Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in <i>Escherichia coli</i>

Kristiansen, Knut Ivan; Weel-Sneve, Ragnhild; Booth, James A.; Bjørås, Magnar

doi:10.1261/rna.058461.116

Cited by 23 publications

(22 citation statements)

References 35 publications

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“…In E. coli MG1655 RNase III cleavage was associated with three of the eight type I TA systems reported in Brantl et al. ( 32 ): dinQ/agrB ( 35 ), tisB/istR1 ( 36 , 37 ), and ibs/sib ( 38 , 39 ). We detected at least one putative cleavage site in each of the putative duplex regions of each of these three systems, as well as in three additional systems, shoB/OhsC, ldr/Rdl and hok/sok .…”

Section: Resultsmentioning

confidence: 79%

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

Altuvia

Bar

Reiss

et al. 2018

Nucleic Acids Research

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Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3′ overhangs, and refined the base-pairing preferences in the cleavage site vicinity. Intriguingly, we observed that the two stem positions between the cleavage sites are highly base-paired, usually involving at least one G-C or C-G base pair. We present a clear distinction between intra-molecular stem structures that are RNase III substrates and intra-molecular stem structures randomly selected across the transcriptome, emphasizing the in vivo specificity of RNase III. Our study provides a comprehensive map of the cleavage sites in both intra-molecular and inter-molecular duplex substrates, providing novel insights into the involvement of RNase III in post-transcriptional regulation in the bacterial cell.

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Section: Resultsmentioning

confidence: 79%

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

Altuvia

Bar

Reiss

et al. 2018

Nucleic Acids Research

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“…The dinQ/agrB system shares many similarities with tisB/istR - 1 with respect to post-transcriptional regulation: the dinQ +1 transcript is translationally inactive and has to be processed at its 5′ end to produce the translationally active +44 transcript. Translation of +44 mRNA is repressed by binding of the antitoxin AgrB (Weel-Sneve et al 2013 ; Kristiansen et al 2016 ) (Fig. 2 b).…”

Section: Sos Induced Toxins: Tisb and Dinqmentioning

confidence: 99%

RNA-based regulation in type I toxin–antitoxin systems and its implication for bacterial persistence

Berghoff

Wagner

2017

Curr Genet

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Bacterial dormancy is a valuable survival strategy upon challenging environmental conditions. Dormant cells tolerate the consequences of high stress levels and may re-populate the environment upon return to favorable conditions. Antibiotic-tolerant bacteria—termed persisters—regularly cause relapsing infections, increase the likelihood of antibiotic resistance, and, therefore, earn increasing attention. Their generation often depends on toxins from chromosomal toxin–antitoxin systems. Here, we review recent insights concerning RNA-based control of toxin synthesis, and discuss possible implications for persister generation.

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“…However, despite these obvious similarities to type I TA systems, the TimR/P system displays some important differences. First, mRNA processing is required for efficient translation of many type I toxin mRNAs, including tisB, hok, zorO, shoB, dinQ, and aapA1 (30,(56)(57)(58)(59)(60)(61). In contrast, the facts that the full-length mRNA, but no shorter isoforms, is detected by Northern blotting analysis (Fig.…”

Section: Discussionmentioning

confidence: 99%

The Small Toxic Salmonella Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR

Andresen

Martínez-Burgo

Zangelin

et al. 2020

mBio

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Small proteins are gaining increased attention due to their important functions in major biological processes throughout the domains of life. However, their small size and low sequence conservation make them difficult to identify. It is therefore not surprising that enterobacterial ryfA has escaped identification as a small protein coding gene for nearly 2 decades. Since its identification in 2001, ryfA has been thought to encode a noncoding RNA and has been implicated in biofilm formation in Escherichia coli and pathogenesis in Shigella dysenteriae. Although a recent ribosome profiling study suggested ryfA to be translated, the corresponding protein product was not detected. In this study, we provide evidence that ryfA encodes a small toxic inner membrane protein, TimP, overexpression of which causes cytoplasmic membrane leakage. TimP carries an N-terminal signal sequence, indicating that its membrane localization is Sec-dependent. Expression of TimP is repressed by the small RNA (sRNA) TimR, which base pairs with the timP mRNA to inhibit its translation. In contrast to overexpression, endogenous expression of TimP upon timR deletion permits cell growth, possibly indicating a toxicity-independent function in the bacterial membrane. IMPORTANCE Next-generation sequencing (NGS) has enabled the revelation of a vast number of genomes from organisms spanning all domains of life. To reduce complexity when new genome sequences are annotated, open reading frames (ORFs) shorter than 50 codons in length are generally omitted. However, it has recently become evident that this procedure sorts away ORFs encoding small proteins of high biological significance. For instance, tailored small protein identification approaches have shown that bacteria encode numerous small proteins with important physiological functions. As the number of predicted small ORFs increase, it becomes important to characterize the corresponding proteins. In this study, we discovered a conserved but previously overlooked small enterobacterial protein. We show that this protein, which we dubbed TimP, is a potent toxin that inhibits bacterial growth by targeting the cell membrane. Toxicity is relieved by a small regulatory RNA, which binds the toxin mRNA to inhibit toxin synthesis.

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Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli

Cited by 23 publications

References 35 publications

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

RNA-based regulation in type I toxin–antitoxin systems and its implication for bacterial persistence

The Small Toxic Salmonella Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR

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