Identification of genes that are associated with DNA repeats in prokaryotes

TLDR

CRISPR consists of direct repeats of 21–37 bp separated by non‑repetitive sequences and is found in prokaryotes, prompting interest in its origin and function. The study used in silico analysis to characterize the structure of CRISPR, a prokaryotic repetitive DNA family absent in eukaryotes and viruses. The authors found that CRISPR loci are flanked by conserved leader sequences, that multiple loci per genome imply mobility, and that four cas genes—adjacent to CRISPRs and encoding helicase and exonuclease motifs—are present only in CRISPR‑positive prokaryotes, indicating a functional relationship.

Abstract

Summary Using in silico analysis we studied a novel family of repetitive DNA sequences that is present among both domains of the prokaryotes (Archaea and Bacteria), but absent from eukaryotes or viruses. This family is characterized by direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non‐repetitive sequences. To appreciate their characteri‐stic structure, we will refer to this family as the clustered regularly interspaced short palindromic repeats (CRISPR). In most species with two or more CRISPR loci, these loci were flanked on one side by a common leader sequence of 300–500 b. The direct repeats and the leader sequences were conserved within a species, but dissimilar between species. The presence of multiple chromosomal CRISPR loci suggests that CRISPRs are mobile elements. Four CRISPR‐associated ( cas ) genes were identified in CRISPR‐containing prokaryotes that were absent from CRISPR‐negative prokaryotes. The cas genes were invariably located adjacent to a CRISPR locus, indicating that the cas genes and CRISPR loci have a functional relationship. The cas3 gene showed motifs characteristic for helicases of the superfamily 2, and the cas 4 gene showed motifs of the RecB family of exonucleases, suggesting that these genes are involved in DNA metabolism or gene expression. The spatial coherence of CRISPR and cas genes may stimulate new research on the genesis and biological role of these repeats and genes.