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Nudler E. Transcription-coupled global genomic repair in E. coli. Trends Biochem Sci 2023; 48:873-882. [PMID: 37558547 DOI: 10.1016/j.tibs.2023.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
The nucleotide excision repair (NER) pathway removes helix-distorting lesions from DNA in all organisms. Escherichia coli has long been a model for understanding NER, which is traditionally divided into major and minor subpathways known as global genome repair (GGR) and transcription-coupled repair (TCR), respectively. TCR has been assumed to be mediated exclusively by Mfd, a DNA translocase of minimal NER phenotype. This review summarizes the evidence that shaped the traditional view of NER in bacteria, and reviews data supporting a new model in which GGR and TCR are inseparable. In this new model, RNA polymerase serves both as the essential primary sensor of bulky DNA lesions genome-wide and as the delivery platform for the assembly of functional NER complexes in living cells.
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Affiliation(s)
- Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
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2
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Martinez B, Bharati BK, Epshtein V, Nudler E. Pervasive Transcription-coupled DNA repair in E. coli. Nat Commun 2022; 13:1702. [PMID: 35354807 PMCID: PMC8967931 DOI: 10.1038/s41467-022-28871-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggest that GGR and TCR are essentially the same process required for complete repair of the bacterial genome. Transcription-Coupled DNA repair has been classically defined as the preferential repair of the template strand (TS) over the non-template strand (NTS). Here the authors challenge this classic model of TCR by using a genome-wide repair assay, CPD-seq, as well as RNA-seq, to show that TCR occurs across the entire E. coli genome – including NTS and intergenic regions.
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Affiliation(s)
- Britney Martinez
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA.,Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA. .,Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, New York, 10016, USA.
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3
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Abstract
Rho is a hexameric bacterial RNA helicase, which became a paradigm of factor-dependent transcription termination. The broadly accepted ("textbook") model posits a series of steps, wherein Rho first binds C-rich Rho utilization (rut) sites on nascent RNA, uses its ATP-dependent translocase activity to catch up with RNA polymerase (RNAP), and either pulls the transcript from the elongation complex or pushes RNAP forward, thus terminating transcription. However, this appealingly simple mechano-chemical model lacks a biological realism and is increasingly at odds with genetic and biochemical data. Here, we summarize recent structural and biochemical studies that have advanced our understanding of molecular details of RNA recognition, termination signaling, and RNAP inactivation in Rho-dependent transcription termination, rebalancing the view in favor of an alternative "allosteric" mechanism. In the revised model, Rho binds RNAP early in elongation assisted by the cofactors NusA and NusG, forming a pre-termination complex (PTC). The formation of PTC allows Rho to continuously sample nascent transcripts for a termination signal, which subsequently traps the elongation complex in an inactive state prior to its dissociation.
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Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, Ny, USA
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4
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Ishihama A, Shimada T. Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators. FEMS Microbiol Rev 2021; 45:6312496. [PMID: 34196371 DOI: 10.1093/femsre/fuab032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two groups of its regulatory proteins, seven species of promoter-recognition subunit sigma and about 300 species of transcription factors. The identification of regulatory targets for all these regulatory proteins is critical toward understanding the genome regulation as a whole. For this purpose, we performed a systematic search in vitro of the whole set of binding sites for each factor by gSELEX system. This review summarizes the accumulated knowledge of regulatory targets for more than 150 TFs from E. coli K-12. Overall TFs could be classified into four families: nucleoid-associated bifunctional TFs; global regulators; local regulators; and single-target regulators, in which the regulatory functions remain uncharacterized for the nucleoid-associated TFs. Here we overview the regulatory targets of two nucleoid-associated TFs, H-NS and its paralog StpA, both together playing the silencing role of a set of non-essential genes. Participation of LeuO and other global regulators have been indicated for the anti-silencing. Finally, we propose the hierarchy of TF network as a key framework of the bacterial genome regulation.
