The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation

Abstract

CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.

Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

“…A search of the 564 non-redundant spacers from P. aeruginosa revealed 33 spacers with high-scoring matches to resistance genes in ResFinder's reference ARG (electronic supplementary material, tables S4 and S5). This is consistent with experimental laboratory studies that showed that spacers can be acquired from ARGs and impede their subsequent uptake [12,59]. To be functional for interference, the type I systems of P. aeruginosa require protospacer adjacent motifs (PAMs).…”

“…These segments of intruder DNA in the CRISPR loci are termed spacers and their complementary target sequences are known as protospacers. The CRISPR arrays are transcribed, processed into short CRISPR RNAs (crRNAs) and, through the formation of Cas ribonucleoprotein complexes and target recognition, lead to degradation of the invading element [12,13].…”

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

“…The biological underpinnings of the non-uniform phyletic spread of CRISPR-Cas systems remain to be elucidated. Considering the high horizontal mobility of CRISPR-cas loci, it appears likely that their loss or retention in prokaryotic genomes depends on the trade-off between the fitness cost that is determined, mostly, by auto-immunity and curtailment of horizontal gene transfer, and the benefits of defence conferred by adaptive immunity [79][80][81][82][83][84] . These benefits, most likely, depend on the abundance and diversity of viruses in specific habitats as well as the biology of host-parasite interactions in specific groups of microorganisms 85,86 .…”

A histidine kinase and a response regulator provide phage resistance to Marinomonas mediterranea via CRISPR-Cas regulation

“…Bacteria in their natural environments are exposed to many invading genetic elements such as phages and plasmids. These elements can constitute mechanisms of horizontal gene transfer conferring valuable attributes to the recipient cells, while they can also provoke cell death 1 . Amongst various bacterial defense mechanisms against invading elements, CRISPR-Cas systems are unique since they confer adaptative immunity to the cells.…”