Structural basis of ECF-σ-factor-dependent transcription initiation

Lin, Wei; Mandal, Sukhendu; Degen, David; Cho, Min Sung; Feng, Yu; Das, Kalyan; Ebright, Richard H.

doi:10.1038/s41467-019-08443-3

Title: Structural basis of ECF-σ-factor-dependent transcription initiation

Abstract

Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.

Authors:

Lin, Wei ^[1];

^[1]; Degen, David ^[1]; Cho, Min Sung ^[1]; Feng, Yu ^[1];

^[2];

^[1]

Rutgers Univ., Piscataway, NJ (United States)
Katholieke Univ. Leuven (Belgium)

Publication Date:: Tue Feb 12 00:00:00 EST 2019

Research Org.:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Org.:: National Institutes of Health (NIH)

OSTI Identifier:: 1498332

Grant/Contract Number:: GM041376

Resource Type:: Accepted Manuscript

Journal Name:: Nature Communications

Additional Journal Information:: Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: ENGLISH

Subject:: 60 APPLIED LIFE SCIENCES; Transcription; X-ray crystallography

Citation Formats


                    Lin, Wei, Mandal, Sukhendu, Degen, David, Cho, Min Sung, Feng, Yu, Das, Kalyan, and Ebright, Richard H. Structural basis of ECF-σ-factor-dependent transcription initiation.  United States: N. p., 2019. 
Web.  doi:10.1038/s41467-019-08443-3.

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                    Lin, Wei, Mandal, Sukhendu, Degen, David, Cho, Min Sung, Feng, Yu, Das, Kalyan, & Ebright, Richard H. Structural basis of ECF-σ-factor-dependent transcription initiation.  United States.  https://doi.org/10.1038/s41467-019-08443-3

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                    Lin, Wei, Mandal, Sukhendu, Degen, David, Cho, Min Sung, Feng, Yu, Das, Kalyan, and Ebright, Richard H. Tue .  
"Structural basis of ECF-σ-factor-dependent transcription initiation".  United States.  https://doi.org/10.1038/s41467-019-08443-3.  https://www.osti.gov/servlets/purl/1498332.

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@article{osti_1498332,

  title        = {Structural basis of ECF-σ-factor-dependent transcription initiation},

  author       = {Lin, Wei and Mandal, Sukhendu and Degen, David and Cho, Min Sung and Feng, Yu and Das, Kalyan and Ebright, Richard H.},

  abstractNote = {Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.},

  doi          = {10.1038/s41467-019-08443-3},

  journal      = {Nature Communications},

  number       = 1,

  volume       = 10,

  place        = {United States},

  year         = {Tue Feb 12 00:00:00 EST 2019},

  month        = {Tue Feb 12 00:00:00 EST 2019}

}

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Works referenced in this record:

Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator.
journal, January 1986

Ebright, R. H.
Proceedings of the National Academy of Sciences, Vol. 83, Issue 2
DOI: 10.1073/pnas.83.2.303

A recombinant Mycobacterium tuberculosis in vitro transcription system
journal, February 2006

Jacques, Jean-FranÃ§ois; Rodrigue, SÃ©bastien; Brzezinski, Ryszard
FEMS Microbiology Letters, Vol. 255, Issue 1
DOI: 10.1111/j.1574-6968.2005.00071.x

Near-atomic resolution visualization of human transcription promoter opening
journal, May 2016

He, Yuan; Yan, Chunli; Fang, Jie
Nature, Vol. 533, Issue 7603
DOI: 10.1038/nature17970

Mechanism of Intrinsic Transcription Termination and Antitermination
journal, April 1999

Yarnell, W. S.
Science, Vol. 284, Issue 5414
DOI: 10.1126/science.284.5414.611

The extracytoplasmic function sigma factors: role and regulation
journal, June 1998

Missiakas, Dominique; Raina, Satish
Molecular Microbiology, Vol. 28, Issue 6
DOI: 10.1046/j.1365-2958.1998.00865.x

The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family: ECF σ factor classification
journal, September 2009

Staroń, Anna; Sofia, Heidi J.; Dietrich, Sascha
Molecular Microbiology, Vol. 74, Issue 3
DOI: 10.1111/j.1365-2958.2009.06870.x

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

Lin, Wei; Mandal, Soma; Degen, David
Molecular Cell, Vol. 66, Issue 2
DOI: 10.1016/j.molcel.2017.03.001