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Affiliation(s)
- Akira Ishihama
- Hosei University, Research Institute for Micro-Nano Technology, Koganei, Tokyo 184-0003, Japan
| | - Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
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5
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Simon I, Delaleau M, Schwartz A, Boudvillain M. A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity. J Mol Biol 2021; 433:167060. [PMID: 34023400 DOI: 10.1016/j.jmb.2021.167060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/30/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
Rho-dependent termination of transcription (RDTT) is a critical regulatory mechanism specific to bacteria. In a subset of species including most Actinobacteria and Bacteroidetes, the Rho factor contains a large, poorly conserved N-terminal insertion domain (NID) of cryptic function. To date, only two NID-bearing Rho factors from high G + C Actinobacteria have been thoroughly characterized. Both can trigger RDTT at promoter-proximal sites or with structurally constrained transcripts that are unsuitable for the archetypal, NID-less Rho factor of Escherichia coli (EcRho). Here, we provide the first biochemical characterization of a NID-bearing Rho factor from a low G + C bacterium. We show that Bacteroides fragilis Rho (BfRho) is a bona fide RNA-dependent NTPase motor able to unwind long RNA:DNA duplexes and to disrupt transcription complexes. The large NID (~40% of total mass) strongly increases BfRho affinity for RNA, is strictly required for RDTT, but does not promote RDTT at promoter-proximal sites or with a structurally constrained transcript. Furthermore, the NID does not preclude modulation of RDTT by transcription factors NusA and NusG or by the Rho inhibitor bicyclomycin. Although the NID contains a prion-like Q/N-rich motif, it does not spontaneously trigger formation of β-amyloids. Thus, despite its unusually large RNA binding domain, BfRho behaves more like the NID-less EcRho than NID-bearing counterparts from high G + C Actinobacteria. Our data highlight the evolutionary plasticity of Rho's N-terminal region and illustrate how RDTT is adapted to distinct genomic contents.
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Affiliation(s)
- Isabelle Simon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France; ED 549, Santé, Sciences Biologiques & Chimie du Vivant, Université d'Orléans, France
| | - Mildred Delaleau
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Annie Schwartz
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France.
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O’Connor NJ, Bordoy AE, Chatterjee A. Engineering Transcriptional Interference through RNA Polymerase Processivity Control. ACS Synth Biol 2021; 10:737-748. [PMID: 33710852 DOI: 10.1021/acssynbio.0c00534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Antisense transcription is widespread in all kingdoms of life and has been shown to influence gene expression through transcriptional interference (TI), a phenomenon in which one transcriptional process negatively influences another in cis. The processivity, or uninterrupted transcription, of an RNA polymerase (RNAP) is closely tied to levels of antisense transcription in bacterial genomes, but its influence on TI, while likely important, is not well-characterized. Here, we show that TI can be tuned through processivity control via three distinct antitermination strategies: the antibiotic bicyclomycin, phage protein Psu, and ribosome-RNAP coupling. We apply these methods toward TI and tune ribosome-RNAP coupling to produce 38-fold transcription-level gene repression due to both RNAP collisions and antisense RNA interference. We then couple protein roadblock and TI to design minimal genetic NAND and NOR logic gates. Together, these results show the importance of processivity control for strong TI and demonstrate TI's potential for synthetic biology.
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Affiliation(s)
- Nolan J. O’Connor
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Antoni E. Bordoy
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Antimicrobial Regeneration Consortium, Boulder, Colorado 80301, United States
- Sachi Bioworks, Inc., Boulder, Colorado 80301, United States
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Irastortza-Olaziregi M, Amster-Choder O. Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises. Front Microbiol 2021; 11:624830. [PMID: 33552035 PMCID: PMC7858274 DOI: 10.3389/fmicb.2020.624830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 01/17/2023] Open
Abstract
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming "RNAP.mRNA.ribosome" complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E. Pre-termination Transcription Complex: Structure and Function. Mol Cell 2020; 81:281-292.e8. [PMID: 33296676 DOI: 10.1016/j.molcel.2020.11.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/11/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
Rho is a general transcription termination factor playing essential roles in RNA polymerase (RNAP) recycling, gene regulation, and genomic stability in most bacteria. Traditional models of transcription termination postulate that hexameric Rho loads onto RNA prior to contacting RNAP and then translocates along the transcript in pursuit of the moving RNAP to pull RNA from it. Here, we report the cryoelectron microscopy (cryo-EM) structures of two termination process intermediates. Prior to interacting with RNA, Rho forms a specific "pre-termination complex" (PTC) with RNAP and elongation factors NusA and NusG, which stabilize the PTC. RNA exiting RNAP interacts with NusA before entering the central channel of Rho from the distal C-terminal side of the ring. We map the principal interactions in the PTC and demonstrate their critical role in termination. Our results support a mechanism in which the formation of a persistent PTC is a prerequisite for termination.
