Noncoding RNA

Desgranges, Emma; Marzi, Stefano; Moreau, Karen; Romby, Pascale; Caldelari, Isabelle

doi:10.1128/microbiolspec.gpp3-0038-2018

Cited by 28 publications

(26 citation statements)

References 123 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These model bacteria express at least three global RBPs—CsrA, Hfq, and ProQ—that form complexes with hundreds of different sRNAs to facilitate extensive post‐transcriptional control of mRNAs (Olejniczak & Storz, ; Holmqvist & Vogel, ; Kavita et al , ; Babitzke et al , ). The situation is very different with Gram‐positive bacteria: Despite much evidence that sRNAs also play important roles in these organisms (Brantl & Brückner, ; Wagner & Romby, ; Quereda & Cossart, ; Wassarman, ; Desgranges et al , ), many aspects of their sRNA biology seem to differ from Gram‐negative species. For example, CsrA circuits work without antagonistic sRNAs, Hfq seems to play a minor role, ProQ is generally absent, and a major sRNA‐related RBP yet awaits to be discovered.…”

Section: Introductionmentioning

confidence: 99%

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

et al. 2020

View full text Add to dashboard Cite

RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNAprotein complexes in Gram-positive species remains scarce. Here, we used the Grad-seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of~88% of the transcripts and~62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1/YhaM with sRNAs that control bacterial competence for DNA uptake. Unexpectedly, the nucleolytic activity of Cbf1 stabilizes these sRNAs, thereby promoting their function as repressors of competence. Overall, these results provide the first RNA/protein complexome resource of a Gram-positive species and illustrate how this can be utilized to identify new molecular factors with functions in RNA-based regulation of virulence-relevant pathways.

show abstract

Section: Introductionmentioning

confidence: 99%

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

et al. 2020

View full text Add to dashboard Cite

show abstract

“…additional levels of control to regulatory networks, contributing to the flexibility and dynamics of target gene expression, often by sensing environmental changes (2,3). The cis-acting riboswitches and antisense sRNAs are encoded on the cDNA strand of protein-coding genes, whereas most trans-acting sRNAs are located within conserved intergenic regions (4,5). Most of the trans-acting sRNAs in S. aureus regulate their target genes by binding to the target mRNAs and indirectly affecting expression of gene products.…”

mentioning

confidence: 99%

“…Most of the trans-acting sRNAs in S. aureus regulate their target genes by binding to the target mRNAs and indirectly affecting expression of gene products. Small RNAs can target both the 5= untranslated regions (5=UTR) and 3=UTR of mRNAs by competing with the ribosome binding site (RBS) and affecting mRNA stability, respectively (5).…”

mentioning

confidence: 99%

Comparative Transcriptomic and Functional Assessments of Linezolid-Responsive Small RNA Genes in Staphylococcus aureus

et al. 2020

View full text Add to dashboard Cite

Staphylococcus aureus contains a repertoire of at least 50 and possibly 500 small RNAs (sRNAs). The functions of most sRNAs are not understood, although some are known to respond to environmental changes, including the presence of antibiotics. Here, in an effort to better understand the roles of sRNAs in the context of antibiotic exposure, we took a clinical methicillin-resistant S. aureus (MRSA) isolate and separately deleted eight sRNAs that were significantly upregulated in response to the last-line antibiotic linezolid as revealed by transcriptome sequencing (RNA-seq) comparisons. We also deleted an additional 10 sRNAs that were either highly expressed or previously found to respond to antibiotic exposure. There were no significant changes for any of the 18 mutants in a variety of phenotypic screens, including MIC screens, growth competition assays in the presence of linezolid, biofilm formation, and resistance to whole-blood killing. These data suggest sRNA functional redundancy, because despite their high expression levels upon antibiotic exposure, individual sRNA genes do not affect readily observable bacterial phenotypes. The sRNA transcriptional changes we measured during antibiotic exposure might also reflect sRNA “indifference,” that is, a general stress response not specifically related to sRNA function. These data underscore the need for sensitive assays and new approaches to try and decipher the functions of sRNA genes in S. aureus. IMPORTANCE Bacterial small RNAs (sRNAs) are RNA molecules that can have important regulatory roles across gene expression networks. There is a growing understanding of the scope and potential breadth of impact of sRNAs on global gene expression patterns in Staphylococcus aureus, a major human pathogen. Here, transcriptome comparisons were used to examine the roles of sRNA genes with a potential role in the response of S. aureus to antibiotic exposure. Although no measurable impact on key bacterial phenotypes was observed after deleting each of 18 sRNAs identified by these comparisons, this research is significant because it underscores the subtle modes of action of these sometimes abundant molecules within the bacterium.

show abstract

“…Bacterial ncRNAs are at the heart of regulatory pathways that allow bacteria to acclimate to changes in the environment, to adjust their metabolism, to regulate the expression of virulence genes and to control many other functions [51][52][53]. Here, we present a workflow for the identification of ncRNAs that appears to be particularly applicable to bacteria of high ecological relevance that are not amenable [58].…”

Section: Conclusion and Possible Implicationsmentioning

confidence: 99%

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

et al. 2020

View full text Add to dashboard Cite

Small regulatory RNAs and antisense RNAs play important roles in the regulation of gene expression in bacteria but are underexplored, especially in natural populations. While environmentally relevant microbes often are not amenable to genetic manipulation or cannot be cultivated in the laboratory, extensive metagenomic and metatranscriptomic datasets for these organisms might be available. Hence, dedicated workflows for specific analyses are needed to fully benefit from this information. Here, we identified abundant sRNAs from oceanic environmental populations of the ecologically important primary producer Prochlorococcus starting from a metatranscriptomic differential RNA-Seq (mdRNA-Seq) dataset. We tracked their homologs in laboratory isolates, and we provide a framework for their further detailed characterization. Several of the experimentally validated sRNAs responded to ecologically relevant changes in cultivation conditions. The expression of the here newly discovered sRNA Yfr28 was highly stimulated in low-nitrogen conditions. Its predicted top targets include mRNAs encoding cell division proteins, a sigma factor, and several enzymes and transporters, suggesting a pivotal role of Yfr28 in the coordination of primary metabolism and cell division. A cis-encoded antisense RNA was identified as a possible positive regulator of atpF encoding subunit b' of the ATP synthase complex. The presented workflow will also be useful for other environmentally relevant microorganisms for which experimental validation abilities are frequently limiting although there is wealth of sequence information available.

show abstract

Noncoding RNA

Cited by 28 publications

References 123 publications

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

Comparative Transcriptomic and Functional Assessments of Linezolid-Responsive Small RNA Genes in Staphylococcus aureus

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

Contact Info

Product

Resources

About