A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding
journal, December 2001

Lim, H. M.; Lee, H. J.; Roy, S.
Proceedings of the National Academy of Sciences, Vol. 98, Issue 26
DOI: 10.1073/pnas.261517398

The complex architecture of mycobacterial promoters
journal, January 2013

Newton-Foot, Mae; Gey van Pittius, Nicolaas C.
Tuberculosis, Vol. 93, Issue 1
DOI: 10.1016/j.tube.2012.08.003

Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions.
journal, August 1994

Lonetto, M. A.; Brown, K. L.; Rudd, K. E.
Proceedings of the National Academy of Sciences, Vol. 91, Issue 16
DOI: 10.1073/pnas.91.16.7573

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors
journal, April 2017

Sineva, Elena; Savkina, Maria; Ades, Sarah E.
Current Opinion in Microbiology, Vol. 36
DOI: 10.1016/j.mib.2017.05.004

Molecular mechanism of promoter opening by RNA polymerase III
journal, January 2018

Vorländer, Matthias K.; Khatter, Heena; Wetzel, Rene
Nature, Vol. 553, Issue 7688
DOI: 10.1038/nature25440

RNA polymerase II–TFIIB structure and mechanism of transcription initiation
journal, October 2009

Kostrewa, Dirk; Zeller, Mirijam E.; Armache, Karim-Jean
Nature, Vol. 462, Issue 7271
DOI: 10.1038/nature08548

Structural basis of RNA polymerase III transcription initiation
journal, January 2018

Abascal-Palacios, Guillermo; Ramsay, Ewan Phillip; Beuron, Fabienne
Nature, Vol. 553, Issue 7688
DOI: 10.1038/nature25441

Structural basis of transcription activation
journal, June 2016

Feng, Y.; Zhang, Y.; Ebright, R. H.
Science, Vol. 352, Issue 6291
DOI: 10.1126/science.aaf4417

Structural Basis of RNA Polymerase I Transcription Initiation
journal, March 2017

Engel, Christoph; Gubbey, Tobias; Neyer, Simon
Cell, Vol. 169, Issue 1
DOI: 10.1016/j.cell.2017.03.003

Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme
journal, June 2014

Basu, Ritwika S.; Warner, Brittany A.; Molodtsov, Vadim
Journal of Biological Chemistry, Vol. 289, Issue 35
DOI: 10.1074/jbc.M114.584037

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation
journal, July 2017

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran
Molecular Cell, Vol. 67, Issue 1
DOI: 10.1016/j.molcel.2017.05.010

Structural insights into transcription initiation by yeast RNA polymerase I
journal, July 2017

Sadian, Yashar; Tafur, Lucas; Kosinski, Jan
The EMBO Journal, Vol. 36, Issue 18
DOI: 10.15252/embj.201796958

Mutational analysis of Escherichia coli σ ²⁸ and its target promoters reveals recognition of a composite −10 region, comprised of an ‘extended −10’ motif and a core −10 element
journal, May 2009

Koo, Byoung-Mo; Rhodius, Virgil A.; Campbell, Elizabeth A.
Molecular Microbiology, Vol. 72, Issue 4
DOI: 10.1111/j.1365-2958.2009.06691.x

Factors and Global Gene Regulation in Mycobacterium tuberculosis
journal, February 2004

Manganelli, R.; Proveddi, R.; Rodrigue, S.
Journal of Bacteriology, Vol. 186, Issue 4
DOI: 10.1128/JB.186.4.895-902.2004

RNA Polymerase Pausing during Initial Transcription
journal, September 2016

Duchi, Diego; Bauer, David L. V.; Fernandez, Laurent
Molecular Cell, Vol. 63, Issue 6
DOI: 10.1016/j.molcel.2016.08.011

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

Zuo, Yuhong; Steitz, Thomas A.
Molecular Cell, Vol. 58, Issue 3
DOI: 10.1016/j.molcel.2015.03.010

Structural basis for −10 promoter element melting by environmentally induced sigma factors
journal, February 2014

Campagne, Sébastien; Marsh, May E.; Capitani, Guido
Nature Structural & Molecular Biology, Vol. 21, Issue 3
DOI: 10.1038/nsmb.2777

GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides
journal, April 2014

Zhang, Yu; Degen, David; Ho, Mary X.
eLife, Vol. 3
DOI: 10.7554/eLife.02450

Structures of the RNA polymerase- 54 reveal new and conserved regulatory strategies
journal, August 2015

