Comparative analysis of CRISPR loci in lactic acid bacteria genomes

International Journal of Food Microbiology

Volumn 131, Issue 1, 2009, Pages 62-70

  Horvath, Philippe ^a   Coûté Monvoisin, Anne Claire ^a   Romero, Dennis A ^b   Boyaval, Patrick ^a   Fremaux, Christophe ^a   Barrangou, Rodolphe ^b  

^a Danisco France SAS   (France)

^b Danisco USA Inc   (United States)

Author keywords

Cas gene; Clustered regularly interspaced short palindromic repeats (CRISPR); Horizontal gene transfer; Lactic acid bacteria; Phage

Indexed keywords

CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; REPETITIVE DNA; SIGNAL PEPTIDE; SPACER DNA; UNCLASSIFIED DRUG;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BIFIDOBACTERIUM; COMPARATIVE STUDY; CONTROLLED STUDY; FIRMICUTES; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENOME ANALYSIS; LACTIC ACID BACTERIUM; LACTOBACILLUS; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN CONTENT; STREPTOCOCCUS;

5' UNTRANSLATED REGIONS; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENOME, BACTERIAL; GRAM-POSITIVE BACTERIA; INVERTED REPEAT SEQUENCES; LACTOBACILLACEAE;

ACTINOBACTERIA; BIFIDOBACTERIUM; FIRMICUTES; LACTOBACILLUS; STREPTOCOCCUS;

EID: 64449088715     PISSN: 01681605     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2008.05.030     Document Type: Article

