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Title: Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

Abstract

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

Authors:
 [1];  [1];  [1];  [1]
  1. Rockefeller Univ., New York, NY (United States)
Publication Date:
Research Org.:
Univ. of Chicago, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1393440
Grant/Contract Number:  
AC02-06CH11357; RO1 GM114450
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES

Citation Formats

Hubin, Elizabeth A., Lilic, Mirjana, Darst, Seth A., and Campbell, Elizabeth A. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. United States: N. p., 2017. Web. doi:10.1038/ncomms16072.
Hubin, Elizabeth A., Lilic, Mirjana, Darst, Seth A., & Campbell, Elizabeth A. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. United States. doi:10.1038/ncomms16072.
Hubin, Elizabeth A., Lilic, Mirjana, Darst, Seth A., and Campbell, Elizabeth A. Thu . "Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures". United States. doi:10.1038/ncomms16072. https://www.osti.gov/servlets/purl/1393440.
@article{osti_1393440,
title = {Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures},
author = {Hubin, Elizabeth A. and Lilic, Mirjana and Darst, Seth A. and Campbell, Elizabeth A.},
abstractNote = {The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.},
doi = {10.1038/ncomms16072},
journal = {Nature Communications},
issn = {2041-1723},
number = ,
volume = 8,
place = {United States},
year = {2017},
month = {7}
}

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Works referenced in this record:

Anatomy of Escherichia coli σ 70 promoters
journal, December 2006

  • Shultzaberger, Ryan K.; Chen, Zehua; Lewis, Karen A.
  • Nucleic Acids Research, Vol. 35, Issue 3
  • DOI: 10.1093/nar/gkl956

Protein–Protein Contacts that Activate and Repress Prokaryotic Transcription
journal, March 1998


Electrostatics of nanosystems: Application to microtubules and the ribosome
journal, August 2001

  • Baker, N. A.; Sept, D.; Joseph, S.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041
  • DOI: 10.1073/pnas.181342398

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
journal, July 2013

  • Das, R. K.; Pappu, R. V.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 33
  • DOI: 10.1073/pnas.1304749110

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach
journal, September 2010


Structure and Function of Lineage-specific Sequence Insertions in the Bacterial RNA Polymerase β′ Subunit
journal, October 2005

  • Chlenov, Mark; Masuda, Shoko; Murakami, Katsuhiko S.
  • Journal of Molecular Biology, Vol. 353, Issue 1
  • DOI: 10.1016/j.jmb.2005.07.073

Cation-pi interactions in structural biology
journal, August 1999

  • Gallivan, J. P.; Dougherty, D. A.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 17
  • DOI: 10.1073/pnas.96.17.9459

Collaboration gets the most out of software
journal, September 2013


Identification of an UP element consensus sequence for bacterial promoters
journal, August 1998

  • Estrem, S. T.; Gaal, T.; Ross, W.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 17
  • DOI: 10.1073/pnas.95.17.9761

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition
journal, April 2017


A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding
journal, October 2008


Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD
journal, December 2014

  • Davis, Elizabeth; Chen, James; Leon, Katherine
  • Nucleic Acids Research, Vol. 43, Issue 1
  • DOI: 10.1093/nar/gku1231

Bacteriophage T7 early promoters: Nucleotide sequences of two RNA polymerase binding sites
journal, December 1975


Protein Disorder Prediction
journal, November 2003


Structure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit
journal, March 2002


The Mechanism of E. coli RNA Polymerase Regulation by ppGpp Is Suggested by the Structure of their Complex
journal, May 2013


Tuberculosis Drug Development: History and Evolution of the Mechanism-Based Paradigm : Figure 1.
journal, April 2015


UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition
journal, August 2000


Molecular systematic studies of eubacteria, using sigma70-type sigma factors of group 1 and group 2.
journal, March 1997


Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble
journal, May 2015


Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA
journal, January 2017


Molecular Evolution of Multisubunit RNA Polymerases: Sequence Analysis
journal, January 2010


Structural Basis of Transcription Initiation
journal, October 2012


The sigma 70 family: sequence conservation and evolutionary relationships.
journal, June 1992


Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis
journal, November 2013


Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ Subunit
journal, December 2011


rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase
journal, June 2006


The PredictProtein server
journal, July 2004

  • Rost, B.; Yachdav, G.; Liu, J.
  • Nucleic Acids Research, Vol. 32, Issue Web Server
  • DOI: 10.1093/nar/gkh377

