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

Campa, Aroa Rey; Smith, Lisa F.; Hampton, Hannah G; Sharma, Sahil; Jackson, Simon A.; Bischler, Thorsten; Sharma, Cynthia M; Fineran, Peter C.

doi:10.1093/nar/gkab704

Cited by 11 publications

(13 citation statements)

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“…pigQ ) – and others which influence it (e.g. crp , ptsG (PTS IIC)) – were identified and previously shown to control type III-A CRISPR-Cas ( 25 , 43 ). Full lists of enriched genes are provided in Supplementary Table S5 and S6 .…”

Section: Resultsmentioning

confidence: 99%

“…In Serratia , the accessory nuclease is NucC (Figure 1A ), which responds to cA 3 and cleaves dsDNA ( 50–52 ). The Serratia type III system provides protection against plasmids and phages ( 22 , 25 , 43 , 50 , 51 ). To test the effect of the alaA-pigU intergenic mutation on type III-A activity, we used a plasmid conjugation-based CRISPR-Cas interference assay using an untargeted control plasmid, or a plasmid with sequences expressed from an arabinose inducible promoter to generate RNA targets of spacer 1 of CRISPR3 (Figure 3A ) ( 22 ).…”

Section: Resultsmentioning

confidence: 99%

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CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

Smith,

Hampton,

Yevstigneyeva

et al. 2023

Nucleic Acids Research

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Bacteria protect themselves from infection by bacteriophages (phages) using different defence systems, such as CRISPR-Cas. Although CRISPR-Cas provides phage resistance, fitness costs are incurred, such as through autoimmunity. CRISPR-Cas regulation can optimise defence and minimise these costs. We recently developed a genome-wide functional genomics approach (SorTn-seq) for high-throughput discovery of regulators of bacterial gene expression. Here, we applied SorTn-seq to identify loci influencing expression of the two type III-A Serratia CRISPR arrays. Multiple genes affected CRISPR expression, including those involved in outer membrane and lipopolysaccharide synthesis. By comparing loci affecting type III CRISPR arrays and cas operon expression, we identified PigU (LrhA) as a repressor that co-ordinately controls both arrays and cas genes. By repressing type III-A CRISPR-Cas expression, PigU shuts off CRISPR-Cas interference against plasmids and phages. PigU also represses interference and CRISPR adaptation by the type I-F system, which is also present in Serratia. RNA sequencing demonstrated that PigU is a global regulator that controls secondary metabolite production and motility, in addition to CRISPR-Cas immunity. Increased PigU also resulted in elevated expression of three Serratia prophages, indicating their likely induction upon sensing PigU-induced cellular changes. In summary, PigU is a major regulator of CRISPR-Cas immunity in Serratia.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

Smith,

Hampton,

Yevstigneyeva

et al. 2023

Nucleic Acids Research

Self Cite

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“…Since certain proteins encoded by bacteria can inhibit the expression and interference of CRISPR-Cas systems, plasmids or phages are likely to obtain these protein homologues in response to CRISPR-Cas immunity. Indeed, it was recently reported that homologues of the CRISPR- cas suppressors AmrZ and RsmA are widely present on plasmids or phages, 62,63 implying that these proteins potentially function to overcome CRISPR-Cas immunity.…”

Section: Discussionmentioning

confidence: 99%

Quorum sensing inhibits Type III-A CRISPR-Cas system activity through repressing positive regulators SarA and ArcR inStaphylococcus aureus

Tang

et al. 2023

Preprint

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CRISPR-Cas is an adaptive immune system that protects prokaryotes from the invasion of foreign genetic elements. The components and immunity mechanisms of CRISPR-Cas have been extensively studied, but the regulation of this system in Staphylococci remains unclear. Here, we show that in the S. aureus Type III-A CRISPR-Cas system, the Pcas of 300 bp located in cas1 displays as a critical regulatory node that initiates the transcription of cas gene clusters. We discovered two transcriptional regulators, SarA and CRP-like ArcR, promote the expression and activity of the CRISPR-Cas system by directly binding to the novel promoter Pcas. Furthermore, we demonstrated that the cell-cell communication, known as quorum sensing (QS), inhibits the activity of CRISPR-Cas system by repressing the positive regulators SarA and ArcR. Bioinformatic analyses suggest that Pcas is conserved in many Type II and III CRISPR-Cas systems in Firmicutes. Our data reveal a new regulatory mechanism for QS-mediated repression of the Type III-A CRISPR-Cas system, which may allow S. aureus to acquire foreign genetic elements encoding antibiotic resistance or virulence factors specifically at high cell density.

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“…Furthermore, the translation efficiency of cas mRNAs, mainly determined by codon usage biases, has also been related to CRISPR-Cas effective functioning (Quax et al 2013b ), and a CRISPR repeat-binding protein was shown to facilitate transcription of a CRISPR locus (Deng et al 2012 ). CRISPR-Cas interference can also be stimulated by Cas protein stabilisation (Yosef et al 2011 ), and suppression of both interference and adaptation by cas mRNA-binding regulatory proteins has recently been reported for several CRISPR-Cas types (Campa et al 2021 ).…”

Section: Crispr-cas Controlmentioning

confidence: 99%

Digging into the lesser-known aspects of CRISPR biology

2021

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A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.

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

Cited by 11 publications

References 91 publications

CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

Quorum sensing inhibits Type III-A CRISPR-Cas system activity through repressing positive regulators SarA and ArcR inStaphylococcus aureus

Digging into the lesser-known aspects of CRISPR biology

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