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...
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References
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.
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.
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.
Cotter PD, Hill C, Ross RP. Bacteriocins: developing innate immunity for food. Nat Rev Micro. 2005;3(10):777–88.
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.
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.
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.
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.
Klaenhammer TR. Bacteriocins of lactic acid bacteria. Biochimie. 1988;70(3):337–49. 0300-9084(88)90206-4.
Knerr PJ, van der Donk WA. Discovery, biosynthesis, and engineering of lantipeptides. Annu Rev Biochem. 2012. doi:10.1146/annurev-biochem-060110-113521.
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.
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.
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].
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.
Piper C, Cotter PD, Ross RP, Hill C. Discovery of medically significant lantibiotics. Curr Drug Discov Technol. 2009;6(1):1–18.
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.
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.
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.
Velásquez JE, van der Donk WA. Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol. 2011;15(1):11–21.
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.
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O’Sullivan, O., Hill, C., Ross, P., Cotter, P. (2013). Bacteriocin Mining in Metagenomes. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_689-3
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DOI: https://doi.org/10.1007/978-1-4614-6418-1_689-3
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