Comparative analysis of CRISPR loci in lactic acid bacteria genomes

Philippe Horvath, Anne Claire Coûté-Monvoisin, Dennis A. Romero, Patrick Boyaval, Christophe Fremaux, Rodolphe Barrangou

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187 Scopus citations

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in bacteria and archaea, that provide acquired immunity against foreign genetic elements. Here, we investigate the occurrence of CRISPR loci in the genomes of lactic acid bacteria (LAB), including members of the Firmicutes and Actinobacteria phyla. A total of 102 complete and draft genomes across 11 genera were studied and 66 CRISPR loci were identified in 26 species. We provide a comparative analysis of the CRISPR/cas content and diversity across LAB genera and species for 37 sets of CRISPR loci. We analyzed CRISPR repeats, CRISPR spacers, leader sequences, and cas gene content, sequences and architecture. Interestingly, multiple CRISPR families were identified within Bifidobacterium, Lactobacillus and Streptococcus, and similar CRISPR loci were found in distant organisms. Overall, eight distinct CRISPR families were identified consistently across CRISPR repeats, cas gene content and architecture, and sequences of the universal cas1 gene. Since the clustering of the CRISPR families does not correlate with the classical phylogenetic tree, we hypothesize that CRISPR loci have been subjected to horizontal gene transfer and further evolved independently in select lineages, in part due to selective pressure resulting from phage predation. Globally, we provide additional insights into the origin and evolution of CRISPR loci and discuss their contribution to microbial adaptation.

Original languageEnglish (US)
Pages (from-to)62-70
Number of pages9
JournalInternational journal of food microbiology
Volume131
Issue number1
DOIs
StatePublished - Apr 30 2009

All Science Journal Classification (ASJC) codes

  • Food Science
  • Microbiology

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    Horvath, P., Coûté-Monvoisin, A. C., Romero, D. A., Boyaval, P., Fremaux, C., & Barrangou, R. (2009). Comparative analysis of CRISPR loci in lactic acid bacteria genomes. International journal of food microbiology, 131(1), 62-70. https://doi.org/10.1016/j.ijfoodmicro.2008.05.030