Why so rare if so essentiel: the determinants of the sparse distribution of CRISPR-Cas systems in bacterial genomes

Abstract

CRISPR-Cas (Cluster of Regularly Interspaced Short Palindromic Repeats) systems confer bacteria and archaea an adaptative immunity against phages and other invading genetic elements playing an important role in bacterial evolution. However, despite the protection they generate and high rate of horizontal transfer, less than 50% of bacterial genomes harbor a CRISPR-Cas system. As a comparison, 90% of archaea encode a CRISPR-Cas system and a bacterial genome codes for two restriction modification systems on average. This review describes CRISPR-Cas systems distribution in bacterial genomes and then details the different hypotheses put forward to explain the relative scarcity of CRISPR-Cas systems. More specifically, phage escape mechanisms, ecological factors such as phage diversity and abundance and intrinsic costs, such as maintenance or autoimmunity, are discussed. Overall, a better understanding of the downsides of encoding CRISPR-Cas systems is essential to explain their evolutionary dynamics and their relative success in different environments and clades.