Isolation of small RNA-binding proteins from<i>E. coli</i>: Evidence for frequent interaction of RNAs with RNA polymerase

Windbichler, Nikolai; Pelchrzim, Frederike von; Mayer, Oliver; Csaszar, Edina; Schroeder, Renée

doi:10.4161/rna.5.1.5694

Cited by 47 publications

(47 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For instance, sRNAs might exert activating functions during the transcription process, such as controlling a transcriptional riboswitch, or interacting with RNA polymerase. The recent observation that RNA polymerase binds several sRNAs and reacts with them, mapping the interaction site of both molecules to the active center cleft of the enzyme (Windbichler et al 2008), would be in support of the latter hypothesis.…”

Section: Future Perspectivesupporting

confidence: 57%

Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence

Brantl

2011

Regulatory RNAs

View full text Add to dashboard Cite

Small RNAs (sRNAs) gained worldwide attention in the late 2002, when the journal Science published a special issue entitled "Small RNAs -Breakthrough of the Year." However, small antisense RNAs in bacteria involved in the regulation of plasmid replication and maintenance, phage life cycles, and transposition had been investigated in great depth for more than 20 years. Whereas these sRNAs were discovered only fortuitously, systematic computer-based searches have only been used since 2001. Currently, it is estimated that a bacterial genome encodes $200-300 sRNAs with diverse functions. To date (2011), about 140 sRNAs are known in Escherichia coli and Salmonella. However, only about 25 of these have been assigned a biological function, indicating that defining their functions continues to be a challenging issue. Systematic searches have also been performed for a few Gram-positive bacterial species. sRNAs in bacteria can be divided into two major groups: The first group regulates gene expression by a base-pairing mechanism with target mRNA, whereas the second group acts by binding of small proteins. This chapter covers mechanisms of action, biological functions, integration in regulatory circuits, and evolutionary aspects of base-pairing and protein-binding sRNAs.

show abstract

Section: Future Perspectivesupporting

confidence: 57%

Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence

Brantl

2011

Regulatory RNAs

View full text Add to dashboard Cite

show abstract

“…Whether these proteins act as RNA chaperones or as regulators remains to be determined. The in vitro binding of E. coli RNA polymerase, ribosomal protein S1, and Hfq to various regulatory sRNAs, that target either mRNA or protein, has been reported [106]. E. coli ribosomal protein S1 is essential for translation initiation [107] and has a positive action on transcription [108].…”

Section: Proteins Associated With Asrnasmentioning

confidence: 97%

“…E. coli ribosomal protein S1 is essential for translation initiation [107] and has a positive action on transcription [108]. The presence of S1 protein and of RNA polymerase in complexes with several asRNAs may reflect the coupling between transcription and translation [106]. Ribonucleases also play an essential role in asRNA regulation.…”

Section: Proteins Associated With Asrnasmentioning

confidence: 99%

RNA-mediated regulation in bacteria: from natural to artificial systems

et al. 2010

View full text Add to dashboard Cite

“…Studies of proteins that facilitate the role of Hfq in sRNA-dependent negative regulation have focused on RNase E and its role in degradation of target mRNAs (32)(33)(34)(35). The N terminus of RNase E encodes an essential endonuclease.…”

Section: Introduction To the Degradosome And Its Role In Srna Regulationmentioning

confidence: 99%

Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices

Lay¹,

Schu²,

Gottesman

2013

Journal of Biological Chemistry

234

184

View full text Add to dashboard Cite

A large group of bacterial small regulatory RNAs (sRNAs) use the Hfq chaperone to mediate pairing with and regulation of mRNAs. Recent findings help to clarify how Hfq acts and highlight the role of the endonuclease RNase E and its associated proteins (the degradosome) in negative regulation by these sRNAs. sRNAs frequently uncouple transcription and translation by blocking ribosome access to the mRNA, allowing other proteins access to the mRNA. As more examples of sRNA-mediated regulation are studied, more variations on how Hfq, RNase E, and other proteins collaborate to bring about sRNAbased regulation are being found. Post-transcriptional Regulation by Small Noncoding RNAs in BacteriaThe idea that RNAs could function as regulators of gene expression has been around since the earliest studies of gene regulation. In their seminal paper entitled "Genetic Regulatory Mechanisms in the Synthesis of Proteins", Jacob and Monod originally hypothesized, "The specific 'repressor' (RNA?), acting with a given operator, is synthesized by a regulator gene" (1). Although the repressor in the case of the lac operon turned out to be the Lac repressor protein, the later discovery of small RNA (sRNA) 3 regulators confirmed their original hypothesis. Currently, examples of this form of gene regulation are widespread among organisms. Here, we will focus on pairing sRNAs in bacteria and, specifically, those that are often termed transencoding sRNAs. These RNAs are expressed from the DNA in trans, i.e. the sRNA genes are far from the genes encoding their mRNA target(s) and have limited complementarity with their target mRNAs. These bacterial sRNAs typically range in length from ϳ50 to 300 nucleotides. Many of these sRNAs are highly expressed when cells are undergoing some type of stress (for instance, oxidative stress, sugar phosphate accumulation, or nutrient starvation). The sRNAs base pair with their mRNA targets, leading to a variety of outcomes. Base pairing can lead to stabilization and/or translational activation of an mRNA target. Usually, activation occurs by base pairing within the 5Ј-UTR, changing folding of the 5Ј-UTR to allow entry of the ribosome and translation to occur (reviewed in Refs. 2 and 3). Another mode of action by sRNAs ultimately leads to translational repression and/or degradation of an mRNA target. In the majority of characterized cases, an sRNA base pairs at or around the ribosome-binding site (RBS) of an mRNA target. This leads to inhibition of translational initiation and, in most cases, the subsequent destabilization of the target. Negative regulation can also occur in other ways, as discussed below. Degradation of the mRNA target reinforces the translational repression and makes it irreversible.In many bacteria, an RNA chaperone, Hfq, is required for efficient base pairing between an sRNA and its target mRNA (reviewed in Ref. 4). In this minireview, we will focus on recent advances in understanding sRNA-mediated negative gene regulation in Escherichia coli and Salmonella enterica. More specifically, ...

show abstract

Isolation of small RNA-binding proteins fromE. coli: Evidence for frequent interaction of RNAs with RNA polymerase

Cited by 47 publications

References 20 publications

Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence

Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence

RNA-mediated regulation in bacteria: from natural to artificial systems

Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices

Contact Info

Product

Resources

About