillus bacteriocins. FEMS Microbiol Rev. 2011;35(1):201–32. doi:10.1111/j.1574-6976.2010.00244.x.PubMedCrossRefGoogle Scholar
  2. Begley M, Cotter PD, Hill C, Ross RP. Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl Environ Microbiol. 2009;75(17):5451–60. doi:10.1128/aem.00730-09.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Bohnebeck U, Lombardot T, Kottmann R, Glockner FO. MetaMine – a tool to detect and analyse gene patterns in their environmental context. BMC Bioinforma. 2008;9:459. doi:10.1186/1471-2105-9-459.CrossRefGoogle Scholar
  4. Cotter PD, Hill C, Ross RP. Bacteriocins: developing innate immunity for food. Nat Rev Micro. 2005;3(10):777–88.CrossRefGoogle Scholar
  5. de Jong A, van Heel AJ, Kok J, Kuipers OP. BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res. 2010;38 suppl 2:W647–51. doi:10.1093/nar/gkq365.PubMedCentralPubMedCrossRefGoogle Scholar
  6. Dobson A, Cotter PD, Ross RP, Hill C. Bacteriocin production: a probiotic trait? Appl Environ Microbiol. 2012;78(1):1–6. doi:10.1128/aem.05576-11.PubMedCentralPubMedCrossRefGoogle Scholar
  7. Glass EM, Wilkening J, Wilke A, Antonopoulos D Meyer F Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010(1), pdb prot5368, doi:2010/1/pdb.prot5368 [pii] 10.1101/pdb.prot5368.Google Scholar
  8. Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I. BACTIBASE second release: a database and tool platform for bacteriocin characterization. BMC Microbiol. 2010;10:22. doi:10.1186/1471-2180-10-22.PubMedCentralPubMedCrossRefGoogle Scholar
  9. Klaenhammer TR. Bacteriocins of lactic acid bacteria. Biochimie. 1988;70(3):337–49. 0300-9084(88)90206-4.PubMedCrossRefGoogle Scholar
  10. Knerr PJ, van der Donk WA. Discovery, biosynthesis, and engineering of lantipeptides. Annu Rev Biochem. 2012. doi:10.1146/annurev-biochem-060110-113521.PubMedGoogle Scholar
  11. Majchrzykiewicz JA, Lubelski J, Moll GN, Kuipers A, Bijlsma JJ, Kuipers OP, 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(4):1498–505. doi:10.1128/AAC.00883-09.PubMedCentralPubMedCrossRefGoogle Scholar
  12. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2008;36 suppl 1:D534–8. doi:10.1093/nar/gkm869.PubMedCentralPubMedGoogle Scholar
  13. Murphy K, O’Sullivan O, Rea MC, Cotter PD, Ross RP, Hill C. Genome mining for radical SAM protein determinants reveals multiple sactibiotic-like gene clusters. PLoS One. 2011;6(7):e20852. doi:10.1371/journal.pone.0020852 PONE-D-11-04704[pii].PubMedCentralPubMedCrossRefGoogle Scholar
  14. O’Sullivan O, Begley M, Ross R, Cotter P, Hill C. Further identification of novel lantibiotic operons using LanM-based genome mining. Probiotics Antimicrob Protein. 2011;3(1):27–40. doi:10.1007/s12602-011-9062-y.CrossRefGoogle Scholar
  15. Piper C, Cotter PD, Ross RP, Hill C. Discovery of medically significant lantibiotics. Curr Drug Discov Technol. 2009;6(1):1–18.PubMedCrossRefGoogle Scholar
  16. Rea M, Cotter P, Hill C, Ross R. Classification of bacteriocins from gram-positive bacteria. In: Drider D, Rebuffat S, editors. Prokaryotic antimicrobial peptides - from genes to applications. New York: Springer; 2011. p. 29.CrossRefGoogle Scholar
  17. Richter M, Lombardot T, Kostadinov I, Kottmann R, Duhaime MB, Peplies J, et al. JCoast - a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinforma. 2008;9:177. doi:10.1186/1471-2105-9-177.CrossRefGoogle Scholar
  18. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 2011;39(Database issue):D546-551. doi:10.1093/nar/gkq1102.Google Scholar
  19. Velásquez JE, van der Donk WA. Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol. 2011;15(1):11–21.PubMedCentralPubMedCrossRefGoogle Scholar
  20. Więckowicz M, Schmidt M, Sip A, Grajek W. Development of a PCR-based assay for rapid detection of class IIa bacteriocin genes. Lett Appl Microbiol. 2011;52(3):281–9. doi:10.1111/j.1472-765X.2010.02999.x.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Orla O’Sullivan
    • 1
    • 2
  • Colin Hill
    • 2
    • 3
  • Paul Ross
    • 1
    • 2
  • Paul Cotter
    • 1
    • 2
  1. 1.Teagasc Food Research Centre, Moorepark, Fermoy, Co.CorkIreland
  2. 2.Alimentary Pharmabiotic CentreUniversity CollegeCorkIreland
  3. 3.Department of MicrobiologyUniversity CollegeCorkIreland