How do base-pairing small RNAs evolve?

Updegrove, Taylor B.; Shabalina, Svetlana A.; Storz, Gisela

doi:10.1093/femsre/fuv014

Cited by 82 publications

(78 citation statements)

References 112 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This role in the iron-sparing response makes FsrA/S512 functionally related to the E. coli sRNA RyhB. As such, this is an example of apparent functional conservation of an sRNA without sequence conservation (101). Three small basic proteins (FbpA, FbpB, and FbpC) have been shown to be involved in different aspects of this regulation, and there are experimental indications that at least FbpB may act as an RNA chaperone (100).…”

Section: Independently Expressed Small Rnas and Rna Antitoxinsmentioning

confidence: 99%

“…Because of this large variability in RNA regulators between species, it may in some contexts be more relevant to speak about the conservation of regulatory RNA functions than of sequence conservation. A good example of such functional conservation is provided by the E. coli RyhB and B. subtilis FsrA/S512 RNA segments in the iron-sparing response (101).…”

Section: Evolutionary Aspects Of Regulatory Rna Regulationmentioning

confidence: 99%

“…One intriguing evolutionary question is whether a regulatory function of a regulatory RNA has to remain conserved when a regulatory RNA sequence is conserved. Indeed, it seems that this is not always the case (101). However, it would still be very interesting to test whether, for instance, RsaE in S. aureus has retained a shared regulatory function with RsaE/S415/RoxS in B. subtilis.…”

Section: Evolutionary Aspects Of Regulatory Rna Regulationmentioning

confidence: 99%

“…This is a question that needs to be addressed in future studies. For a more general discussion on evolutionary aspects of regulatory RNA regulation, please see the recent review by Updegrove et al (101).…”

Section: Evolutionary Aspects Of Regulatory Rna Regulationmentioning

confidence: 99%

See 3 more Smart Citations

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

View full text Add to dashboard Cite

SUMMARY Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans -acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella . Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis . A recent study identified 1,583 putative regulatory RNAs in B. subtilis , whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis , and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis . Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis .

show abstract

Section: Independently Expressed Small Rnas and Rna Antitoxinsmentioning

confidence: 99%

Section: Evolutionary Aspects Of Regulatory Rna Regulationmentioning

confidence: 99%

Section: Evolutionary Aspects Of Regulatory Rna Regulationmentioning

confidence: 99%

Section: Evolutionary Aspects Of Regulatory Rna Regulationmentioning

confidence: 99%

See 2 more Smart Citations

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

View full text Add to dashboard Cite

show abstract

“…These noncoding RNAs recognize complementary sequences in their target mRNAs, and induce the activation or repression of translation (Waters and Storz 2009;Updegrove et al 2015). This regulation is important for the adaptation of enterobacteria to changing environmental conditions (De Lay and Gottesman 2012), maintenance of cellular homeostasis (Papenfort et al 2013), and virulence of pathogenic species Tree et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

Wróblewska

Olejniczak

2016

RNA

View full text Add to dashboard Cite

The bacterial protein Hfq participates in the regulation of translation by small noncoding RNAs (sRNAs). Several mechanisms have been proposed to explain the role of Hfq in the regulation by sRNAs binding to the 5 ′ -untranslated mRNA regions. However, it remains unknown how Hfq affects those sRNAs that target the coding sequence. Here, the contribution of Hfq to the annealing of three sRNAs, RybB, SdsR, and MicC, to the coding sequence of Salmonella ompD mRNA was investigated. Hfq bound to ompD mRNA with tight, subnanomolar affinity. Moreover, Hfq strongly accelerated the rates of annealing of RybB and MicC sRNAs to this mRNA, and it also had a small effect on the annealing of SdsR. The experiments using truncated RNAs revealed that the contributions of Hfq to the annealing of each sRNA were individually adjusted depending on the structures of interacting RNAs. In agreement with that, the mRNA structure probing revealed different structural contexts of each sRNA binding site. Additionally, the annealing of RybB and MicC sRNAs induced specific conformational changes in ompD mRNA consistent with local unfolding of mRNA secondary structure. Finally, the mutation analysis showed that the long AU-rich sequence in the 5 ′ -untranslated mRNA region served as an Hfq binding site essential for the annealing of sRNAs to the coding sequence. Overall, the data showed that the functional specificity of Hfq in the annealing of each sRNA to the ompD mRNA coding sequence was determined by the sequence and structure of the interacting RNAs.

show abstract

Hfq chaperone brings speed dating to bacterial sRNA

2018

View full text Add to dashboard Cite

Hfq is a ubiquitous, Sm-like RNA binding protein found in most bacteria and some archaea. Hfq binds small regulatory RNAs (sRNAs), facilitates base pairing between sRNAs and their mRNA targets, and directly binds and regulates translation of certain mRNAs. Because sRNAs regulate many stress response pathways in bacteria, Hfq is essential for adaptation to different environments and growth conditions. The chaperone activities of Hfq arise from multipronged RNA binding by three different surfaces of the Hfq hexamer. The manner in which the structured Sm core of Hfq binds RNA has been well studied, but recent work shows that the intrinsically disordered C-terminal domain of Hfq modulates sRNA binding, creating a kinetic hierarchy of RNA competition for Hfq and ensuring the release of double-stranded sRNA-mRNA complexes. A combination of structural, biophysical, and genetic experiments reveals how Hfq recognizes its RNA substrates and plays matchmaker for sRNAs and mRNAs in the cell. The interplay between structured and disordered domains of Hfq optimizes sRNA-mediated post-transcriptional regulation, and is a common theme in RNA chaperones. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry.

show abstract

How do base-pairing small RNAs evolve?

Cited by 82 publications

References 112 publications

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

Hfq chaperone brings speed dating to bacterial sRNA

Contact Info

Product

Resources

About