Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity

Alexandra E. Briner, Rodolphe Barrangou

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5'-AAAA-3'. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.

Original languageEnglish (US)
Pages (from-to)994-1001
Number of pages8
JournalApplied and environmental microbiology
Volume80
Issue number3
DOIs
StatePublished - Feb 1 2014

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Clustered Regularly Interspaced Short Palindromic Repeats
Lactobacillus buchneri
Lactobacillus
genotyping
loci
fermentation
gene
immunization
silage
immune system
pickles
plasmid
homology
bioethanol
vegetable
polymorphism
genotype
genome
divergence
spoilage

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

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Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity. / Briner, Alexandra E.; Barrangou, Rodolphe.

In: Applied and environmental microbiology, Vol. 80, No. 3, 01.02.2014, p. 994-1001.

Research output: Contribution to journalArticle

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