CRISPR-Cas systems are defense systems that protect bacteria and archaea (two forms of single-cell organisms that do not have a nucleus in their cells) against selfish elements, such as viruses. Archaea resemble bacteria in cell shape and size, but they are closer in evolutionary relation to nucleus-containing cells, such as those of fungi, plants, or animals than they are to bacteria. Much like our own immune system, when viruses or virus-like elements inject their genomes into such cells, the system can sample a piece of the selfish DNA and the next time it will meet a similar invading DNA it will cut its genome to pieces and thereby protect the cell from infection. Such defense systems are common in bacteria and even more so in archaea, the vast majority of which have them. However, just as countries must incur large costs to have defense forces to keep invaders out so do cells, and CRISPR-Cas systems do have their costs. One such cost is the potential reduction in genetic novelty. Some viruses of archaea and bacteria can actually benefit their hosts by various mechanisms, especially by killing off competitor strains and species, while keeping a “low profile” in their own host cell. If a CRISPR-Cas system is too active and defensive, it can therefore prevent the cell from acquiring beneficial traits. As an example, bacterial strains that have CRISPR-Cas systems that are active tend to have fewer antibiotic resistance genes than their counterparts in which the system has been inactivated or lost. The “borders” that CRISPR-Cas systems create may even be sufficient to reduce the flow of genetic material between cells and ultimately lead to their divergence into different species.
Another potential cost of CRISPR-Cas system is that it may interfere with DNA repair processes in the cell because its components may clash with repair enzymes that help the cell deal with the damages of UV radiation or toxic chemicals that damage DNA. To date, CRISPR-associated proteins have been shown to contribute to DNA-repair In some bacteria and interfere in others, but this has not been studied in archaea. Our aims are to explore the role of CRISPR-Cas systems in shaping gene exchange, speciation, and genetic novelty in archaea and how they interact with DNA repair processes in the cell.
