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

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 ob-served 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.

Automated summary

CRISPR-Cas systems are a type of acquired immunity found in 40% of bacterial genomes, which use small DNA fragments called spacers to prevent viral infections. However, the majority of these spacers, known as CRISPR dark matter, have not been associated with specific viruses. Through analyzing spacers from tens of thousands of genomes, researchers have reduced the amount of CRISPR dark matter from 80% to as low as 15% in some bacterial species. Additionally, it has been observed that genomes with CRISPR-Cas systems also have specific sets of membrane proteins, suggesting a connection between bacterial competitiveness and the acquisition of CRISPR-Cas.