Yang, Y.; Darbari, V. C.; Zhang, N.
Science, Vol. 349, Issue 6250
DOI: 10.1126/science.aab1478

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I
journal, June 2017

Han, Yan; Yan, Chunli; Nguyen, Thi Hoang Duong
eLife, Vol. 6
DOI: 10.7554/eLife.27414

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

Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine
eLife, Vol. 6
DOI: 10.7554/eLife.22520

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution
journal, May 2002

Vassylyev, Dmitry G.; Sekine, Shun-ichi; Laptenko, Oleg
Nature, Vol. 417, Issue 6890
DOI: 10.1038/nature752

Structural Basis of Transcription Initiation
journal, October 2012

Zhang, Y.; Feng, Y.; Chatterjee, S.
Science, Vol. 338, Issue 6110
DOI: 10.1126/science.1227786

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation
journal, February 2015

Campagne, Sébastien; Allain, Frédéric H-T; Vorholt, Julia A.
Current Opinion in Structural Biology, Vol. 30
DOI: 10.1016/j.sbi.2015.01.006

The σ factors of Mycobacterium tuberculosis
journal, November 2006

Rodrigue, Sébastien; Provvedi, Roberta; Jacques, Pierre-Étienne
FEMS Microbiology Reviews, Vol. 30, Issue 6
DOI: 10.1111/j.1574-6976.2006.00040.x

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

Feklistov, Andrey; Darst, Seth A.
Cell, Vol. 147, Issue 6
DOI: 10.1016/j.cell.2011.10.041

The Mycobacterium tuberculosis Extracytoplasmic-Function Sigma Factor SigL Regulates Polyketide Synthases and Secreted or Membrane Proteins and Is Required for Virulence
journal, September 2005

Hahn, M. -Y.; Raman, S.; Anaya, M.
Journal of Bacteriology, Vol. 187, Issue 20
DOI: 10.1128/JB.187.20.7062-7071.2005

Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism
journal, November 2009

Liu, Xin; Bushnell, David A.; Wang, Dong
Science, Vol. 327, Issue 5962
DOI: 10.1126/science.1182015

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
DOI: 10.1146/annurev-micro-092412-155737

Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope
journal, April 2016

Helmann, John D.
Current Opinion in Microbiology, Vol. 30
DOI: 10.1016/j.mib.2016.02.002

Use of “Loss-of-Contact” Substitutions to Identify Residues Involved in an Amino Acid-Base Pair Contact: Effect of Substitution of Gln18 of Lac Repressor by Gly, Ser, and Leu
journal, October 1985

Ebright, Richard H.
Journal of Biomolecular Structure and Dynamics, Vol. 3, Issue 2
DOI: 10.1080/07391102.1985.10508417

Transcription initiation complex structures elucidate DNA opening
journal, May 2016

Plaschka, C.; Hantsche, M.; Dienemann, C.
Nature, Vol. 533, Issue 7603
DOI: 10.1038/nature17990

Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution
journal, May 2002

Murakami, Katsuhiko S.; Masuda, Shoko; Darst, Seth A.
Science, Vol. 296, Issue 5571, p. 1280-1284
DOI: 10.1126/science.1069594

Signaling diversity and evolution of extracytoplasmic function (ECF) σ factors
journal, April 2013

Mascher, Thorsten
Current Opinion in Microbiology, Vol. 16, Issue 2
DOI: 10.1016/j.mib.2013.02.001

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
DOI: 10.1073/pnas.1520555113

Optimization of recombinant Mycobacterium tuberculosis RNA polymerase expression and purification
journal, July 2014

Banerjee, Rajdeep; Rudra, Paulami; Prajapati, Ranjit Kumar
Tuberculosis, Vol. 94, Issue 4
DOI: 10.1016/j.tube.2014.03.008

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
journal, June 1989

Cunningham, B.; Wells, J.
Science, Vol. 244, Issue 4908
DOI: 10.1126/science.2471267

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

The sigma factors of Mycobacterium tuberculosis: regulation of the regulators: The σ-factors of M. tuberculosis
journal, November 2009

Sachdeva, Preeti; Misra, Richa; Tyagi, Anil K.
FEBS Journal, Vol. 277, Issue 3
DOI: 10.1111/j.1742-4658.2009.07479.x

Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase
journal, October 2016

Lerner, Eitan; Chung, SangYoon; Allen, Benjamin L.
Proceedings of the National Academy of Sciences, Vol. 113, Issue 43
DOI: 10.1073/pnas.1605038113

Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence
journal, February 2014

Manganelli, Riccardo
Microbiology Spectrum, Vol. 2, Issue 1
DOI: 10.1128/microbiolspec.MGM2-0007-2013

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process.
journal, November 1986

Kammerer, W.; Deuschle, U.; Gentz, R.
The EMBO Journal, Vol. 5, Issue 11
DOI: 10.1002/j.1460-2075.1986.tb04597.x

Delays in Tapping Energy Sources
journal, January 1975

Abelson, P. H.
Science, Vol. 187, Issue 4171
DOI: 10.1126/science.187.4171.17

enoLOGOS: a versatile web tool for energy normalized sequence logos
journal, July 2005

Workman, C. T.; Yin, Y.; Corcoran, D. L.
Nucleic Acids Research, Vol. 33, Issue Web Server
DOI: 10.1093/nar/gki439

Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
journal, January 2013

Rhodius, Virgil A.; Segall‐Shapiro, Thomas H.; Sharon, Brian D.
Molecular Systems Biology, Vol. 9, Issue 1
DOI: 10.1038/msb.2013.58

Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria
journal, April 2018

Dulin, David; Bauer, David L. V.; Malinen, Anssi M.
Nature Communications, Vol. 9, Issue 1
DOI: 10.1038/s41467-018-03902-9

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

Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex.
journal, June 1990

Zhang, X. P.; Ebright, R. H.
Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
DOI: 10.1073/pnas.87.12.4717

Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape
journal, January 2014

Pupov, Danil; Kuzin, Ivan; Bass, Irina
Nucleic Acids Research, Vol. 42, Issue 7
DOI: 10.1093/nar/gkt1384

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Otwinowski, Zbyszek; Minor, Wladek
Macromolecular Crystallography Part A, 307-326
DOI: 10.1016/S0076-6879(97)76066-X

Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures.
journal, November 1986

Deuschle, U.; Kammerer, W.; Gentz, R.
The EMBO Journal, Vol. 5, Issue 11
DOI: 10.1002/j.1460-2075.1986.tb04596.x

Supercoiling response of the lac ps promoter in vitro
journal, August 1985

Borowiec, James A.; Gralla, Jay D.
Journal of Molecular Biology, Vol. 184, Issue 4
DOI: 10.1016/0022-2836(85)90305-5

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)
journal, April 2018

Lin, Wei; Das, Kalyan; Degen, David
Molecular Cell, Vol. 70, Issue 1
DOI: 10.1016/j.molcel.2018.02.026

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation
journal, June 2018

Glyde, Robert; Ye, Fuzhou; Jovanovic, Milija
Molecular Cell, Vol. 70, Issue 6
DOI: 10.1016/j.molcel.2018.05.021

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures
journal, July 2017

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.
Nature Communications, Vol. 8, Issue 1
DOI: 10.1038/ncomms16072

PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019

Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-13641-0

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021

Tillu, Vikas A.; Rae, James; Gao, Ya
Nature Communications, Vol. 12, Issue 1
DOI: 10.1038/s41467-021-21035-4

Near-atomic resolution visualization of human transcription promoter opening
journal, May 2017

He, Yuan; Yan, Chunli; Fang, Jie
Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1
DOI: 10.1107/s0108767317097483

σ Factors and Global Gene Regulation in Mycobacterium tuberculosis
journal, April 2004

Manganelli, Riccardo; Provvedi, Roberta; Rodrigue, Sebastien
Journal of Bacteriology, Vol. 186, Issue 8
DOI: 10.1128/jb.186.8.2516.2004

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

Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
Apollo - University of Cambridge Repository
DOI: 10.17863/cam.45787

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process.
journal, November 1986

Kammerer, W.; Deuschle, U.; Gentz, R.
The EMBO Journal, Vol. 5, Issue 11
DOI: 10.1002/j.1460-2075.1986.tb04597.x

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

Feklistov, Andrey; Darst, Seth A.
Cell, Vol. 147, Issue 6
DOI: 10.1016/j.cell.2011.10.041

Structural Basis of RNA Polymerase I Transcription Initiation
journal, March 2017

Engel, Christoph; Gubbey, Tobias; Neyer, Simon
Cell, Vol. 169, Issue 1
DOI: 10.1016/j.cell.2017.03.003

