The type III-B CRISPR-Cas System Affects Energy Metabolism and Adaptation in the Archaeon Saccharolobus solfataricus

Type III CRISPR-Cas immune systems that recognize and cleave extrachromosomal RNA when active, are particularly widespread in archaea. Mechanistically, these systems have the potential to regulate gene expression of host genes on a post-transcriptional level, but very little is known about any potential accessory roles of type III-B systems beyond immunity. We have created knockout mutants of a type III-B CRISPR-Cas complex in the thermoacidophilic archaeon Saccharolobus solfataricus to investigate potential secondary functions of the type III-B system. Deletion mutants exhibited an accelerate growth but were less quickly adaptable to changes in carbon sources in their growth media. In line with this phenotype, upregulated genes were significantly enriched in functional categories of energy production and conversion, as well as with carbohydrate or amino acid transport and metabolism in RNAseq studies. Generally, a significant accumulation of genes encoding transmembrane proteins in the upregulated proportion of the transcriptome suggests interconnections between the type III-B CRISPR-Cas system and various membrane-associated processes. Notably, the deletion mutants did not lose their general virus- or plasmid defense activities indicating that this particular system might have been partially adopted for cellular regulatory roles.