Dataset Information

Involvement of RNase J in CRISPR RNA maturation and degradosome formation in cyanobacteria

ABSTRACT: Many bacteria and archaea use CRISPR-Cas systems, which provide RNA-based, adaptive, and inheritable immune defenses against invading viruses and other foreign genetic elements. The proper processing of CRISPR guide RNAs (crRNAs) is a crucial step in the maturation of the defense complexes and is frequently performed by specialized ribonucleases encoded by cas genes. However, some systems employ enzymes associated with degradosome or housekeeping functions, such as RNase III or the endoribonuclease RNase E. Here, the endo- and 5´-exoribonuclease RNase J was identified as additional enzyme involved in crRNA maturation, acting jointly with RNase E in the crRNA maturation of a type III-Bv CRISPR-Cas system, and possibly together with a further RNase. Co-IP experiments revealed a small set of proteins that were co-enriched with RNase J, among them PNPase. Despite a measured, strong 3’ exonucleolytic activity of the recombinant enzyme, PNPase was not confirmed to contribute to crRNA maturation. However, the co-IP results indicate that PNPase is a component of the cyanobacterial degradosome that can recruit either RNase E or RNase J, together with additional enriched proteins.

INSTRUMENT(S):

ORGANISM(S): Synechocystis Sp. Pcc 6803

TISSUE(S): Photosynthetic Cell

SUBMITTER: Friedel Drepper

LAB HEAD: Pitter Huesgen

PROVIDER: PXD060866 | Pride | 2025-10-06

REPOSITORIES: Pride

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Publications

Involvement of RNase J in CRISPR RNA maturation in the cyanobacterium <i>Synechocystis</i> sp. PCC 6803.

Bilger Raphael R Drepper Friedel F Knapp Bettina B Berndt Tanja T Landerer Helena H Putzer Harald H Huesgen Pitter F PF Hess Wolfgang R WR

microLife 20250901

Many bacteria and archaea use CRISPR-Cas systems, which provide RNA-based, adaptive, and inheritable immune defenses against invading viruses and other foreign genetic elements. The proper processing of CRISPR guide RNAs (crRNAs) is a crucial step in the maturation of the defense complexes and is frequently performed by specialized ribonucleases encoded by <i>cas</i> genes. However, some systems employ enzymes associated with degradosome or housekeeping functions, such as RNase III or the endori ...[more]

PMID: 41019300

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Project description:The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. RNA degradation can be initiated by an endonucleolytic cleavage and then by further promoted by exoribonucleolytic decay. In this study, we analyzed the importance of the Rhodobacter sphaeroides PNPase regarding the physiology and sRNA homeostasis. Moreover, we developed a pipeline to globally identify differential RNA 3’-ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants. The Rhodobacter sphaeroides PNPase mutant exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. Furthermore, the transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, the PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. The RNA 3’-end analysis reveals that 82% of all differential 3’-ends are enriched in the pnp mutant and are mostly located in coding sequences or untranslated regions (UTR). A fair percentage of these ends was also identified as differential RNA 3’-end in RNase E and RNase III mutant strains. The PNPase has a major influence in RNA processing and maturation and thus modulates the transcriptome. This includes regulatory sRNAs, stressing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The 3’-end analysis indicates a sequential processing of UTR- and non-UTR derived sRNAs by several ribonucleases. Moreover, we provide a modular pipeline which greatly facilitates the identification of RNA 5’/3’-ends. It is publicly available on GitHub and is distributed under ICS licence.

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	CS014b_experimentalDesignTemplate_pride.txt	Txt
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Dataset Information

Involvement of RNase J in CRISPR RNA maturation and degradosome formation in cyanobacteria

Dataset's files

Publications

Involvement of RNase J in CRISPR RNA maturation in the cyanobacterium <i>Synechocystis</i> sp. PCC 6803.

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Dataset Information

Involvement of RNase J in CRISPR RNA maturation and degradosome formation in cyanobacteria

Dataset's files

Publications

Involvement of RNase J in CRISPR RNA maturation in the cyanobacterium &lt;i&gt;Synechocystis&lt;/i&gt; sp. PCC 6803.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Involvement of RNase J in CRISPR RNA maturation in the cyanobacterium <i>Synechocystis</i> sp. PCC 6803.