1
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Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG. Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand. Nat Struct Mol Biol 2023; 30:902-913. [PMID: 37264140 PMCID: PMC10523900 DOI: 10.1038/s41594-023-01002-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/20/2023] [Indexed: 06/03/2023]
Abstract
Folding of nascent transcripts can be modulated by the RNA polymerase (RNAP) that carries out their transcription, and vice versa. A pause of RNAP during transcription of a preQ1 riboswitch (termed que-PEC) is stabilized by a previously characterized template consensus sequence and the ligand-free conformation of the nascent RNA. Ligand binding to the riboswitch induces RNAP pause release and downstream transcription termination; however, the mechanism by which riboswitch folding modulates pausing is unclear. Here, we report single-particle cryo-electron microscopy reconstructions of que-PEC in ligand-free and ligand-bound states. In the absence of preQ1, the RNA transcript is in an unexpected hyper-translocated state, preventing downstream nucleotide incorporation. Strikingly, on ligand binding, the riboswitch rotates around its helical axis, expanding the surrounding RNAP exit channel and repositioning the transcript for elongation. Our study reveals the tight coupling by which nascent RNA structures and their ligands can functionally regulate the macromolecular transcription machinery.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jason C Porta
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Indrajit Deb
- Biophysics Program, University of Michigan, Ann Arbor, MI, USA
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emily Ellinger
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Katarina Meze
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Aaron T Frank
- Biophysics Program, University of Michigan, Ann Arbor, MI, USA
- Arrakis Therapeutics, Waltham, MA, USA
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022; 82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
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3
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Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA. Nat Commun 2022; 13:4668. [PMID: 35970830 PMCID: PMC9378689 DOI: 10.1038/s41467-022-32315-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/26/2022] [Indexed: 12/16/2022] Open
Abstract
Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis-element, put, which suppresses pausing and termination during transcription of the early phage genes. The putRNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted putRNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of putRNA-associated EC, putRNA-absent EC, and σ70-bound EC suggest that the putRNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ70 might modulate putRNA folding via σ70-dependent pausing during elongation.
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4
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Miguel-Arribas A, Wu LJ, Michaelis C, Yoshida KI, Grohmann E, Meijer WJJ. Conjugation Operons in Gram-Positive Bacteria with and without Antitermination Systems. Microorganisms 2022; 10:microorganisms10030587. [PMID: 35336162 PMCID: PMC8955417 DOI: 10.3390/microorganisms10030587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
Genes involved in the same cellular process are often clustered together in an operon whose expression is controlled by an upstream promoter. Generally, the activity of the promoter is strictly controlled. However, spurious transcription undermines this strict regulation, particularly affecting large operons. The negative effects of spurious transcription can be mitigated by the presence of multiple terminators inside the operon, in combination with an antitermination system. Antitermination systems modify the transcription elongation complexes and enable them to bypass terminators. Bacterial conjugation is the process by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugation involves many genes that are mostly organized in one or a few large operons. It has recently been shown that many conjugation operons present on plasmids replicating in Gram-positive bacteria possess a bipartite antitermination system that allows not only many terminators inside the conjugation operon to be bypassed, but also the differential expression of a subset of genes. Here, we show that some conjugation operons on plasmids belonging to the Inc18 family of Gram-positive broad host-range plasmids do not possess an antitermination system, suggesting that the absence of an antitermination system may have advantages. The possible (dis)advantages of conjugation operons possessing (or not) an antitermination system are discussed.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Medical Faculty, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK;
| | - Claudia Michaelis
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Elisabeth Grohmann
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
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5
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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6
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Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021; 49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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7
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Antitermination protein P7 of bacteriophage Xp10 distinguishes different types of transcriptional pausing by bacterial RNA polymerase. Biochimie 2020; 170:57-64. [DOI: 10.1016/j.biochi.2019.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022]
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8
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Abstract
Bacteriophages employ small proteins to usurp host molecular machinery, thereby interfering with central metabolic processes in infected bacteria. Generally, phages inhibit or redirect host transcription to favor transcription of their own genomes. Mechanistic and structural studies of phage-modulated host transcription may provide inspirations for the development of novel antibacterial substances.
