GalK limits type I-F CRISPR-Cas expression in a CRP-dependent manner

Abstract

CRISPR-Cas adaptive immune systems protect bacteria from phage predation, and other foreign genetic elements such as plasmids. Significant advances have been made regarding how CRISPR-Cas systems elicit immunity; however, comparatively little is known about their regulation. To study CRISPR-Cas regulation, we describe the construction of suicide lacZ-reporter plasmids with different antibiotic resistance cassettes. Through recombination into the host chromosome, single-copy expression can be achieved, thus preserving natural gene expression and maintaining a reporter expression output that reflects regulation within a normal genomic context. Previous work determined that the galactose metabolism gene galM, decreased the expression of the cas operon in Pectobacterium atrosepticum. We used the new integrative reporters to investigate galK, a gene that is located elsewhere in the genome and is responsible for the conversion of α-D-Galactose to Galactose-1-P during galactose metabolism. Deletion of galK led to elevated cas expression in a CRP-dependent manner but had no effect on CRISPR array expression. These results highlight that the metabolic status of the host cell is linked to the induction of CRISPR-Cas immunity.

The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR–Cas immune systems

“…This may enable the integration of quorum sensing signalling with metabolic status to fine-tune adaptive immunity. The cAMP receptor protein (CRP), which is also involved in carbon utilisation, regulates CRISPR–Cas systems in E. coli , Serratia, P. atrosepticum and Thermus thermophilus ( 20 , 78–81 ), and is connected to the Csr pathways ( 82 ). Therefore, in Serratia , CRP might integrate further information into the Rsm pathway to control adaptive immunity.…”

Avoidance of Self during CRISPR Immunization

“…Across systems and host species, though, patterns of expression are variable [38]. The cas genes can be up-regulated in response to various stimuli that may correspond to increased infection risk, including nutrient concentrations [78,79,80], temperature [81], and host density [82,83]. Systems may even be up-regulated as a direct response to viral contact or ongoing infection [38,84].…”

“…For a comprehensive discussion of CRISPR regulation, a large and active research area in itself, see Patterson et al [38]. How CRISPR is regulated so that the host can dynamically control infection risk is still something of a mystery, but promising new methods to quickly and accurately measure the expression of cas genes in a range of genetic backgrounds and ecological scenarios are being developed [80].…”

“…Therefore, if pathogen exposure varies in time, hosts can maximize their capacity for self vs. non-self recognition by employing a strategy that combines induction with various mechanisms to bias the Cas acquisition machinery's substrate preference (discussed earlier). Possibly of note, cas genes are typically found as a single operon [17], and often are co-transcribed (e.g., [80]). This implies a temporal coupling of the Cas acquisition and effector complexes, consistent with the idea that at times of increased infection the host will want to both use and add to its spacer repertoire.…”

Immune Lag Is a Major Cost of Prokaryotic Adaptive Immunity During Viral Outbreaks

“…The cas genes and CRISPR arrays of many hosts are transcriptionally upregulated in response to infection [53, 54], or in situations where there is a high risk of infection ( e.g ., in a biofilm; [55, 56, 57, 58, 59]). The specific regulatory cues used by the CRISPR locus are diverse [54], and new methods are being developed to probe them [60]. Consider the case where the CRISPR locus is specifically upregulated in response to infection.…”