Deciphering how the Cas2 ribonuclease non-canonically controls Legionella pneumophila thermal tolerance and virulence

PROJECT SUMMARY / ABSTRACT Legionella pneumophila (Lp) is the agent of Legionnaires’ disease. In water systems, Lp grows in amoebae and biofilms, and in the lungs, it infects macrophages. CRISPR-Cas systems are a common feature of Lp, where they expectedly confer immunity to invading genetic elements. Yet, through an analysis of Lp 130b, which has the most common Lp CRISPR-Cas type (type II-B), we discovered that Cas2 majorly promotes Lp infection of amoebae. Compatible with this, cas2 mRNA is hyperexpressed during Lp infection of amoebae and during stationary phase, the growth stage linked to the infectious Lp phenotype. Critically, the infection role of Cas2 was distinct from adaptive immunity, i.e., i) a cas2 mutant’s infection defect occurred in the absence of any foreign genetic element, ii) mutants lacking other cas genes or the CRISPR array were not impaired, and iii) introduction of Cas2 into a Lp strain that naturally lacks a CRISPR-Cas locus caused that strain to be more infective for amoebae. We purified Lp Cas2 and showed that it has RNase activity, and by testing a mutant form of Cas2 that lacked the ability to cleave ssRNAs, we showed that RNase activity is critical for the ability of Cas2 to promote infection of amoebae. This work has endured as the sole example of Cas2 clearly promoting a non-canonical or infectious phenotype. Thus, we posited that Cas2, by virtue of its ability to cleave/degrade RNA, influences the amount or configuration of an mRNA that encodes or regulates a key infectivity factor. We now identify expression of a previously undefined small heat shock protein gene (hspC2) as being increased by the presence of Cas2. Mutant analysis found that HspC2, along with Cas2, promotes Lp growth in amoebae and macrophages as well as biofilm formation, thereby revealing a role for a sHsp in pathogenesis and new insight into how Cas2 impacts Lp infectivity. We also confirmed a role for Cas2 in Lp thermal tolerance and biofilm formation. Given these data, we propose that the Lp Cas2-HspC2 axis can be a new model or paradigm for decoding how Cas proteins non-canonically impact gene expression, thermal tolerance, and virulence. Thus, we now aim to discern whether Cas2 i) acts directly by binding and then cleaving/degrading (only) a part of hspC2 mRNA such that the transcript is more stable, ii) acts indirectly by binding and degrading wholesale the RNA for a repressor of hspC2 transcription, or iii) again acts indirectly but by binding and then cleaving a part of the mRNA for a transcriptional activator of hspC2 such that the resulting RNA is more stable. This proposal has the potential to i) advance our understanding of Lp physiology and virulence, potentially revealing new targets for restricting Lp spread, ii) define a new mode of bacterial gene regulation controlled by multi- purpose Cas2 proteins, and iii) ultimately uncover a form of nuclease activity that might have broad application.