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors
journal, April 2017

Sineva, Elena; Savkina, Maria; Ades, Sarah E.
Current Opinion in Microbiology, Vol. 36
DOI: 10.1016/j.mib.2017.05.004

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

Lin, Wei; Mandal, Soma; Degen, David
Molecular Cell, Vol. 66, Issue 2
DOI: 10.1016/j.molcel.2017.03.001

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation
journal, February 2015

Campagne, Sébastien; Allain, Frédéric H-T; Vorholt, Julia A.
Current Opinion in Structural Biology, Vol. 30
DOI: 10.1016/j.sbi.2015.01.006

The complex architecture of mycobacterial promoters
journal, January 2013

Newton-Foot, Mae; Gey van Pittius, Nicolaas C.
Tuberculosis, Vol. 93, Issue 1
DOI: 10.1016/j.tube.2012.08.003

A hybrid sigma subunit directs RNA polymerase to a hybrid promoter in Escherichia coli
journal, January 1995

Kumar, Ashok; Grimes, Brenda; Logan, Mary
Journal of Molecular Biology, Vol. 246, Issue 5
DOI: 10.1016/s0022-2836(05)80105-6

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

Mekler, Vladimir; Kortkhonjia, Ekaterine; Mukhopadhyay, Jayanta
Cell, Vol. 108, Issue 5
DOI: 10.1016/s0092-8674(02)00667-0

Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination
journal, March 2004

Stols, Lucy; Millard, Cynthia Sanville; Dementieva, Irina
Journal of Structural and Functional Genomics, Vol. 5, Issue 1/2
DOI: 10.1023/b:jsfg.0000029196.87615.6e

Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
journal, January 2013

Rhodius, Virgil A.; Segall‐Shapiro, Thomas H.; Sharon, Brian D.
Molecular Systems Biology, Vol. 9, Issue 1
DOI: 10.1038/msb.2013.58

RNA polymerase II–TFIIB structure and mechanism of transcription initiation
journal, October 2009

Kostrewa, Dirk; Zeller, Mirijam E.; Armache, Karim-Jean
Nature, Vol. 462, Issue 7271
DOI: 10.1038/nature08548

Transcription initiation complex structures elucidate DNA opening
journal, May 2016

Plaschka, C.; Hantsche, M.; Dienemann, C.
Nature, Vol. 533, Issue 7603
DOI: 10.1038/nature17990

Structural basis for −10 promoter element melting by environmentally induced sigma factors
journal, February 2014

Campagne, Sébastien; Marsh, May E.; Capitani, Guido
Nature Structural & Molecular Biology, Vol. 21, Issue 3
DOI: 10.1038/nsmb.2777

Identification of cancer driver genes based on nucleotide context
journal, February 2020

Dietlein, Felix; Weghorn, Donate; Taylor-Weiner, Amaro
Nature Genetics, Vol. 52, Issue 2
DOI: 10.1038/s41588-019-0572-y

The extracytoplasmic function sigma factors: role and regulation
journal, June 1998

Missiakas, Dominique; Raina, Satish
Molecular Microbiology, Vol. 28, Issue 6
DOI: 10.1046/j.1365-2958.1998.00865.x

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
DOI: 10.1073/pnas.1520555113

Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase
journal, October 2016

Lerner, Eitan; Chung, SangYoon; Allen, Benjamin L.
Proceedings of the National Academy of Sciences, Vol. 113, Issue 43
DOI: 10.1073/pnas.1605038113

A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding
journal, December 2001

Lim, H. M.; Lee, H. J.; Roy, S.
Proceedings of the National Academy of Sciences, Vol. 98, Issue 26
DOI: 10.1073/pnas.261517398

Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator.
journal, January 1986

Ebright, R. H.
Proceedings of the National Academy of Sciences, Vol. 83, Issue 2
DOI: 10.1073/pnas.83.2.303

Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex.
journal, June 1990

Zhang, X. P.; Ebright, R. H.
Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
DOI: 10.1073/pnas.87.12.4717

Region 3.2 of the σ Subunit Contributes to the Binding of the 3′-Initiating Nucleotide in the RNA Polymerase Active Center and Facilitates Promoter Clearance during Initiation
journal, May 2006

Kulbachinskiy, Andrey; Mustaev, Arkady
Journal of Biological Chemistry, Vol. 281, Issue 27
DOI: 10.1074/jbc.c600060200

