BAGEL2: Mining for bacteriocins in genomic data

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  de Jong, Anne ^a   van Heel, Auke J ^a   Kok, Jan ^a   Kuipers, Oscar P ^a,b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b Kluyver Center for Genomics of Industrial Fermentation   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOCIN; ANTIINFECTIVE AGENT;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; BIOSYNTHESIS; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA BASE; ENTEROCOCCUS FAECALIS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; LACTOBACILLUS PLANTARUM; PRIORITY JOURNAL; STREPTOCOCCUS PNEUMONIA; VALIDITY; WEB BROWSER; CHEMISTRY; DATA MINING; GENETICS; GENOMICS; INTERNET; OPEN READING FRAME; PROTEIN MOTIF;

AMINO ACID MOTIFS; ANTI-BACTERIAL AGENTS; BACTERIOCINS; DATA MINING; GENOME, BACTERIAL; GENOMICS; INTERNET; OPEN READING FRAMES; SOFTWARE;

BACTERIA (MICROORGANISMS);

EID: 77954305252     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq365     Document Type: Article

References (20)

1. Cotter,P.D., Hill,C. and Ross,R.P. (2005) Bacteriocins: Developing innate immunity for food. Nat. Rev. Microbiol., 3, 777-788.
2. Gillor,O., Nigro,L.M. and Riley,M.A. (2005) Genetically engineered bacteriocins and their potential as the next generation of antimicrobials. Curr. Pharm. Des., 11, 1067-1075.
3. de Jong,A., van Hijum,S.A.F.T., Bijlsma,J.J.E., Kok,J. and Kuipers,O.P. (2006) BAGEL: A web-based bacteriocin genome mining tool. Nucleic Acids Res., 34, W273.
4. Knoll,C., Divol,B. and du Toit,M. (2008) Genetic screening of lactic acid bacteria of oenological origin for bacteriocin-encoding genes. Food Microbiol., 25, 983-991.
5. Navarro,L., Rojo-Bezares,B., Sáenz,Y., Díez,L., Zarazaga,M., Ruiz-Larrea,F. and Torres,C. (2008) Comparative study of the pln locus of the quorum-sensing regulated bacteriocin-producing L. plantarum J51 strain. Int. J. Food Microbiol., 128, 390-394.
6. Holtsmark,I., Eijsink,V.H. and Brurberg,M. (2008) Bacteriocins from plant pathogenic bacteria. FEMS Microbiol. Lett., 280, 1-7.
7. Bierbaum,G. and Sahl,H.G. (2009) Lantibiotics: mode of action, biosynthesis and bioengineering. Curr. Pharm. Biotechnol., 10, 2-18.
8. Nissen-Meyer,J., Rogne,P., Oppegard,C., Haugen,H.S. and Kristiansen,P.E. (2009) Structure-function relationships of the non-lanthionine-containing peptide (class II) bacteriocins produced by Gram-positive bacteria. Curr. Pharm. Biotechnol., 10, 19-37.
9. Maqueda,M., Sanchez-Hidalgo,M., Fernandez,M., Montalban-Lopez,M., Valdivia,E. and Martinez-Bueno,M. (2008) Genetic features of circular bacteriocins produced by gram-positive bacteria. FEMS Microbiol. Rev., 32, 2-22.
10. Drider,D., Fimland,G., Hechard,Y., McMullen,L.M. and Prevost,H. (2006) The continuing story of class IIa bacteriocins. Microbiol. Mol. Biol. Rev., 70, 564.
11. Willey,J.M. and Van der Donk,W.A. (2007) Lantibiotics: peptides of diverse structure and function. Annu. Rev. Microbiol., 61, 477-501.
12. Goto,Y., Li,B., Claesen,J., Shi,Y., Bibb,M.J. and van der Donk,W.A. (2010) Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights. PLoS Biology, 8, e1000339.
13. Begley,M., Cotter,P.D., Hill,C. and Ross,R.P. (2009) Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl. Environ. Microbiol., 75, 5451.
14. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
15. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
16. Delcher,A.L., Bratke,K.A., Powers,E.C. and Salzberg,S.L. (2007) Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics, 23, 673.
17. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
18. Bailey,T.L. and Gribskov,M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 14, 48-54.
19. Dufour,A., Hindre,T., Haras,D. and Le Pennec,J.P. (2007) The biology of lantibiotics from the lacticin 481 group is coming of age. FEMS Microbiol. Rev., 31, 134-167.
20. Wooley,J.C., Godzik,A. and Friedberg,I. (2010) A primer on metagenomics. PLoS Comput. Biol., 6, e1000667.