Not All Predicted CRISPR-Cas Systems Are Equal: Isolated Cas Genes and Classes of CRISPR Like Elements

BMC Bioinformatics. 2017 Feb 6;18(1):92. doi: 10.1186/s12859-017-1512-4.

Abstract

Background: The CRISPR-Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR-Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs.

Results: Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don't contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements.

Conclusion: This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR-Cas systems.

Keywords: CRISPR–Cas system; STAR-like element; Tandem repeat; false-CRISPR.

MeSH terms

  • CRISPR-Cas Systems*
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Enhancer Elements, Genetic*
  • Genetic Loci
  • Genome, Bacterial*
  • Genomics
  • Molecular Sequence Annotation
  • Phylogeny
  • Software
  • Staphylococcus aureus / genetics
  • Streptococcus pyogenes / genetics
  • Streptococcus thermophilus / genetics