A Haloarchaeal Transcriptional Regulator That Represses the Expression of CRISPR-Associated Genes.

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) systems provide acquired heritable protection to bacteria and archaea against selfish DNA elements, such as viruses. These systems must be tightly regulated because they can capture DNA fragments from foreign selfish elements, and also occasionally from self-chromosomes, resulting in autoimmunity. Most known species from the halophilic archaeal genus contain type I-B CRISPR-Cas systems, and the strongest hotspot for self-spacer acquisition by was a locus that contained a putative transposable element, as well as the gene , which was a very frequent target for self-targeting spacers. To test whether this gene is CRISPR-associated, we investigated it using bioinformatics, deletion, over-expression, and comparative transcriptomics. We show that is a global transcriptional regulator that can repress diverse genes, since its deletion results in significantly higher expression of multiple genes, especially those involved in nutrient transport. When over-expressed, strongly repressed the transcript production of all genes tested, both those involved in spacer acquisition (, and ) and those required for destroying selfish genetic elements ( and ). Considering that is highly conserved in haloarchaea, with homologs that are present in species that do not encode the CRISPR-Cas system, we conclude that it is a global regulator that is also involved in gene regulation, either directly or indirectly.