Antisense RNA asPcrL regulates expression of photosynthesis genes in <i>Rhodobacter sphaeroides</i> by promoting RNase III-dependent turn-over of <i>puf</i> mRNA

Reuscher, Carina M.; Klug, Gabriele

doi:10.1080/15476286.2020.1857520

Cited by 13 publications

(18 citation statements)

References 80 publications

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“…GadY antisense RNA has been shown to interact with Hfq in E. coli but the specific role of Hfq in this RNA-mediated regulation remains unclear [ 92 ]. In Rhodobacter sphaeroides , the Hfq protein binds to and destabilizes both an antisense RNA asPcrL and its target puf -mRNA [ 93 ].…”

Section: Discussionmentioning

confidence: 99%

“…For example, in E. coli , Hfq was shown to promote the RNase E-mediated degradation of Hfq-bound sRNAs [ 94 ]. Furthermore, RNase III being a double-strand specific RNase, the recruitment of Hfq could interfere with RNase III-mediated degradation of RNAs [ 93 , 95 ]. In some cases, the action of antisense RNAs on trans -encoded targets could potentially require Hfq for efficient base-pairing [ 96 ].…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…Furthermore, FnrL is an oxygen-responsive regulator of some photosynthesis genes [ 21 , 22 , 23 ]. In addition to transcription factors, sRNAs influence the expression of photosynthesis genes by having modulating effects as part of regulatory feed-forward loops [ 24 , 25 , 26 , 27 ]. The sRNAs, PcrX and asPcrL, interact with parts of the polycistronic puf mRNA that encodes the pigment-binding proteins of the reaction center (RC) and light harvesting (LH) complexes and the assembly factor PufX.…”

Section: Introductionmentioning

confidence: 99%

“…The sRNAs, PcrX and asPcrL, interact with parts of the polycistronic puf mRNA that encodes the pigment-binding proteins of the reaction center (RC) and light harvesting (LH) complexes and the assembly factor PufX. They affect the stability of puf mRNA segments and, consequently, the stoichiometry of RC/LHI and LHII complexes [ 26 , 27 ]. LHII proteins are encoded by the puc mRNAs that are not affected by PrcX or asPcrL.…”

Section: Introductionmentioning

confidence: 99%

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A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides

Eisenhardt

Remes

Grützner

et al. 2021

IJMS

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Adaptation of bacteria to a changing environment is often accompanied by remodeling of the transcriptome. In the facultative phototroph Rhodobacter sphaeroides the alternative sigma factors RpoE, RpoHI and RpoHII play an important role in a variety of stress responses, including heat, oxidative stress and nutrient limitation. Photooxidative stress caused by the simultaneous presence of chlorophylls, light and oxygen is a special challenge for phototrophic organisms. Like alternative sigma factors, several non-coding sRNAs have important roles in the defense against photooxidative stress. RNAseq-based transcriptome data pointed to an influence of the stationary phase-induced StsR sRNA on levels of mRNAs and sRNAs with a role in the photooxidative stress response. Furthermore, StsR also affects expression of photosynthesis genes and of genes for regulators of photosynthesis genes. In vivo and in vitro interaction studies revealed that StsR, that is under control of the RpoHI and RpoHII sigma factors, targets rpoE mRNA and affects its abundance by altering its stability. RpoE regulates expression of the rpoHII gene and, consequently, expression of stsR. These data provide new insights into a complex regulatory network of protein regulators and sRNAs involved in defense against photooxidative stress and the regulation of photosynthesis genes.

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Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products

Evguenieva‐Hackenberg

2021

WIREs RNA

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Gene expression strategies ensuring bacterial survival and competitiveness rely on cis‐ and trans‐acting RNA‐regulators (riboregulators). Among the cis‐acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans‐acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome‐dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans‐acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA‐containing, antibiotic‐dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA‐based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule‐RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs

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Antisense RNA asPcrL regulates expression of photosynthesis genes in Rhodobacter sphaeroides by promoting RNase III-dependent turn-over of puf mRNA

Cited by 13 publications

References 80 publications

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

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

A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides

Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products

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