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The Rsm (Csr) post-transcriptional regulatory system directly controls CRISPR-Cas immunity

ABSTRACT: The Rsm (Csr) post-transcriptional regulatory system directly controls CRISPR-Cas immunity

PROVIDER: PRJNA679240 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13080662.fastq.gz	Fastqsanger.gz
	SRR13080663.fastq.gz	Fastqsanger.gz
	SRR13080664.fastq.gz	Fastqsanger.gz
	SRR13080665.fastq.gz	Fastqsanger.gz
	SRR15498200.fastq.gz	Fastqsanger.gz

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The Rsm (Csr) post-transcriptional regulatory system directly controls CRISPR-Cas immunity

Project description:RIP-seq analysis to identify RsmA bound RNAs using co-immunoprecipitation and sequencing in Serratia sp. ATCC 39006. We report the binding sites of RsmA (CsrA homologue) in Serratia sp. ATCC39006

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CSR-1A post-translational modification

Project description:CSR-1 is an essential Argonaute protein that binds to a subclass of 22G-RNAs targeting most germline-expressed genes. Here we show that the two isoforms of CSR-1 have distinct expression patterns; CSR-1B is ubiquitously expressed throughout the germline and during all stages of development while CSR-1A expression is restricted to germ cells undergoing spermatogenesis. Furthermore, CSR-1A associates preferentially with 22G-RNAs mapping to spermatogenesis-specific genes whereas CSR-1B-bound small RNAs map predominantly to oogenesis-specific genes. Interestingly, the exon unique to CSR-1A contains multiple dimethylarginine modifications, which are necessary for the preferential binding of CSR-1A to spermatogenesis-specific 22G-RNAs. Thus, we have discovered a regulatory mechanism for C. elegans Argonaute proteins that allows for specificity of small RNA binding between similar Argonaute proteins with overlapping temporal and spatial localization.

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

Project description:CRISPR-Cas systems provide bacteria with adaptive immunity against phages and plasmids; however, pathways regulating their activity are not well defined. We recently developed a high-throughput genome-wide method (SorTn-seq) and used this to uncover CRISPR-Cas regulators. Here, we demonstrate that the widespread Rsm/Csr pathway regulates the expression of multiple CRISPR-Cas systems in Serratia (type I-E, I-F and III-A). The main pathway component, RsmA (CsrA), is an RNA-binding post-transcriptional regulator of carbon utilisation, virulence and motility. RsmA binds cas mRNAs and suppresses type I and III CRISPR-Cas interference in addition to adaptation by type I systems. Coregulation of CRISPR-Cas and flagella by the Rsm pathway allows modulation of adaptive immunity when changes in receptor availability would alter susceptibility to flagella-tropic phages. Furthermore, we show that Rsm controls CRISPR-Cas in other genera, suggesting conservation of this regulatory strategy. Finally, we identify genes encoding RsmA homologues in phages, which have the potential to manipulate the physiology of host bacteria and might provide an anti-CRISPR activity.

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Genome-wide analysis of targets for post-transcriptional regulation by Rsm proteins in Pseudomonas putida KT2440

Project description:Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences that are bound in vivo by Rsm proteins, in order to identify potential regulatory targets for each of them. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to identify 709 targets, 75 of them common to the three proteins. Relevant targets include genes encoding proteins involved in metabolism, transport and secretion, stress responses, signal transduction and regulation, and the turnover of the second messenger c-di-GMP. The role of Rsm proteins in the utilization of basic amino acids and bacterial fitness in the plant rhizosphere are also exposed.

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Project description:Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5' untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.

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