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Affiliation(s)
- Markus C Wahl
- Freie Universität Berlin, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Ranjan Sen
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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9
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Sedlyarova N, Rescheneder P, Magán A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E. Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. Mol Cell 2017; 67:30-43.e6. [PMID: 28648779 PMCID: PMC5535762 DOI: 10.1016/j.molcel.2017.05.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/10/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
Abstract
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 inhibitory 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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Affiliation(s)
- Nadezda Sedlyarova
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, 1030 Vienna, Austria
| | - Andrés Magán
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Niko Popitsch
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria
| | - Natascha Rziha
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Ivana Bilusic
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bob Zimmermann
- Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Meghan Lybecker
- University of Colorado, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Renée Schroeder
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria.
| | - 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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10
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Kriner MA, Groisman EA. RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader. Nucleic Acids Res 2016; 45:631-642. [PMID: 28123036 PMCID: PMC5314796 DOI: 10.1093/nar/gkw889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 09/20/2016] [Accepted: 09/30/2016] [Indexed: 11/14/2022] Open
Abstract
Transcription termination events in bacteria often require the RNA helicase Rho. Typically, Rho promotes termination at the end of coding sequences, but it can also terminate transcription within leader regions to implement regulatory decisions. Rho-dependent termination requires initial recognition of a Rho utilization (rut) site on a nascent RNA by Rho's primary binding surface. However, it is presently unclear what factors determine the location of transcription termination, how RNA secondary structures influence this process and whether mechanistic differences distinguish constitutive from regulated Rho-dependent terminators. We previously demonstrated that the 5′ leader mRNA of the Salmonella corA gene can adopt two mutually exclusive conformations that dictate accessibility of a rut site to Rho. We now report that the corA leader also controls two subsequent steps of Rho-dependent termination. First, the RNA conformation that presents an accessible rut site promotes pausing of RNA polymerase (RNAP) at a single Rho-dependent termination site over 100 nt downstream. Second, an additional RNA stem-loop promotes Rho activity and controls the location at which Rho-dependent termination occurs, despite having no effect on initial Rho binding to the corA leader. Thus, the multi-step nature of Rho-dependent termination may facilitate regulation of a given coding region by multiple cytoplasmic signals.
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Affiliation(s)
- Michelle A Kriner
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.,Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA .,Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
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11
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Zhang J, Landick R. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci 2016; 41:293-310. [PMID: 26822487 DOI: 10.1016/j.tibs.2015.12.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023]
Abstract
The vectorial (5'-to-3' at varying velocity) synthesis of RNA by cellular RNA polymerases (RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived, pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here, we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure. We categorize and rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
| | - Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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12
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Casjens SR, Hendrix RW. Bacteriophage lambda: Early pioneer and still relevant. Virology 2015; 479-480:310-30. [PMID: 25742714 PMCID: PMC4424060 DOI: 10.1016/j.virol.2015.02.010] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/13/2015] [Accepted: 02/05/2015] [Indexed: 12/14/2022]
Abstract
Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT 84112, USA; Biology Department, University of Utah, Salt Lake City, UT 84112, USA.
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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13
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Distinct pathways of RNA polymerase regulation by a phage-encoded factor. Proc Natl Acad Sci U S A 2015; 112:2017-22. [PMID: 25646468 DOI: 10.1073/pnas.1416330112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. Here, we dissect the transcription antitermination mechanism of Xanthomonas oryzae virus Xp10 protein p7, which binds host RNA polymerase (RNAP) and regulates both transcription initiation and termination. We show that p7 suppresses intrinsic termination by decreasing RNAP pausing and increasing the transcription complex stability, in cooperation with host-encoded factor NusA. Uniquely, the antitermination activity of p7 depends on the ω subunit of the RNAP core and is modulated by ppGpp. In contrast, the inhibition of transcription initiation by p7 does not require ω but depends on other RNAP sites. Our results suggest that p7, a bifunctional transcription factor, uses distinct mechanisms to control different steps of transcription. We propose that regulatory functions of the ω subunit revealed by our analysis may extend to its homologs in eukaryotic RNAPs.