References (38)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 215 (1990) 403-410
2. Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D.A., and Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 (2007) 1709-1712
3. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., and Wheeler D.L. GenBank. Nucleic Acids Research 36 (2008) D25-30
4. Berger B., Pridmore R.D., Barretto C., Delmas-Julien F., Schreiber K., Arigoni F., and Brüssow H. Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics. Journal of Bacteriology 189 (2007) 1311-1321
5. Bernal A., Ear U., and Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Research 29 (2001) 126-127
6. Bolotin A., Quinquis B., Sorokin A., and Ehrlich S.D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151 (2005) 2551-2561
7. Callanan M., Kaleta P., O'Callaghan J., O'Sullivan O., Jordan K., McAuliffe O., Sangrador-Vegas A., Slattery L., Fitzgerald G.F., Beresford T., and Ross R.P. Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. Journal of Bacteriology 190 (2008) 727-735
8. Deveau H., Barrangou R., Garneau J.E., Labonté J., Fremaux C., Boyaval P., Romero D.A., Horvath P., and Moineau S. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. Journal of Bacteriology 190 (2008) 1390-1400
9. Glaser P., Rusniok C., Buchrieser C., Chevalier F., Frangeul L., Msadek T., Zouine M., Couvé E., Lalioui L., Poyart C., Trieu-Cuot P., and Kunst F. Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Molecular Microbiology 45 (2002) 1499-1513
10. Godde J.S., and Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. Journal of Molecular Evolution 62 (2006) 718-729
11. Grissa I., Vergnaud G., and Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Research 35 (2007) W52-57
12. Grissa I., Vergnaud G., and Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 23 (2007) 172
13. Haft D.H., Selengut J.D., and White O. The TIGRFAMs database of protein families. Nucleic Acids Research 31 (2003) 371-373
14. Haft D.H., Selengut J., Mongodin E.F., and Nelson K.E. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Computational Biology 1 (2005) e60
15. Hartke, A., Zuniga, M., Deutscher, J., 2008. Unpublished results.
16. Horvath P., Romero D.A., Coûté-Monvoisin A.C., Richards M., Deveau H., Moineau S., Boyaval P., Fremaux C., and Barrangou R. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. Journal of Bacteriology 190 (2008) 1401-1412
17. Jansen R., Van Embden J.D., Gaastra W., and Schouls L.M. Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology 43 (2002) 1565-1575
18. Klaenhammer T.R., Altermann E., Arigoni F., Bolotin A., Breidt F., Broadbent J., Cano R., Chaillou S., Deutscher J., Gasson M., van de Guchte M., Guzzo J., Hartke A., Hawkins T., Hols P., Hutkins R., Kleerebezem M., Kok J., Kuipers O., Lubbers M., Maguin E., McKay L., Mills D., Nauta A., Overbeek R., Pel H., Pridmore D., Saier M., van Sinderen D., Sorokin A., Steele J., O'Sullivan D., de Vos W., Weimer B., Zagorec M., and Siezen R. Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek 82 (2002) 29-58
19. Klaenhammer T.R., Barrangou R., Buck B.L., Azcarate-Peril M.A., and Altermann E. Genomic features of lactic acid bacteria effecting bioprocessing and health. FEMS Microbiology Reviews 29 (2005) 393-409
20. Kleerebezem M., and Hugenholtz J. Metabolic pathway engineering in lactic acid bacteria. Current Opinion in Biotechnology 14 (2003) 232-237
21. Kunin V., Sorek R., and Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology 8 (2007) R61
22. Kunin V., He S., Warnecke F., Peterson S.B., Garcia Martin H., Haynes M., Ivanova N., Blackall L.L., Breitbart M., Rohwer F., McMahon K.D., and Hugenholtz P. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research 18 (2008) 293-297
23. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 23 (2007) 2947-2948
24. Lillestøl R., Redder P., Garrett R., and Brügger K. A putative viral defence mechanism in archaeal cells. Archaea 2 (2006) 59-72
25. Liu M., van Enckevort F.H., and Siezen R.J. Genome update: lactic acid bacteria genome sequencing is booming. Microbiology 151 (2005) 3811-3814
26. Makarova K.S., and Koonin E.V. Evolutionary genomics of lactic acid bacteria. Journal of Bacteriology 189 (2007) 1199-1208
27. Makarova K.S., Grishin N.V., Shabalina S.A., Wolf Y.I., and Koonin E.V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct 1 (2006) 1-26
28. Makarova K.S., Slesarev A., Wolf Y., Sorokin A., Mirkin B., Koonin E., Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V., Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D.M., Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A., Baldwin K., Lee J.H., Díaz-Muñiz I., Dosti B., Smeianov V., Wechter W., Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y., Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J., Hutkins R., O'Sullivan D., Steele J., Unlu G., Saier M., Klaenhammer T., Richardson P., Kozyavkin S., Weimer B., and Mills D. Comparative genomics of the lactic acid bacteria. Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 15611-15616
29. Mojica F.J., Díez-Villaseñor C., García-Martínez J., and Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular Evolution 60 (2005) 174-182
30. Pfeiler E.A., and Klaenhammer T.R. The genomics of lactic acid bacteria. Trends in Microbiology 15 (2007) 546-553
31. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., and Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 16 (2000) 944-945
32. Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., Zwahlen M.C., Desiere F., Bork P., Delley M., Pridmore R.D., and Arigoni F. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proceedings of the National Academy of Sciences of the United States of America 99 (2002) 14422-14427
33. Selengut J.D., Haft D.H., Davidsen T., Ganapathy A., Gwinn-Giglio M., Nelson W.C., Richter A.R., and White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Research 35 (2007) D260-264
34. Sonnhammer E.L., and Durbin R. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167 (1995) GC1-GC10
35. Sorek R., Kunin V., and Hugenholtz P. CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology 6 (2008) 181-186
36. Tomita H., and Ike Y. Genetic analysis of transfer-related regions of the vancomycin resistance Enterococcus conjugative plasmid pHTbeta: identification of oriT and a putative relaxase gene. Journal of Bacteriology 187 (2005) 7727-7737
37. Tyson G.W., and Banfield J.F. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology 10 (2008) 200-207
38. Xu P., Alves J.M., Kitten T., Brown A., Chen Z., Ozaki L.S., Manque P., Ge X., Serrano M.G., Puiu D., Hendricks S., Wang Y., Chaplin M.D., Akan D., Paik S., Peterson D.L., Macrina F.L., and Buck G.A. Genome of the opportunistic pathogen Streptococcus sanguinis. Journal of Bacteriology 189 (2007) 3166-3175