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

Murakami, Katsuhiko S.
Journal of Biological Chemistry, Vol. 288, Issue 13
DOI: 10.1074/jbc.m112.430900

Transcription Factor B Contacts Promoter DNA Near the Transcription Start Site of the Archaeal Transcription Initiation Complex
journal, November 2003

Renfrow, Matthew B.; Naryshkin, Nikolai; Lewis, L. Michelle
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DOI: 10.1074/jbc.m311433200

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journal, October 1985

Ebright, Richard H.
Journal of Biomolecular Structure and Dynamics, Vol. 3, Issue 2
DOI: 10.1080/07391102.1985.10508417

enoLOGOS: a versatile web tool for energy normalized sequence logos
journal, July 2005

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DOI: 10.1093/nar/gki439

Features and development of Coot
journal, March 2010

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DOI: 10.1107/s0907444910007493

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journal, May 2009

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Molecular Microbiology, Vol. 72, Issue 4
DOI: 10.1111/j.1365-2958.2009.06691.x

A recombinant Mycobacterium tuberculosis in vitro transcription system
journal, February 2006

FEMS Microbiology Letters, Vol. 255, Issue 1
DOI: 10.1111/j.1574-6968.2005.00071.x

The sigma factors of Mycobacterium tuberculosis: regulation of the regulators: The σ-factors of M. tuberculosis
journal, November 2009

Sachdeva, Preeti; Misra, Richa; Tyagi, Anil K.
FEBS Journal, Vol. 277, Issue 3
DOI: 10.1111/j.1742-4658.2009.07479.x

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journal, November 2009

Liu, Xin; Bushnell, David A.; Wang, Dong
Science, Vol. 327, Issue 5962
DOI: 10.1126/science.1182015

Structural Basis of Transcription Initiation
journal, October 2012

Zhang, Y.; Feng, Y.; Chatterjee, S.
Science, Vol. 338, Issue 6110
DOI: 10.1126/science.1227786

Delays in Tapping Energy Sources
journal, January 1975

Abelson, P. H.
Science, Vol. 187, Issue 4171
DOI: 10.1126/science.187.4171.17

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
journal, June 1989

Cunningham, B.; Wells, J.
Science, Vol. 244, Issue 4908
DOI: 10.1126/science.2471267

Structures of the RNA polymerase- 54 reveal new and conserved regulatory strategies
journal, August 2015

Yang, Y.; Darbari, V. C.; Zhang, N.
Science, Vol. 349, Issue 6250
DOI: 10.1126/science.aab1478

Structural basis of transcription activation
journal, June 2016

Feng, Y.; Zhang, Y.; Ebright, R. H.
Science, Vol. 352, Issue 6291
DOI: 10.1126/science.aaf4417

Posttranslational Regulation of Mycobacterium tuberculosis Extracytoplasmic-Function Sigma Factor L and Roles in Virulence and in Global Regulation of Gene Expression
journal, March 2006

Dainese, E.; Rodrigue, S.; Delogu, G.
Infection and Immunity, Vol. 74, Issue 4
DOI: 10.1128/iai.74.4.2457-2461.2006

Identification of Mycobacterial Factor Binding Sites by Chromatin Immunoprecipitation Assays
journal, December 2006

Rodrigue, S.; Brodeur, J.; Jacques, P. -E.
Journal of Bacteriology, Vol. 189, Issue 5
DOI: 10.1128/jb.01371-06

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journal, September 2014

Feklístov, Andrey; Sharon, Brian D.; Darst, Seth A.
Annual Review of Microbiology, Vol. 68, Issue 1
DOI: 10.1146/annurev-micro-092412-155737

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:

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
DOI: 10.1093/nar/gkz470

Deciphering the essentiality and function of the anti‐σ ^M factors in Bacillus subtilis
journal, March 2019

Zhao, Heng; Roistacher, Daniel M.; Helmann, John D.
Molecular Microbiology, Vol. 112, Issue 2
DOI: 10.1111/mmi.14216

Where to begin? Sigma factors and the selectivity of transcription initiation in bacteria
journal, June 2019

Helmann, John D.
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DOI: 10.1111/mmi.14309

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journal, December 2019

Xu, Juncao; Cui, Kaijie; Shen, Liqiang
eLife, Vol. 8
DOI: 10.7554/elife.50928

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription
journal, March 2020

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DOI: 10.1073/pnas.1920747117