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Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly H Kim
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Sergey Proshkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119991, Russia
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Venu Kamarthapu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Binod Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119991, Russia
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
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9
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Boots JL, von Pelchrzim F, Weiss A, Zimmermann B, Friesacher T, Radtke M, Żywicki M, Chen D, Matylla-Kulińska K, Zagrovic B, Schroeder R. RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription in cis. Transcription 2020; 11:217-229. [PMID: 32663063 PMCID: PMC7714431 DOI: 10.1080/21541264.2020.1790990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We identified a variety of Pol II-binding aptamers (RAPs), prominent in repeat elements such as ACRO1 satellites, LINE1 retrotransposons and CA simple repeats, and also in several protein-coding genes. ACRO1 repeat, when translated in silico, exhibits ~50% identity with the Pol II CTD sequence. Taken together with a recent proposal that proteins in general tend to interact with RNAs similar to their cognate mRNAs, this suggests a mechanism for RAP binding. Using a reporter construct, we show that ACRO1 potently inhibits Pol II elongation in cis. We propose a novel mode of transcriptional regulation in humans, in which the nascent RNA binds Pol II to silence its own expression.
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Affiliation(s)
- Jennifer L. Boots
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Frederike von Pelchrzim
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Adam Weiss
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Theres Friesacher
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Maximilian Radtke
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Marek Żywicki
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Doris Chen
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Katarzyna Matylla-Kulińska
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Renée Schroeder
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria,CONTACT Renée Schroeder Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
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Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters. mSystems 2020; 5:5/4/e00250-20. [PMID: 32694125 PMCID: PMC7566282 DOI: 10.1128/msystems.00250-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Efforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the Z. mobilis genome presented in this work, we provide crucial knowledge for the development of synthetic genetic parts tailored to Z. mobilis. This information is vital as researchers continue to develop Z. mobilis for synthetic biology applications. Our methods and statistical analyses also provide ways to rapidly advance the understanding of poorly characterized bacteria via empirical data that enable the experimental validation of sequence-based prediction for genome characterization and annotation. Zymomonas mobilis is an ethanologenic alphaproteobacterium with promise for the industrial conversion of renewable plant biomass into fuels and chemical bioproducts. Limited functional annotation of the Z. mobilis genome is a current barrier to both fundamental studies of Z. mobilis and its development as a synthetic biology chassis. To gain insight, we collected sample-matched multiomics data, including RNA sequencing (RNA-seq), transcription start site (TSS) sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry, across different growth conditions and used these data to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. We developed statistical methods for annotating transcript 5′ and 3′ ends, enabling the identification of 3,940 TSSs and their corresponding promoters and 2,091 transcription termination sites, which were distinguished from RNA processing sites by the lack of an adjacent RNA 5′ end. Our results revealed that Z. mobilis σA −35 and −10 promoter elements closely resemble canonical Escherichia coli −35 and −10 elements, with one notable exception: the Z. mobilis −10 element lacks the highly conserved −7 thymine observed in E. coli and other previously characterized σA promoters. The σA promoters of another alphaproteobacterium, Caulobacter crescentus, similarly lack the conservation of −7 thymine in their −10 elements. Our results anchor the development of Z. mobilis as a platform for synthetic biology and establish strategies for empirical genome annotation that can complement purely computational methods. IMPORTANCE Efforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the Z. mobilis genome presented in this work, we provide crucial knowledge for the development of synthetic genetic parts tailored to Z. mobilis. This information is vital as researchers continue to develop Z. mobilis for synthetic biology applications. Our methods and statistical analyses also provide ways to rapidly advance the understanding of poorly characterized bacteria via empirical data that enable the experimental validation of sequence-based prediction for genome characterization and annotation.
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Bossi L, Figueroa-Bossi N, Bouloc P, Boudvillain M. Regulatory interplay between small RNAs and transcription termination factor Rho. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194546. [PMID: 32217107 DOI: 10.1016/j.bbagrm.2020.194546] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/12/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
The largest and best studied group of regulatory small RNAs (sRNAs) in bacteria act by modulating translation or turnover of messenger RNAs (mRNAs) through base-pairing interactions that typically take place near the 5' end of the mRNA. This allows the sRNA to bind the complementary target sequence while the remainder of the mRNA is still being made, creating conditions whereby the action of the sRNA can extend to transcriptional steps, most notably transcription termination. Increasing evidence corroborates the existence of a functional interplay between sRNAs and termination factor Rho. Two general mechanisms have emerged. One mechanism operates in translated regions subjected to sRNA repression. By inhibiting ribosome binding co-transcriptionally, the sRNA uncouples translation from transcription, allowing Rho to bind the nascent RNA and promote termination. In the second mechanism, which functions in 5' untranslated regions, the sRNA antagonizes termination directly by interfering with Rho binding to the RNA or the subsequent translocation along the RNA. Here, we review the above literature in the context of other mechanisms that underlie the participation of Rho-dependent transcription termination in gene regulation. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
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