MtvS Interacts With RNA Polymerase to Regulate the Francisella Type V-A CRISPR-Cas System

CRISPR-Cas systems endow bacteria and archaea with adaptive immunity against mobile genetic elements, playing a fundamental role in shaping microbial communities. Many organisms harbor more than one CRISPR-Cas system, and little is known about whether and how they are differentially regulated, in many instances due to the impossibility of studying CRISPR immunity in native hosts. Here we studied the regulation of endogenous type II-B and type V-A CRISPR-Cas systems in opportunistic human pathogen Francisella novicida U112. Fluorescence microscopy and transcriptomics experiments revealed that while the type II-B system is constitutively expressed, the type V-A CRISPR-Cas system is differentially expressed at stationary phase and high cell density. Using mass spectrometry and genetics we identified MtvS as a factor required for the differential expression of the type V-A CRISPR-Cas locus. Surprisingly, MtvS-dependent expression of the type V-A CRISPR-Cas system at high cell density is linked to a quorum sensing-like behavior. In addition, MtvS modulates transcription of many genes in stationary phase, some of which are required for Francisella virulence. Pull-down experiments revealed MtvS interacts with the β’ subunit of the RNA polymerase and therefore may constitute a noncanonical alternative sigma factor involved in the regulation of the expression of CRISPR loci and other genes.