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
DOI: 10.1093/nar/gkz470

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All organisms—bacteria, archaea, and eukaryotes—have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. In this paper, we report four sets of crystal structures ofmore »« less
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Title: Structural basis of ECF-σ-factor-dependent transcription initiation

Abstract

Citation Formats

Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator. journal, January 1986

A recombinant Mycobacterium tuberculosis in vitro transcription system journal, February 2006

Near-atomic resolution visualization of human transcription promoter opening journal, May 2016

Mechanism of Intrinsic Transcription Termination and Antitermination journal, April 1999

The extracytoplasmic function sigma factors: role and regulation journal, June 1998

The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family: ECF σ factor classification journal, September 2009

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

A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding journal, December 2001

The complex architecture of mycobacterial promoters journal, January 2013

Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions. journal, August 1994

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors journal, April 2017

Molecular mechanism of promoter opening by RNA polymerase III journal, January 2018

RNA polymerase II–TFIIB structure and mechanism of transcription initiation journal, October 2009

Structural basis of RNA polymerase III transcription initiation journal, January 2018

Structural basis of transcription activation journal, June 2016

Structural Basis of RNA Polymerase I Transcription Initiation journal, March 2017

Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme journal, June 2014

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation journal, July 2017

Structural insights into transcription initiation by yeast RNA polymerase I journal, July 2017

Mutational analysis of Escherichia coli σ 28 and its target promoters reveals recognition of a composite −10 region, comprised of an ‘extended −10’ motif and a core −10 element journal, May 2009

Factors and Global Gene Regulation in Mycobacterium tuberculosis journal, February 2004

RNA Polymerase Pausing during Initial Transcription journal, September 2016

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

Structural basis for −10 promoter element melting by environmentally induced sigma factors journal, February 2014

GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides journal, April 2014

Structures of the RNA polymerase- 54 reveal new and conserved regulatory strategies journal, August 2015

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I journal, June 2017

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

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution journal, May 2002

Structural Basis of Transcription Initiation journal, October 2012

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation journal, February 2015

The σ factors of Mycobacterium tuberculosis journal, November 2006

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

The Mycobacterium tuberculosis Extracytoplasmic-Function Sigma Factor SigL Regulates Polyketide Synthases and Secreted or Membrane Proteins and Is Required for Virulence journal, September 2005

Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism journal, November 2009

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective journal, September 2014

Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope journal, April 2016

Use of “Loss-of-Contact” Substitutions to Identify Residues Involved in an Amino Acid-Base Pair Contact: Effect of Substitution of Gln18 of Lac Repressor by Gly, Ser, and Leu journal, October 1985

Transcription initiation complex structures elucidate DNA opening journal, May 2016

Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution journal, May 2002

Signaling diversity and evolution of extracytoplasmic function (ECF) σ factors journal, April 2013

Structures of E . coli σ S -transcription initiation complexes provide new insights into polymerase mechanism journal, March 2016

Optimization of recombinant Mycobacterium tuberculosis RNA polymerase expression and purification journal, July 2014

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis journal, June 1989

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

The sigma factors of Mycobacterium tuberculosis: regulation of the regulators: The σ-factors of M. tuberculosis journal, November 2009

Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase journal, October 2016

Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence journal, February 2014

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. journal, November 1986

Delays in Tapping Energy Sources journal, January 1975

enoLOGOS: a versatile web tool for energy normalized sequence logos journal, July 2005

Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters journal, January 2013

Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria journal, April 2018

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

Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex. journal, June 1990

Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape journal, January 2014

[20] Processing of X-ray diffraction data collected in oscillation mode book, January 1997

Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. journal, November 1986

Supercoiling response of the lac ps promoter in vitro journal, August 1985

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3) journal, April 2018

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation journal, June 2018

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures journal, July 2017

PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome journal, December 2019

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation journal, February 2021

Near-atomic resolution visualization of human transcription promoter opening journal, May 2017

σ Factors and Global Gene Regulation in Mycobacterium tuberculosis journal, April 2004

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

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. journal, November 1986

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

Structural Basis of RNA Polymerase I Transcription Initiation journal, March 2017

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors journal, April 2017

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

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation journal, February 2015

The complex architecture of mycobacterial promoters journal, January 2013

A hybrid sigma subunit directs RNA polymerase to a hybrid promoter in Escherichia coli journal, January 1995

