CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex
Abstract
A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.
- Authors:
-
- Rockefeller Univ., New York, NY (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- National Center for Research Resources (NCRR); National Institute of Biomedical Imaging and Bioengineering (NIBIB); National Institute of General Medical Sciences (NIGMS)
- OSTI Identifier:
- 1233324
- Grant/Contract Number:
- 1S10RR027037; P30-EB-009998; F32 GM103170
- Resource Type:
- Accepted Manuscript
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Volume: 4; Journal Issue: 2015; Journal ID: ISSN 2050-084X
- Publisher:
- eLife Sciences Publications, Ltd.
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Bae, Brian, Chen, James, Davis, Elizabeth, Leon, Katherine, Darst, Seth A., and Campbell, Elizabeth A. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. United States: N. p., 2015.
Web. doi:10.7554/eLife.08505.
Bae, Brian, Chen, James, Davis, Elizabeth, Leon, Katherine, Darst, Seth A., & Campbell, Elizabeth A. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. United States. https://doi.org/10.7554/eLife.08505
Bae, Brian, Chen, James, Davis, Elizabeth, Leon, Katherine, Darst, Seth A., and Campbell, Elizabeth A. Tue .
"CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex". United States. https://doi.org/10.7554/eLife.08505. https://www.osti.gov/servlets/purl/1233324.
@article{osti_1233324,
title = {CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex},
author = {Bae, Brian and Chen, James and Davis, Elizabeth and Leon, Katherine and Darst, Seth A. and Campbell, Elizabeth A.},
abstractNote = {A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.},
doi = {10.7554/eLife.08505},
journal = {eLife},
number = 2015,
volume = 4,
place = {United States},
year = {Tue Sep 08 00:00:00 EDT 2015},
month = {Tue Sep 08 00:00:00 EDT 2015}
}
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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
Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis
journal, May 2006
- Strong, M.; Sawaya, M. R.; Wang, S.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 21
Mechanism of initiation of transcription by Bacillus subtilis RNA polymerase at several promoters
journal, January 1992
- Whipple, Frederick W.; Sonenshein, Abraham L.
- Journal of Molecular Biology, Vol. 223, Issue 2
An unusual rRNA operon constellation: in Thermus thermophilus HB8 the 23S/5S rRNA operon is a separate entity from the 16S rRNA operon
journal, October 1987
- Hartmann, Roland K.; Ulbrich, Norbert; Erdmann, Volker A.
- Biochimie, Vol. 69, Issue 10
rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase
journal, June 2006
- Haugen, Shanil P.; Berkmen, Melanie B.; Ross, Wilma
- Cell, Vol. 125, Issue 6
Linking Crystallographic Model and Data Quality
journal, May 2012
- Karplus, P. A.; Diederichs, K.
- Science, Vol. 336, Issue 6084
The regulation of bacterial transcription initiation
journal, January 2004
- Browning, Douglas F.; Busby, Stephen J. W.
- Nature Reviews Microbiology, Vol. 2, Issue 1
[10] Footprinting protein-DNA complexes in Vivo
book, January 1991
- Sasse-Dwight, Selina; Gralla, Jay D.
- Protein \3- DNA Interactions
Structure of a Ternary Transcription Activation Complex
journal, January 2004
- Jain, Deepti; Nickels, Bryce E.; Sun, Li
- Molecular Cell, Vol. 13, Issue 1
Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective
journal, September 2014
- Feklístov, Andrey; Sharon, Brian D.; Darst, Seth A.
- Annual Review of Microbiology, Vol. 68, Issue 1
The α-helix dipole and the properties of proteins
journal, June 1978
- Hol, W. G. J.; van Duijnen, P. T.; Berendsen, H. J. C.
- Nature, Vol. 273, Issue 5662
Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis
journal, August 2012
- Weiss, L. A.; Harrison, P. G.; Nickels, B. E.
- Journal of Bacteriology, Vol. 194, Issue 20
Improved R-factors for diffraction data analysis in macromolecular crystallography
journal, April 1997
- Diederichs, Kay; Karplus, P. Andrew
- Nature Structural Biology, Vol. 4, Issue 4
Purification and Initial Characterization of RNA Polymerase from Thermus thermophilus Strain HB8 †
journal, November 2000
- Xue, Yu; Hogan, Brian P.; Erie, Dorothy A.
- Biochemistry, Vol. 39, Issue 46
RNA Polymerases from Bacillus subtilisand Escherichia coli Differ in Recognition of Regulatory Signals In Vitro
journal, January 2000
- Artsimovitch, Irina; Svetlov, Vladimir; Anthony, Larry
- Journal of Bacteriology, Vol. 182, Issue 21
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
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
journal, September 1998
- Brünger, A. T.; Adams, P. D.; Clore, G. M.
- Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
journal, September 2015
- Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka
- eLife, Vol. 4
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
A Basal Promoter Element Recognized by Free RNA Polymerase σ Subunit Determines Promoter Recognition by RNA Polymerase Holoenzyme
journal, July 2006
- Feklistov, Andrey; Barinova, Nataliya; Sevostyanova, Anastasiya
- Molecular Cell, Vol. 23, Issue 1
Structural Basis of Transcription: RNA Polymerase II at 2.8 Angstrom Resolution
journal, April 2001
- Cramer, P.
- Science, Vol. 292, Issue 5523
Transcription activation at Class I CAP-dependent promoters
journal, May 1993
- Ebright, Richard H.
- Molecular Microbiology, Vol. 8, Issue 5
Changing the mechanism of transcriptional activation by phage repressor
journal, April 1997
- Li, M.; McClure, W. R.; Susskind, M. M.
- Proceedings of the National Academy of Sciences, Vol. 94, Issue 8
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
Hierarchies of base pair preferences in the P22 ant promoter.
journal, January 1991
- Moyle, H.; Waldburger, C.; Susskind, M. M.
- Journal of Bacteriology, Vol. 173, Issue 6
Structure and function of CarD, an essential mycobacterial transcription factor
journal, July 2013
- Srivastava, D. B.; Leon, K.; Osmundson, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 31
Promoter recognition and discrimination by EsigmaS RNA polymerase
journal, November 2001
- Gaal, Tamas; Ross, Wilma; Estrem, Shawn T.
- Molecular Microbiology, Vol. 42, Issue 4
Still Looking for the Magic Spot: The Crystallographically Defined Binding Site for ppGpp on RNA Polymerase Is Unlikely to Be Responsible for rRNA Transcription Regulation
journal, March 2008
- Vrentas, Catherine E.; Gaal, Tamas; Berkmen, Melanie B.
- Journal of Molecular Biology, Vol. 377, Issue 2
Region 4 of σ as a target for transcription regulation: Region 4 of σ
journal, May 2003
- Dove, Simon L.; Darst, Seth A.; Hochschild, Ann
- Molecular Microbiology, Vol. 48, Issue 4
Distinct Functions of Regions 1.1 and 1.2 of RNA Polymerase σ Subunits from Escherichia coli and Thermus aquaticus in Transcription Initiation
journal, May 2012
- Miropolskaya, Nataliya; Ignatov, Artem; Bass, Irina
- Journal of Biological Chemistry, Vol. 287, Issue 28
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
Analysis of RNA polymerase-promoter complex formation
journal, January 2009
- Ross, Wilma; Gourse, Richard L.
- Methods, Vol. 47, Issue 1
CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence
journal, July 2009
- Stallings, Christina L.; Stephanou, Nicolas C.; Chu, Linda
- Cell, Vol. 138, Issue 1
Protein–Protein and Protein–DNA Interactions of σ70 Region 4 Involved in Transcription Activation by λcI
journal, November 2002
- Nickels, Bryce E.; Dove, Simon L.; Murakami, Katsuhiko S.
- Journal of Molecular Biology, Vol. 324, Issue 1
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction
journal, August 2010
- Westblade, Lars F.; Campbell, Elizabeth A.; Pukhrambam, Chirangini
- Nucleic Acids Research, Vol. 38, Issue 22
Structure of the Mtb CarD/RNAP β-Lobes Complex Reveals the Molecular Basis of Interaction and Presents a Distinct DNA-Binding Domain for Mtb CarD
journal, October 2013
- Gulten, Gulcin; Sacchettini, James C.
- Structure, Vol. 21, Issue 10
DNA Recognition by Proteins with the Helix-Turn-Helix Motif
journal, June 1990
- Harrison, Stephen C.; Aggarwal, Aneel K.
- Annual Review of Biochemistry, Vol. 59, Issue 1
Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007
- Krissinel, Evgeny; Henrick, Kim
- Journal of Molecular Biology, Vol. 372, Issue 3
Crystal structure of the nucleosome core particle at 2.8 Å resolution
journal, September 1997
- Luger, Karolin; Mäder, Armin W.; Richmond, Robin K.
- Nature, Vol. 389, Issue 6648
Structural Basis for Bacterial Transcription-Coupled DNA Repair
journal, February 2006
- Deaconescu, Alexandra M.; Chambers, Anna L.; Smith, Abigail J.