MEME SUITE: tools for motif discovery and searching
journal, May 2009

  • Bailey, T. L.; Boden, M.; Buske, F. A.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp335

Polypeptides containing highly conserved regions of transcription initiation factor σ70 exhibit specificity of binding to promoter DNA
journal, August 1992


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Transcription activation by catabolite activator protein (CAP)
journal, October 1999

  • Busby, Steve; Ebright, Richard H.
  • Journal of Molecular Biology, Vol. 293, Issue 2
  • DOI: 10.1006/jmbi.1999.3161

C-h⋯π-interactions in proteins
journal, March 2001

  • Brandl, Maria; Weiss, Manfred S.; Jabs, Andreas
  • Journal of Molecular Biology, Vol. 307, Issue 1
  • DOI: 10.1006/jmbi.2000.4473

Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis
journal, October 2011

  • Saecker, Ruth M.; Record, M. Thomas; deHaseth, Pieter L.
  • Journal of Molecular Biology, Vol. 412, Issue 5
  • DOI: 10.1016/j.jmb.2011.01.018

Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA
journal, May 2015

  • Hubin, Elizabeth A.; Tabib-Salazar, Aline; Humphrey, Laurence J.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 23
  • DOI: 10.1073/pnas.1504942112

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

A Basal Promoter Element Recognized by Free RNA Polymerase σ Subunit Determines Promoter Recognition by RNA Polymerase Holoenzyme
journal, July 2006


Structural Basis of Transcription Activation: The CAP-alpha CTD-DNA Complex
journal, August 2002


Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
journal, June 1998

  • Cole, S. T.; Brosch, R.; Parkhill, J.
  • Nature, Vol. 393, Issue 6685
  • DOI: 10.1038/31159

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ 70 Holoenzyme
journal, February 2013


Domain 1.1 of the σ70 Subunit of Escherichia coli RNA Polymerase Modulates the Formation of Stable Polymerase/Promoter Complexes
journal, June 2001

  • Vuthoori, Srilatha; Bowers, Christina Wilson; McCracken, Andrea
  • Journal of Molecular Biology, Vol. 309, Issue 3
  • DOI: 10.1006/JMBI.2001.4690

Promoter recognition and discrimination by EsigmaS RNA polymerase
journal, November 2001


Escherichia coli K-12: a cooperatively developed annotation snapshot--2005
journal, January 2006


Autoregulation of a bacterial   factor explored by using segmental isotopic labeling and NMR
journal, June 2002

  • Camarero, J. A.; Shekhtman, A.; Campbell, E. A.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 13
  • DOI: 10.1073/pnas.132033899

Region 1 of σ70 is required for efficient isomerization and initiation of transcription by Escherichia coli RNA polymerase
journal, March 1997

  • Wilson, Christina; Dombroski, Alicia J.
  • Journal of Molecular Biology, Vol. 267, Issue 1
  • DOI: 10.1006/jmbi.1997.0875

Sequence logos: a new way to display consensus sequences
journal, January 1990

  • Schneider, Thomas D.; Stephens, R. Michael
  • Nucleic Acids Research, Vol. 18, Issue 20
  • DOI: 10.1093/nar/18.20.6097

CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism
journal, February 2015

  • Rammohan, Jayan; Ruiz Manzano, Ana; Garner, Ashley L.
  • Nucleic Acids Research, Vol. 43, Issue 6
  • DOI: 10.1093/nar/gkv078

Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter.
journal, March 1975

  • Pribnow, D.
  • Proceedings of the National Academy of Sciences, Vol. 72, Issue 3
  • DOI: 10.1073/pnas.72.3.784

CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence
journal, July 2009


Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of  70 domain 1.1
journal, November 2013

  • Bae, B.; Davis, E.; Brown, D.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 49
  • DOI: 10.1073/pnas.1314576110

Massively Systematic Transcript End Readout, “MASTER”: Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields
journal, December 2015


Structural Biology of Bacterial RNA Polymerase
journal, May 2015


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex
journal, March 2002


Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex
journal, May 2002


Structure of a bacterial RNA polymerase holoenzyme open promoter complex
journal, September 2015

  • Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka
  • eLife, Vol. 4
  • DOI: 10.7554/eLife.08504

    Works referencing / citing this record:

    Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis
    journal, December 2019

    • Wan, Tao; Li, Shanren; Beltran, Daisy Guiza
    • Nucleic Acids Research, Vol. 48, Issue 2
    • DOI: 10.1093/nar/gkz1133