The adaptive immune system known as CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) is found in 90% of fully sequenced thermophiles, but in less than 50% of mesophilic bacteria. Why the discrepancy? In their study in mBio this week, researchers from Harvard Medical School and from the National Center for Biotechnology Information at NIH used a computer model to sort this out. The upshot? When viruses mutate quickly, as they do at middle-of-the-road temperatures, they can overwhelm CRISPR-Cas systems.
CRISPRs in bacteria and archaea use “spacers”, DNA sequences that are designed based on a viral or plasmid template to correspond to sequences in these attacking viruses or plasmids. When the host is invaded, it transcribes these spacers into RNA, cleaves it up into fragments of the right length, then the spacers bind their target viral or plasmid sequences (called “protospacers”) and tag them for degradation. Combined with the Cas machinery that makes it all work, CRISPR-Cas systems amount to adaptive immune systems that immunize the host against invasions. However, it’s not a foolproof system: viruses can evade CRISPR-Cas with as little as a single mutation in their protospacer. And when viruses mutate quickly and nimbly, it seems a CRISPR-Cas system would be little use but costly to keep up.
The authors of the mBio paper hypothesized that if the mutation rate of these attacking viruses gets too high it will overwhelm the ability of CRISPR-Cas systems to fend them off, making the CRISPR-Cas system a waste of energy and resources for the host. And one place where mutation rates are relatively high is in mesophilic systems.
In hot situations, the authors write, life is tougher. The cost of a wrong mutational turn is costlier and more likely to end badly. Hence, mutation rates in all manner of microbes, including viruses, are higher in mesophilic systems. Is that why mesophiles use CRISPR-Cas systems less than thermophiles? After studying the results of their model experiments, the authors say “yes”.
Using a population genetic model in which hosts with and without CRISPR-Cas compete under pressure from mutating, lytic viruses, they looked at what might happen when viral mutation rates decline to levels seen in thermophilic systems. As they predicted, the simulations show CRISPR-Cas competitors win out over non-CRISPR strains at reduced viral mutation rates but that the tables are turned once viral mutation rates pass a certain threshold. Increasing viral adaptability seems to depress the value of a CRISPR-Cas system, selecting against adaptability in bacteria or archaea that might otherwise carry them.
“These results offer a simple, testable viral diversity hypothesis to explain why mesophilic bacteria disproportionately lack CRISPR-Cas immunity,” write the authors.
If bacteria and archaea have been under attack from viruses day and night for billions of years, and the CRISPR-Cas system only works under certain circumstances, why haven’t they evolved a system like ours: an immune system that can preemptively adapt and respond to practically any viral variant? The problem, the authors hypothesize, is space. With genomes smaller than 13 Mb, no prokaryote can house the billions of randomly generated spacer sequences it would need to arm an immune system like vertebrates possess. The best they can do is “chase the diversifying viral population, trying to stay apace.”