sRNA-Mediated Control of Transcription Termination in E. coli

Sedlyarova, Nadezda; Shamovsky, Ilya; Bharati, Binod K.; Epshtein, Vitaly; Chen, Jiandong; Gottesman, Susan; Schroeder, Renée; Nudler, Evgeny

doi:10.1016/j.cell.2016.09.004

Cited by 189 publications

(189 citation statements)

References 64 publications

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“…To estimate how many of these “antisense” RAPs were actually transcribed, we correlated the antisense RAP dataset with our recent total transcriptome profile of E. coli (Sedlyarova et al, 2016). We identified more than 20% of all the antisense RAPs being expressed under normal growth conditions in rich medium (Figure 6A; Table S3).…”

Section: Resultsmentioning

confidence: 99%

“…In experiments with oxidative stress induction, bacterial cells grown to early exponential phase (OD 600 ≈ 0.4-0.5) were treated with 4 mM H2O2 for 20 or 60 minutes (as indicated) prior to harvesting. In experiments with BCM treatment (followed by RNA extraction), bacterial cells grown to early exponential phase (OD 600 ≈ 0.4-0.5) were treated with BCM as indicated (25 / 50 / 75 μg/mL; final concentrations selected based on previous studies (Dutta et al, 2011; Sedlyarova et al, 2016)) and cultivated for 15-20 minutes before harvesting.…”

Section: Methods and Resourcesmentioning

confidence: 99%

“…In bacteria all steps of transcription, from initiation to elongation and termination, are prone to regulation by trans -acting proteins and small RNAs (Belogurov and Artsimovitch, 2015; Browning and Busby, 2016; Decker and Hinton, 2013; Sedlyarova et al, 2016). Additionally, the nascent RNA itself can contain cis -acting regulatory signals.…”

Section: Introductionmentioning

confidence: 99%

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Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

et al. 2017

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Summary In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP) we deep-sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches we characterized a subset of RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment. The mechanism of iRAPs involves active uncoupling of transcription and translation, making nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.

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Section: Resultsmentioning

confidence: 99%

Section: Methods and Resourcesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

et al. 2017

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“…In other cases, the sRNA:mRNA interaction can target the mRNA for rapid degradation, often by the multienzyme RNA degradosome assembly (Fei et al 2015;Wagner and Romby 2015). sRNAs can also operate on actively transcribed genes by modulating the process of transcription termination (Sedlyarova et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Structure of the Escherichia coli ProQ RNA-binding protein

Gonzalez

Hardwick

Maslen

et al. 2017

RNA

123

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The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.

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“…Other sRNAs control Rho-dependent termination at the 5′ UTR of the transcripts by blocking the action of Rho and resulting in increased translation of the transcripts (107). The association of many sRNAs with a functionally important cognate RNA-binding protein (Hfq) is critical for its functionality.…”

Section: Processing and Decay Of Small Regulatory Rnasmentioning

confidence: 99%

Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

Mohanty¹,

Kushner

2018

Microbiol Spectr

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Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this chapter we discuss the various enzymes that control transcription, translation and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5′ and 3′ termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript, are matured to individual 16S, 23S and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and non-translated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase as well as proteins that regulate the catalytic activity of particular ribonucleases. Under certain stress conditions an additional group of specialized endonucleases facilitate the cell’s ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I participate in multiple RNA processing and decay pathways.

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sRNA-Mediated Control of Transcription Termination in E. coli

Cited by 189 publications

References 64 publications

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

Structure of the Escherichia coli ProQ RNA-binding protein

Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

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