Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems

Abstract

CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.

Biological warfare between two bacterial viruses in a genomic archipelago sheds light on the spread of CRISPR-Cas systems

“…A small proportion of genomes of the pathogenic bacterium A. baumannii have long been known to exhibit two subtypes of type I-F CRISPR-Cas systems (8, 9). These were named as subtypes I-Fa and I-Fb.…”

“…The pangenome used was the one constructed with 9,696 genomes in Rubio et al, 2023 (8). All genomes are structurally and functionally annotated, as well as the reference genes of the pangenome itself.…”

“…As found in 40% of bacterial genomes, A. baumannii posesses the acquired CRISPR-Cas defense system against bacterial viruses (bacteriophages, known as phages) and other mobile genetic elements (7). However, this system appears in only 13% of its sequenced genomes (8, 9). These CRISPR-Cas systems are mainly targeted against phages, but also against plasmids to a lesser extent (10).…”

“…These CRISPR-Cas systems are mainly targeted against phages, but also against plasmids to a lesser extent (10). Finally, it has been discussed that they could also be targeted against phage-plasmids (8), which are phages that can act as plasmids under certain conditions (11).…”

“…A. baumannii mainly presents class I CRISPR-Cas systems, divided into 2 type I subtypes: I-Fa (also classified as I-F2) and I-Fb (also classified as I-F1) (8, 15–17). Remarkably, Global Clone 2 does not usually present CRISPR-Cas systems (9).…”