RNase J is required for processing of a small number of RNAs in<i>Rhodobacter sphaeroides</i>

Weber, Lennart; Remes, Bernhard; Förstner, Konrad U.; Klug, Gabriele

doi:10.4161/rna.29440

Cited by 12 publications

(8 citation statements)

References 62 publications

(97 reference statements)

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“…In addition to RNase E, endoribonuclease G, which has strong homology to the N-terminal part of RNase E, and the double-strand–specific RNase III participate in endonucleolytic cleavage of RNA in Gram-negative bacteria ( Evguenieva-Hackenberg & Klug, 2009 ). R. sphaeroides also harbors an RNase J enzyme ( Rische-Grahl et al, 2014 ), which was shown to exhibit endonucleolytic activity in B. subtilis ( Even et al, 2005 ).…”

Section: Resultsmentioning

confidence: 99%

RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth

et al. 2018

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Section: Resultsmentioning

confidence: 99%

RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth

et al. 2018

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“…The indirect effects of CrhR truncation on RNA turnover could be associated with the observed up-regulation of RNase J (slr0551). Although not studied in cyanobacteria, RNase J is known to perform functions in all aspects of RNA metabolism in a range of organisms [53][54][55]. Moreover, yeast two-hybrid screens indicated that the DEAD-box RNA helicase HP4 interacted with the RNase J homolog in C. reinhardtii [53].…”

Section: Altered Mrna Expression Correlates With Altered Cellular Mormentioning

confidence: 99%

Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803

et al. 2019

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DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift. Despite its proposed effect on RNA metabolism and its known relevance in cold-stress adaptation, the reported impact of a CrhR knockout on the cold adaption of the transcriptome only identified eight affected genes. Here, we utilized a custom designed microarray to assess the impact of the absence of CrhR RNA helicase activity on the transcriptome, independent of cold stress. CrhR truncation impacts an RNA subset comprising~10% of the ncRNA and alsõ 10% of the mRNA transcripts. While equal numbers of mRNAs showed increased as well as decreased abundance, more than 90% of the ncRNAs showed enhanced expression in the absence of CrhR, indicative of a negative effect on ncRNA transcription or stability. We further tested the effect of CrhR on the stability of strongly responding RNAs that identify examples of post-transcriptional and transcriptional regulation. The data suggest that CrhR impacts multiple aspects of RNA metabolism in Synechocystis.

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“…To get more insight into the interplay of RNase E, RNase III and PNPase we analyzed the correlation of 3′ ends from the wild type, the pnp mutant, an RNase III mutant and a strain with reduced RNase E activity. In the RNase III mutant strain, the rnc gene was removed by homologous recombination [24]. Since RNase E is an essential enzyme in Rhodobacter sphaeroides, the rne mutant strain was achieved by replacing the native rne by the gene of the thermosensitive RNase E from E. coli [54].…”

Section: Intersection Analysismentioning

confidence: 99%

“…These are the RNase R, RNase D and RNase PH which catalyze mainly tRNA and rRNA processing reactions and all act in 3′-to-5′ direction [ 21 – 23 ]. In addition, RNase J1 is responsible for the maturation of the 23S rRNA and very few other transcripts [ 24 , 25 ]. In contrast to the other RNases, it processes RNA molecules in 5′-to-3′ end direction [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E

2021

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Background The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the Escherichia coli degradosome, PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay by acting as a 3′-to-5′ exoribonuclease. Furthermore, PNPase can catalyze the reverse reaction by elongating RNA molecules in 5′-to-3′ end direction which has a destabilizing effect on the prolonged RNA molecule. RNA degradation is often initiated by an endonucleolytic cleavage, followed by exoribonucleolytic decay from the new 3′ end. Results The PNPase mutant from the facultative phototrophic Rhodobacter sphaeroides exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. The transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. Moreover, we globally identified and compared differential RNA 3′ ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants for the first time in a Gram-negative organism. The genome wide RNA 3′ end analysis revealed that 885 3′ ends are degraded by PNPase. A fair percentage of these RNA 3′ ends was also identified at the same genomic position in RNase E or RNase III mutant strains. Conclusion The PNPase has a major influence on RNA processing and maturation and thus modulates the transcriptome of R. sphaeroides. This includes sRNAs, emphasizing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The global 3′ end analysis indicates a sequential RNA processing: 5.9% of all RNase E-dependent and 9.7% of all RNase III-dependent RNA 3′ ends are subsequently degraded by PNPase. 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 license.

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RNase J is required for processing of a small number of RNAs inRhodobacter sphaeroides

Cited by 12 publications

References 62 publications

RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth

RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth

Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803

Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E

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