Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae

Ekaterina Semenova, Maxim Nagornykh, Mikhail Pyatnitskiy, Irena I. Artamonova, Konstantin Severinov

Research output: Contribution to journalArticlepeer-review

59 Citations (Scopus)


Clustered regularly interspaced short palindromic repeat (CRISPR) is a bacterial immunity system that requires a perfect sequence match between the CRISPR cassette spacer and a protospacer in invading DNA for exclusion of foreign genetic elements. CRISPR cassettes are hypervariable, possibly reflecting different exposure of strains of the same species to foreign genetic elements. Here, we determined CRISPR cassette sequences of two Xanthomonas oryzae strains and found that one of the strains remains sensitive to phage Xop411 despite carrying a cassette that has a spacer exactly matching a fragment of the Xop411 genome. To explain this apparent paradox, we identified X. oryzae CRISPR spacers of likely phage origin and defined a consensus sequence of a motif adjacent to X. oryzae phage protospacers. Our analysis revealed that the Xop411 protospacer that matches the CRISPR spacer has this motif mutated, which likely explains the phage's ability to infect its host. While similar observations were made previously with Streptococcus thermophilus and its phages, the conserved motif in X. oryzae phages is located on a protospacer side opposite to the S. thermophilus phages' motif. The results thus point to a considerable degree of variety of CRISPR-mediated phage resistance mechanisms in different bacteria.

Original languageEnglish
Pages (from-to)110-116
Number of pages7
JournalFEMS Microbiology Letters
Issue number1
Publication statusPublished - Jul 2009
Externally publishedYes


  • Bacteriophage
  • Small RNA
  • Xanthomonas oryzae


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