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      Escherichia coli NusG Links the Lead Ribosome with the Transcription Elongation Complex

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          Summary

          It has been known for more than 50 years that transcription and translation are physically coupled in bacteria, but whether or not this coupling may be mediated by the two-domain protein N-utilization substance (Nus) G in Escherichia coli is still heavily debated. Here, we combine integrative structural biology and functional analyses to provide conclusive evidence that NusG can physically link transcription with translation by contacting both RNA polymerase and the ribosome. We present a cryo-electron microscopy structure of a NusG:70S ribosome complex and nuclear magnetic resonance spectroscopy data revealing simultaneous binding of NusG to RNAP and the intact 70S ribosome, providing the first direct structural evidence for NusG-mediated coupling. Furthermore, in vivo reporter assays show that recruitment of NusG occurs late in transcription and strongly depends on translation. Thus, our data suggest that coupling occurs initially via direct RNAP:ribosome contacts and is then mediated by NusG.

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          Highlights

          • NusG can contact RNAP and lead ribosome simultaneously

          • NusG recruitment occurs late during transcription and depends on translation

          • NusG-mediated coupling happens during late translation

          Abstract

          Biochemistry; Biochemistry Methods; Structural Biology; Three-Dimensional Reconstruction of Biomolecular Structures

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          Most cited references46

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

          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.

            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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              Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli.

              Transcription of the bacterial genome by the RNA polymerase must terminate at specific points. Transcription can be terminated by Rho factor, an essential protein in enterobacteria. We used the antibiotic bicyclomycin, which inhibits Rho, to assess its role on a genome-wide scale. Rho is revealed as a global regulator of gene expression that matches Escherichia coli transcription to translational needs. We also found that genes in E. coli that are most repressed by Rho are prophages and other horizontally acquired portions of the genome. Elimination of these foreign DNA elements increases resistance to bicyclomycin. Although rho remains essential, such reduced-genome bacteria no longer require Rho cofactors NusA and NusG. Deletion of the cryptic rac prophage in wild-type E. coli increases bicyclomycin resistance and permits deletion of nusG. Thus, Rho termination, supported by NusA and NusG, is required to suppress the toxic activity of foreign genes.
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                Author and article information

                Contributors
                Journal
                iScience
                iScience
                iScience
                Elsevier
                2589-0042
                09 July 2020
                21 August 2020
                09 July 2020
                : 23
                : 8
                : 101352
                Affiliations
                [1 ]Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
                [2 ]Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany
                [3 ]Department of Biological Sciences, Columbia University, New York, NY 10027, USA
                [4 ]Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
                [5 ]University of Michigan, Ann Arbor, MI 48109, USA
                Author notes
                []Corresponding author meg8@ 123456cumc.columbia.edu
                [∗∗ ]Corresponding author stefan.knauer@ 123456uni-bayreuth.de
                [∗∗∗ ]Corresponding author jf2192@ 123456cumc.columbia.edu
                [6]

                Present address: University of California at San Francisco, San Francisco, CA 94158, USA

                [7]

                Present address: NSERM U1212, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France

                [8]

                Present address: Bristol-Myers Squibb Pharmaceutical Co., New Brunswick, NJ 08901, USA

                [9]

                Present address: California Institute of Technology, Pasadena, CA 91125, USA

                [10]

                Lead Contact

                Article
                S2589-0042(20)30539-3 101352
                10.1016/j.isci.2020.101352
                7390762
                32726726
                ce20b40a-9698-4b86-b3d3-70bac2250296
                © 2020 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 11 March 2020
                : 4 June 2020
                : 3 July 2020
                Categories
                Article

                biochemistry,biochemistry methods,structural biology,three-dimensional reconstruction of biomolecular structures

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