- Cell, Vol. 124, Issue 3
The rRNA Operons of Mycobacterium Smegmatis and Mycobacterium Tuberculosis: Comparison of Promoter Elements and of Neighbouring Upstream Genes
journal, March 1996
- Gonzalez-y-Merchand, J. A.; Colston, M. J.; Cox, R. A.
- Microbiology, Vol. 142, Issue 3
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Structural Insights into RNA Polymerase Recognition and Essential Function of Myxococcus xanthus CdnL
journal, October 2014
- Gallego-García, Aránzazu; Mirassou, Yasmina; García-Moreno, Diana
- PLoS ONE, Vol. 9, Issue 10
Super-resolution biomolecular crystallography with low-resolution data
journal, April 2010
- Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.
- Nature, Vol. 464, Issue 7292
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Activation and Repression of Transcription by Differential Contact: Two Sides of a Coin
journal, June 1998
- Roy, Siddhartha; Garges, Susan; Adhya, Sankar
- Journal of Biological Chemistry, Vol. 273, Issue 23
Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure
journal, August 2005
- Lejeune, Diane; Delsaux, Nicolas; Charloteaux, Benoît
- Proteins: Structure, Function, and Bioinformatics, Vol. 61, Issue 2
Works referencing / citing this record:
Local and global regulation of transcription initiation in bacteria
journal, August 2016
- Browning, Douglas F.; Busby, Stephen J. W.
- Nature Reviews Microbiology, Vol. 14, Issue 10
Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding
journal, January 2019
- Boyaci, Hande; Chen, James; Jansen, Rolf
- Nature, Vol. 565, Issue 7739
Mycobacterium tuberculosis CarD, an essential global transcriptional regulator forms amyloid-like fibrils
journal, July 2018
- Kaur, Gundeep; Kaundal, Soni; Kapoor, Srajan
- Scientific Reports, Vol. 8, Issue 1
Structures of E . coli σ S -transcription initiation complexes provide new insights into polymerase mechanism
journal, March 2016
- Liu, Bin; Zuo, Yuhong; Steitz, Thomas A.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 15
The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression
journal, November 2018
- Galburt, Eric A.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 50
Transcription initiation in mycobacteria: a biophysical perspective
journal, December 2019
- Boyaci, Hande; Saecker, Ruth M.; Campbell, Elizabeth A.
- Transcription, Vol. 11, Issue 2
Lysine acetylation of the housekeeping sigma factor enhances the activity of the RNA polymerase holoenzyme
journal, January 2020
- Kim, Ji-Eun; Choi, Joon-Sun; Kim, Jong-Seo
- Nucleic Acids Research, Vol. 48, Issue 5
Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA
journal, March 2018
- Wu, Xiaoxian; Haakonsen, Diane L.; Sanderlin, Allen G.
- Nucleic Acids Research, Vol. 46, Issue 6
Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex
journal, June 2018
- Bernal-Bernal, Diego; Abellón-Ruiz, Javier; Iniesta, Antonio A.
- Nucleic Acids Research, Vol. 46, Issue 13
CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase
journal, May 2019
- Jensen, Drake; Manzano, Ana Ruiz; Rammohan, Jayan
- Nucleic Acids Research, Vol. 47, Issue 13
Structures and mechanism of transcription initiation by bacterial ECF factors
journal, May 2019
- Fang, Chengli; Li, Lingting; Shen, Liqiang
- Nucleic Acids Research, Vol. 47, Issue 13
The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa
journal, July 2019
- Bergkessel, Megan; Babin, Brett M.; VanderVelde, David
- Molecular Microbiology, Vol. 112, Issue 3
Structural basis of transcription activation
journal, June 2016
- Feng, Y.; Zhang, Y.; Ebright, R. H.
- Science, Vol. 352, Issue 6291
Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks
journal, February 2016
- Flentie, Kelly; Garner, Ashley L.; Stallings, Christina L.
- Journal of Bacteriology, Vol. 198, Issue 9
Bacterial Survival under Extreme UV Radiation: A Comparative Proteomics Study of Rhodobacter sp., Isolated from High Altitude Wetlands in Chile
journal, June 2017
- Pérez, Vilma; Hengst, Martha; Kurte, Lenka
- Frontiers in Microbiology, Vol. 8
Identification of the Tolfenamic Acid Binding Pocket in PrbP from Liberibacter asiaticus
journal, August 2017
- Pan, Lei; Gardner, Christopher L.; Pagliai, Fernando A.
- Frontiers in Microbiology, Vol. 8
E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation
journal, December 2019
- Chen, James; Gopalkrishnan, Saumya; Chiu, Courtney
- eLife, Vol. 8
The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa
journal, December 2018
- Bergkessel, Megan; Babin, Brett M.; VanderVelde, David G.
- Molecular Microbiology