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14
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Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator. Proc Natl Acad Sci U S A 2014; 111:E1999-2007. [PMID: 24778260 DOI: 10.1073/pnas.1319193111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Up to half of all transcription termination events in bacteria rely on the RNA-dependent helicase Rho. However, the nucleic acid sequences that promote Rho-dependent termination remain poorly characterized. Defining the molecular determinants that confer Rho-dependent termination is especially important for understanding how such terminators can be regulated in response to specific signals. Here, we identify an extraordinarily long-lived pause at the site where Rho terminates transcription in the 5'-leader region of the Mg(2+) transporter gene mgtA in Salmonella enterica. We dissect the sequence elements required for prolonged pausing in the mgtA leader and establish that the remarkable longevity of this pause is required for a riboswitch to stimulate Rho-dependent termination in the mgtA leader region in response to Mg(2+) availability. Unlike Rho-dependent terminators described previously, where termination occurs at multiple pause sites, there is a single site of transcription termination directed by Rho in the mgtA leader. Our data suggest that Rho-dependent termination events that are subject to regulation may require elements distinct from those operating at constitutive Rho-dependent terminators.
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15
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Abstract
Antiterminator RNA directly modifies the transcription elongation complex so that it terminates less efficiently at intrinsic and factor-dependent terminators. These unusual RNAs were first discovered in bacteriophage HK022, where the nascent transcripts of the phage put sites promote full expression of phage genes during lytic infection. The activity of antiterminator RNA depends on specific structural elements that form as the transcript exits RNA polymerase. To further our understanding of the critical sequence features that permit RNA to serve as a transcriptional antiterminator, we have identified eight antiterminator RNA sequences in bacteriophages or prophages. There is strong sequence conservation among most of the put sequences, but sequence divergence is tolerated if critical structural elements are preserved. The most diverged antiterminator RNA is found in bacteriophage HK639. The HK639 putL transcript is an efficient antiterminator, and it has a novel structural feature that is critical for its activity. HK639 also displays a unique pattern of sensitivity to amino acid substitutions in the β' subunit zinc binding domain of RNA polymerase, adding to existing evidence that this domain interacts specifically with antiterminator RNA.
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16
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Santangelo TJ, Artsimovitch I. Termination and antitermination: RNA polymerase runs a stop sign. Nat Rev Microbiol 2011; 9:319-29. [PMID: 21478900 DOI: 10.1038/nrmicro2560] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Termination signals induce rapid and irreversible dissociation of the nascent transcript from RNA polymerase. Terminators at the end of genes prevent unintended transcription into the downstream genes, whereas terminators in the upstream regulatory leader regions adjust expression of the structural genes in response to metabolic and environmental signals. Premature termination within an operon leads to potentially deleterious defects in the expression of the downstream genes, but also provides an important surveillance mechanism. This Review discusses the actions of bacterial and phage antiterminators that allow RNA polymerase to override a terminator when the circumstances demand it.
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Affiliation(s)
- Thomas J Santangelo
- Department of Microbiology and The RNA Group, The Ohio State University, Columbus, Ohio 43210, USA
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17
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Zhang J, Lau MW, Ferré-D'Amaré AR. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 2010; 49:9123-31. [PMID: 20931966 DOI: 10.1021/bi1012645] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diverse small molecules interact with catalytic RNAs (ribozymes) as substrates and cofactors, and their intracellular concentrations are sensed by gene-regulatory mRNA domains (riboswitches) that modulate transcription, splicing, translation, or RNA stability. Although recognition mechanisms vary from RNA to RNA, structural analyses reveal recurring strategies that arise from the intrinsic properties of RNA such as base pairing and stacking with conjugated heterocycles, and cation-dependent recognition of anionic functional groups. These studies also suggest that, to a first approximation, the magnitude of ligand-induced reorganization of an RNA is inversely proportional to the complexity of the riboswitch or ribozyme. How these small molecule binding-induced changes in RNA lead to alteration in gene expression is less well understood. While different riboswitches have been proposed to be under either kinetic or thermodynamic control, the biochemical and structural mechanisms that give rise to regulatory consequences downstream of small molecule recognition by RNAs mostly remain to be elucidated.
