Abstract
CRISPR-Cas systems provide with adaptive immunity to bacteria, by targeting and degrading specific nucleic acid from invaders, such as plasmids and bacteriophages. Thus, CRISPR-Cas provide protection from phage infections, but also limit the acquisition of new traits by horizontal gene transfer, a key mechanism in bacterial evolution. However, when selective pressure to acquire new elements is strong, these systems can be lost or inactivated. Moreover, CRISPR-Cas systems occasionally make mistakes and target their own sequences, causing a form of ‘autoimmunity’. This autoimmunity has been observed to cause chromosomal deletions, including genomic regions that have been integrated through horizontal gene transfer, such as genomic islands. Interestingly, CRISPR-Cas systems have been found in about 40% of sequenced bacteria, and their distribution is sporadic, with unrelated strains carrying similar systems to distant species and vice versa. Based on the downsides of carrying these systems, one could hypothesise that their prevalence should be much lower. Alternatively, based on the immunity benefits, they might be expected to be more widespread. During this thesis I have studied the autoimmunity effects, as well as the capability of recovering a region previously deleted due to self targeting. Moreover, I have studied the mobility of these systems, trying to understand their distribution and prevalence in bacterial genomes. Finally, I have investigated the regulation of CRISPR-Cas systems and how fine-tuning mechanisms can lower the trade-offs associated with their activity, as well as activate these systems when they are most needed. We I identified the Rsm pathway, a post-transcriptional regulatory system, as a CRISPR-Cas regulator. I have characterised the Rsm pathway and its effects in Serratia, identified the direct targets of RsmA, the RNA-binding protein that leads the Rsm pathway, and connected this pathway to other global regulators, such as quorum sensing.