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

Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination journal, March 2004

Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator.
journal, January 1986

A recombinant Mycobacterium tuberculosis in vitro transcription system
journal, February 2006

Near-atomic resolution visualization of human transcription promoter opening
journal, May 2016

Mechanism of Intrinsic Transcription Termination and Antitermination
journal, April 1999

The extracytoplasmic function sigma factors: role and regulation
journal, June 1998

The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family: ECF σ factor classification
journal, September 2009

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

A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding
journal, December 2001

The complex architecture of mycobacterial promoters
journal, January 2013

Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions.
journal, August 1994

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors
journal, April 2017

Molecular mechanism of promoter opening by RNA polymerase III
journal, January 2018

RNA polymerase II–TFIIB structure and mechanism of transcription initiation
journal, October 2009

Structural basis of RNA polymerase III transcription initiation
journal, January 2018

Structural basis of transcription activation
journal, June 2016

Structural Basis of RNA Polymerase I Transcription Initiation
journal, March 2017

Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme
journal, June 2014

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation
journal, July 2017

Structural insights into transcription initiation by yeast RNA polymerase I
journal, July 2017

Mutational analysis of Escherichia coli σ ²⁸ and its target promoters reveals recognition of a composite −10 region, comprised of an ‘extended −10’ motif and a core −10 element
journal, May 2009

Factors and Global Gene Regulation in Mycobacterium tuberculosis
journal, February 2004

RNA Polymerase Pausing during Initial Transcription
journal, September 2016

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

Structural basis for −10 promoter element melting by environmentally induced sigma factors
journal, February 2014

GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides
journal, April 2014

Structures of the RNA polymerase- 54 reveal new and conserved regulatory strategies
journal, August 2015

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I
journal, June 2017

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

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution
journal, May 2002

Structural Basis of Transcription Initiation
journal, October 2012

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation
journal, February 2015

The σ factors of Mycobacterium tuberculosis
journal, November 2006

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

The Mycobacterium tuberculosis Extracytoplasmic-Function Sigma Factor SigL Regulates Polyketide Synthases and Secreted or Membrane Proteins and Is Required for Virulence
journal, September 2005

Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism
journal, November 2009

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective
journal, September 2014

Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope
journal, April 2016

Use of “Loss-of-Contact” Substitutions to Identify Residues Involved in an Amino Acid-Base Pair Contact: Effect of Substitution of Gln18 of Lac Repressor by Gly, Ser, and Leu
journal, October 1985

Transcription initiation complex structures elucidate DNA opening
journal, May 2016

Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution
journal, May 2002

Signaling diversity and evolution of extracytoplasmic function (ECF) σ factors
journal, April 2013

Structures of E . coli σ ^S -transcription initiation complexes provide new insights into polymerase mechanism
journal, March 2016

Optimization of recombinant Mycobacterium tuberculosis RNA polymerase expression and purification
journal, July 2014

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
journal, June 1989

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

The sigma factors of Mycobacterium tuberculosis: regulation of the regulators: The σ-factors of M. tuberculosis
journal, November 2009

Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase
journal, October 2016

Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence
journal, February 2014

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process.
journal, November 1986

Delays in Tapping Energy Sources
journal, January 1975

enoLOGOS: a versatile web tool for energy normalized sequence logos
journal, July 2005

Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
journal, January 2013

Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria
journal, April 2018

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

Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex.
journal, June 1990

Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape
journal, January 2014

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures.
journal, November 1986

Supercoiling response of the lac ps promoter in vitro
journal, August 1985

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)
journal, April 2018

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation
journal, June 2018

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures
journal, July 2017

PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021

Near-atomic resolution visualization of human transcription promoter opening
journal, May 2017

σ Factors and Global Gene Regulation in Mycobacterium tuberculosis
journal, April 2004

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

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process.
journal, November 1986

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

Structural Basis of RNA Polymerase I Transcription Initiation
journal, March 2017

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors
journal, April 2017

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

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation
journal, February 2015

The complex architecture of mycobacterial promoters
journal, January 2013

A hybrid sigma subunit directs RNA polymerase to a hybrid promoter in Escherichia coli
journal, January 1995

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

Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination
journal, March 2004

Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
journal, January 2013

RNA polymerase II–TFIIB structure and mechanism of transcription initiation
journal, October 2009

Transcription initiation complex structures elucidate DNA opening
journal, May 2016