Poly(A) polymerase is required for RyhB sRNA stability and function in <i>Escherichia coli</i>

Sinha, Dhriti; Matz, Lisa M.; Cameron, Todd A.; Lay, Nicholas R. De

doi:10.1261/rna.067181.118

Cited by 22 publications

(17 citation statements)

References 91 publications

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“…1). Interestingly, the reduction of RyhB levels in a strain lacking poly(A) polymerase may be attributed to reduced degradation of the 3′ETS LeuZ RyhB sponge in this mutant background (114).…”

Section: Competition Rna Decoys Rna Mimics and Rna Spongesmentioning

confidence: 92%

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

et al. 2020

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The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.

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Section: Competition Rna Decoys Rna Mimics and Rna Spongesmentioning

confidence: 92%

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

et al. 2020

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“…Signal was visualized on a phosphorimager (Fuji FLA‐3000) and quantified using the Image Quant image analyzer (ImageGauge V4.22). Decay curves corresponding to rifampicin chase experiments were generated using GraphPad Prism version 8.0 (Sinha et al , ).…”

Section: Methodsmentioning

confidence: 99%

Oxygen‐dependent regulation of SPI1 type three secretion system by small RNAs in Salmonella enterica serovar Typhimurium

Kim

Golubeva

Vanderpool

et al. 2018

Molecular Microbiology

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Summary Salmonella Typhimurium induces inflammatory diarrhea and uptake into intestinal epithelial cells using the Salmonella pathogenicity island 1 (SPI1) type III secretion system (T3SS). Three AraC‐like regulators, HilD, HilC and RtsA, form a feed‐forward regulatory loop that activates transcription of hilA, encoding the activator of the T3SS structural genes. Many environmental signals and regulatory systems are integrated into this circuit to precisely regulate SPI1 expression. A subset of these regulatory factors affects translation of hilD, but the mechanisms are poorly understood. Here, we identified two sRNAs, FnrS and ArcZ, which repress hilD translation, leading to decreased production of HilA. FnrS and ArcZ are oppositely regulated in response to oxygen, one of the key environmental signals affecting expression of SPI1. Mutational analysis demonstrates that FnrS and ArcZ bind to the hilD mRNA 5′ UTR, resulting in translational repression. Deletion of fnrS led to increased HilD production under low‐aeration conditions, whereas deletion of arcZ abolished the regulatory effect on hilD translation aerobically. The fnrS arcZ double mutant has phenotypes in a mouse oral infection model consistent with increased expression of SPI1. Together, these results suggest that coordinated regulation by these two sRNAs maximizes HilD production at an intermediate level of oxygen.

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“…However, on shorter poly(A) tails (<10 nt), Hfq has poor accessibility, making the transcripts susceptible to the activity of PNPase and RNase II (Regnier and Hajnsdorf, 2013). Interestingly, in E. coli, the absence of PAP I disrupts the regulatory role of some sRNAs, leading to an unexpected destabilization of some sRNAs and transcripts, e.g., RyhB and MicA (Sinha et al, 2018). This appears to result from accumulation of transcripts that are normally degraded in a PAP I-dependent fashion.…”

Section: Roles Of Ribosomes Translation Srnas and Rna-binding Protmentioning

confidence: 99%

Regulation of mRNA Stability During Bacterial Stress Responses

Vargas-Blanco

Shell

2020

Front. Microbiol.

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Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5 ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.

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Poly(A) polymerase is required for RyhB sRNA stability and function in Escherichia coli

Cited by 22 publications

References 91 publications

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

Oxygen‐dependent regulation of SPI1 type three secretion system by small RNAs in Salmonella enterica serovar Typhimurium

Regulation of mRNA Stability During Bacterial Stress Responses

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