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Affiliation(s)
- Jinwei Zhang
- Howard Hughes Medical Institute, Seattle, Washington 98109-1024, USA
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18
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Abstract
Since the discovery of the first signal-sensing RNA structure by Grundy and Henkin in 1993, the list of cis-acting riboregulators has grown dramatically. Riboswitches fold into elaborate structures and respond to binding of small metabolites by altering the folding pattern of the surrounding transcript, thereby altering the gene expression programme. Riboswitches that use short-range mechanisms to control transcription attenuation and translation initiation and mediate mRNA cleavage have been characterized in many Gram-positive bacteria. Their action typically relies on alternative RNA structures that are differentially stabilized by the ligand binding. In this issue of Molecular Microbiology, Irnov and Winkler describe a novel Bacillus subtilis riboregulator called EAR that shares structural complexity with riboswitches but possesses a unique mechanism of action. EAR increases expression of exopolysaccharide genes and biofilm formation, and appears to act as a processive, long-range antiterminator, the first such example outside of Escherichia coli. While it is unclear whether EAR senses a biofilm-inducing signal, the results suggest that its action depends on yet unidentified auxiliary factors. Interestingly, efficient capsule biogenesis in E. coli and Bacteroides fragilis also depends on processive antiterminators but utilizes the protein-based mechanisms instead.
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Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology and The RNA Group, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
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Irnov I, Winkler WC. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol 2010; 76:559-75. [DOI: 10.1111/j.1365-2958.2010.07131.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Abstract
In Bacteria, transcription is catalyzed by a single RNA polymerase (RNAP) whose promoter selectivity and activity is governed by a wide variety of transcription factors. The net effect of these transcriptional regulators is to determine which genes are transcribed, and at what levels, under any specific growth condition. RNAP thus serves as a nexus of gene regulation that integrates the information coming from a variety of sensory systems to appropriately modulate gene expression. The techniques presented in this volume provide a set of tools and approaches for investigating the factors controlling RNAP activity at both individual promoters and on a genomic scale. This introductory chapter provides a brief overview of RNAP and the transcription cycle and introduces general principles of how the fundamental steps of transcription are influenced by both DNA (promoter) sequences and trans-acting factors.
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Affiliation(s)
- John D Helmann
- Department of Microbiology, Cornell University, 327 Wing Hall, Ithaca, NY 14853-8101, USA.
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Lewis DEA, Komissarova N, Le P, Kashlev M, Adhya S. DNA sequences in gal operon override transcription elongation blocks. J Mol Biol 2008; 382:843-58. [PMID: 18691599 DOI: 10.1016/j.jmb.2008.07.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/12/2008] [Accepted: 07/23/2008] [Indexed: 12/01/2022]
Abstract
The DNA loop that represses transcription from galactose (gal) promoters is infrequently formed in stationary-phase cells because the concentration of the loop architectural protein HU is significantly low at that state, resulting in expression of the operon in the absence of the gal inducer D-galactose. Unexpectedly, transcription from the gal promoters under these conditions overrides physical block because of the presence of the Gal repressor bound to an internal operator (O(I)) located downstream of the promoters. We have shown here that although a stretch of pyrimidine residues (UUCU) in the RNA:DNA hybrid located immediately upstream of O(I) weakens the RNA:DNA hybrid and favors RNA polymerase (RNAP) pausing and backtracking, a stretch of purines (GAGAG) in the RNA present immediately upstream of the pause sequence in the hybrid acts as an antipause element by stabilizing the RNA:DNA duplex and preventing backtracking. This facilitates forward translocation of RNAP, including overriding of the DNA-bound Gal repressor barrier at O(I). When the GAGAG sequence is separated from the pyrimidine sequence by a 5-bp DNA insertion, RNAP backtracking is favored from a weak hybrid to a more stable hybrid. RNAP backtracking is sensitive to Gre factors, D-galactose, and antisense oligonucleotides. The ability of a native DNA sequence to override transcription elongation blocks in the gal operon uncovers a previously unknown way of regulating gal metabolism in Escherichia coli. It also explains the synthesis of gal enzymes in the absence of inducer for biosynthetic reactions.
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Affiliation(s)
- Dale E A Lewis
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA.
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