CRISPRTarget: bioinformatic prediction and analysis of crRNA targets

A. Biswas, J.N. Gagnon, S.J.J. Brouns, P.C. Fineran, C.M. Brown

Research output: Contribution to journalArticleAcademicpeer-review

130 Citations (Scopus)

Abstract

The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems
Original languageEnglish
Pages (from-to)817-827
JournalRNA Biology
Volume10
Issue number5
DOIs
Publication statusPublished - 2013

Keywords

  • short palindromic repeats
  • bacterial immune-system
  • cas systems
  • pectobacterium-atrosepticum
  • streptococcus-thermophilus
  • salmonella-enterica
  • dynamic properties
  • antiviral defense
  • adaptive immunity
  • genome sequence

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