Type I-F CRISPR–Cas provides protection from DNA, but not RNA phages

Buyukyoruk, Murat; Wiedenheft, Blake

doi:10.1038/s41421-019-0123-9

Cited by 7 publications

(8 citation statements)

References 9 publications

(15 reference statements)

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“…However, the exact mechanism implicating crRNA targeting for regulatory purposes remains the subject of debate. For example, in contrast to the previously reported regulatory potential for type I-F CRISPR-Cas in Pseudomonas aeruginosa (98), more recent studies did not find evidence of RNA targeting (103,104). The possible implication of Hfq RNA chaperone in crRNA interactions with potential mRNA targets implies that crRNAs could be additional components in the regulatory RNA networks and suggests an alternative mechanism for crRNA regulatory actions independent from the Cas machinery.…”

Section: Discussioncontrasting

confidence: 76%

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogenClostridioides difficile

Boudry

Piattelli

Drouineau

et al. 2020

Preprint

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Noncoding RNAs (ncRNA) have emerged as important components of regulatory networks governing bacterial physiology and virulence. Previous deep-sequencing analysis identified a large diversity of ncRNAs in the human enteropathogen Clostridioides (Clostridium) difficile. Some of them are trans-encoded RNAs that could require the RNA chaperone protein Hfq for their action. Recent analysis suggested a pleiotropic role of Hfq in C. difficile with the most pronounced effect on sporulation, a key process during the infectious cycle of this pathogen. However, a global view of RNAs interacting with C. difficile Hfq is missing. In the present study, we performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) to identify Hfq-associated RNAs in C. difficile. Our work revealed a large set of Hfq-interacting mRNAs and ncRNAs, including mRNA leaders and coding regions, known and potential new ncRNAs. In addition to trans-encoded RNAs, new categories of Hfq ligands were found including cis-antisense RNAs, riboswitches and CRISPR RNAs. ncRNA-mRNA and ncRNA-ncRNA pairings were postulated through computational predictions. Investigation of one of the Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation in C. difficile. Altogether, these data provide essential molecular basis for further studies of post-transcriptional regulatory network in this enteropathogen.

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Section: Discussioncontrasting

confidence: 76%

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogenClostridioides difficile

Boudry

Piattelli

Drouineau

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…However, the exact mechanism implicating crRNA targeting for regulatory purposes remains the subject of debate. For example, in contrast to the previously reported regulatory potential for type I-F CRISPR-Cas in Pseudomonas aeruginosa [ 106 ], more recent studies did not find evidence of RNA targeting [ 111 , 112 ]. The possible implication of the RNA chaperone Hfq in crRNA interactions with potential mRNA targets implies that crRNAs could be additional components in the regulatory RNA networks and suggests an alternative mechanism for crRNA regulatory actions independent from the Cas machinery.…”

Section: Discussionmentioning

confidence: 88%

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile

et al. 2021

View full text Add to dashboard Cite

Noncoding RNAs (ncRNA) have emerged as important components of regulatory networks governing bacterial physiology and virulence. Previous deep-sequencing analysis identified a large diversity of ncRNAs in the human enteropathogen Clostridioides (Clostridium) difficile . Some of them are trans -encoded RNAs that could require the RNA chaperone protein Hfq for their action. Recent analysis suggested a pleiotropic role of Hfq in C. difficile with the most pronounced effect on sporulation, a key process during the infectious cycle of this pathogen. However, a global view of RNAs interacting with C. difficile Hfq is missing. In the present study, we performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) to identify Hfq-associated RNAs in C. difficile . Our work revealed a large set of Hfq-interacting mRNAs and ncRNAs, including mRNA leaders and coding regions, known and potential new ncRNAs. In addition to trans -encoded RNAs, new categories of Hfq ligands were found including cis -antisense RNAs, riboswitches and CRISPR RNAs. ncRNA-mRNA and ncRNA-ncRNA pairings were postulated through computational predictions. Investigation of one of the Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation in C. difficile . Altogether, these data provide essential molecular basis for further studies of post-transcriptional regulatory network in this enteropathogen.

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“…7b ). To investigate the biological relevance of the non-specific DNA binding activity, we used a phage plaquing assay by transforming the type I-F CRISPR-Cas system from P. aeruginosa into Escherichia coli to target lambda (λ) phage 28 . By co-transforming AcrIF24 or its mutants in E. coli cells, their Acr activity were tested.…”

Section: Resultsmentioning

confidence: 99%

Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24

et al. 2022

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CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding.

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Type I-F CRISPR–Cas provides protection from DNA, but not RNA phages

Cited by 7 publications

References 9 publications

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogenClostridioides difficile

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogenClostridioides difficile

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile

Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24

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