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      Regulation of Transcription Elongation and Termination

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          Abstract

          This article will review our current understanding of transcription elongation and termination in E. coli. We discuss why transcription elongation complexes pause at certain template sites and how auxiliary host and phage transcription factors affect elongation and termination. The connection between translation and transcription elongation is described. Finally we present an overview indicating where progress has been made and where it has not.

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          A pause sequence enriched at translation start sites drives transcription dynamics in vivo.

          Matthew Larson, Rachel A. Mooney, Jason M Peters … (2014)
          Transcription by RNA polymerase (RNAP) is interrupted by pauses that play diverse regulatory roles. Although individual pauses have been studied in vitro, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. Using nascent transcript sequencing, we identified a 16-nucleotide consensus pause sequence in Escherichia coli that accounts for known regulatory pause sites as well as ~20,000 new in vivo pause sites. In vitro single-molecule and ensemble analyses demonstrate that these pauses result from RNAP-nucleic acid interactions that inhibit next-nucleotide addition. The consensus sequence also leads to pausing by RNAPs from diverse lineages and is enriched at translation start sites in both E. coli and Bacillus subtilis. Our results thus reveal a conserved mechanism unifying known and newly identified pause events. Copyright © 2014, American Association for the Advancement of Science.
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            A NusE:NusG complex links transcription and translation.

            Björn M. Burmann, Markus Wahl, Max E. Gottesman … (2010)
            Bacterial NusG is a highly conserved transcription factor that is required for most Rho activity in vivo. We show by nuclear magnetic resonance spectroscopy that Escherichia coli NusG carboxyl-terminal domain forms a complex alternatively with Rho or with transcription factor NusE, a protein identical to 30S ribosomal protein S10. Because NusG amino-terminal domain contacts RNA polymerase and the NusG carboxy-terminal domain interaction site of NusE is accessible in the ribosomal 30S subunit, NusG may act as a link between transcription and translation. Uncoupling of transcription and translation at the ends of bacterial operons enables transcription termination by Rho factor, and competition between ribosomal NusE and Rho for NusG helps to explain why Rho cannot terminate translated transcripts.
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              The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation.

              Patricia Vazquez, Catherine E Vrentas, Wilma Ross … (2013)
              The global regulatory nucleotide ppGpp ("magic spot") regulates transcription from a large subset of Escherichia coli promoters, illustrating how small molecules can control gene expression promoter-specifically by interacting with RNA polymerase (RNAP) without binding to DNA. However, ppGpp's target site on RNAP, and therefore its mechanism of action, has remained unclear. We report here a binding site for ppGpp on E. coli RNAP, identified by crosslinking, protease mapping, and analysis of mutant RNAPs that fail to respond to ppGpp. A strain with a mutant ppGpp binding site displays properties characteristic of cells defective for ppGpp synthesis. The binding site is at an interface of two RNAP subunits, ω and β', and its position suggests an allosteric mechanism of action involving restriction of motion between two mobile RNAP modules. Identification of the binding site allows prediction of bacterial species in which ppGpp exerts its effects by targeting RNAP. Copyright © 2013 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Deborah M. Hinton: Role: Academic Editor
                Sivaramesh Wigneshweraraj: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Biomolecules
                Journal ID (iso-abbrev): Biomolecules
                Journal ID (publisher-id): biomolecules
                Title: Biomolecules
                Publisher: MDPI
                ISSN (Electronic): 2218-273X
                Publication date (Electronic): 29 May 2015
                Publication date Collection: June 2015
                Volume: 5
                Issue: 2
                Pages: 1063-1078
                Affiliations
                [1 ]Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA; E-Mail: rw378@ 123456cumc.columbia.edu
                [2 ]Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: meg8@ 123456columbia.edu .
                Article
                Publisher ID: biomolecules-05-01063
                DOI: 10.3390/biom5021063
                PMC ID: 4496710
                PubMed ID: 26035374
                SO-VID: 7f4b2763-2616-4b59-b5a0-8fd014b9167e
                Copyright © © 2015 by the authors; licensee MDPI, Basel, Switzerland.
                License:

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 09 April 2015
                Date accepted : 21 May 2015
                Categories
                Subject: Review

                Keywords: transcription elongation,transcription pausing,transcription termination,nus factors,transcription antitermination,transcription-translation coupling
                Data availability:
                Keywords: transcription elongation, transcription pausing, transcription termination, nus factors, transcription antitermination, transcription-translation coupling

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