Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.
- Authors:
-
- The Rockefeller Univ., New York, NY (United States)
- Saint Louis Univ. School of Medicine, St. Louis, MO (United States)
- Univ. of Wisconsin-Madison, Madison, WI (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1223793
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Volume: 4; 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, Feklistov, Andrey, Lass-Napiorkowska, Agnieszka, Landick, Robert, and Darst, Seth A. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. United States: N. p., 2015.
Web. doi:10.7554/eLife.08504.
Bae, Brian, Feklistov, Andrey, Lass-Napiorkowska, Agnieszka, Landick, Robert, & Darst, Seth A. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. United States. https://doi.org/10.7554/eLife.08504
Bae, Brian, Feklistov, Andrey, Lass-Napiorkowska, Agnieszka, Landick, Robert, and Darst, Seth A. Tue .
"Structure of a bacterial RNA polymerase holoenzyme open promoter complex". United States. https://doi.org/10.7554/eLife.08504. https://www.osti.gov/servlets/purl/1223793.
@article{osti_1223793,
title = {Structure of a bacterial RNA polymerase holoenzyme open promoter complex},
author = {Bae, Brian and Feklistov, Andrey and Lass-Napiorkowska, Agnieszka and Landick, Robert and Darst, Seth A.},
abstractNote = {Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.},
doi = {10.7554/eLife.08504},
journal = {eLife},
number = ,
volume = 4,
place = {United States},
year = {Tue Sep 08 00:00:00 EDT 2015},
month = {Tue Sep 08 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
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
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
journal, September 2012
- Adelman, Karen; Lis, John T.
- Nature Reviews Genetics, Vol. 13, Issue 10
Topological unwinding of strong and weak promoters by RNA polymerase
journal, June 1987
- Amouyal, M.; Buc, H.
- Journal of Molecular Biology, Vol. 195, Issue 4
CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex
journal, September 2015
- Bae, Brian; Chen, James; Davis, Elizabeth
- eLife, Vol. 4
Region 2.5 of the Escherichia coli RNA polymerase σ70 subunit is responsible for the recognition of the 'extended −10' motif at promoters
journal, July 1997
- Barne, Kerry A.; Bown, Jon A.; Busby, Stephen J. W.
- The EMBO Journal, Vol. 16, Issue 13
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
Nucleosomes Unfold Completely at a Transcriptionally Active Promoter
journal, June 2003
- Boeger, Hinrich; Griesenbeck, Joachim; Strattan, J. Seth
- Molecular Cell, Vol. 11, Issue 6
C-h⋯π-interactions in proteins
journal, March 2001
- Brandl, Maria; Weiss, Manfred S.; Jabs, Andreas
- Journal of Molecular Biology, Vol. 307, Issue 1
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
Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps
journal, May 1985
- Buc, Henri; McClure, William R.
- Biochemistry, Vol. 24, Issue 11
Structure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit
journal, March 2002
- Campbell, Elizabeth A.; Muzzin, Oriana; Chlenov, Mark
- Molecular Cell, Vol. 9, Issue 3
DNA-melting at the Bacillus subtilis flagellin promoter nucleates near −10 and expands unidirectionally
journal, March 1997
- Chen, Ya-Fen; Helmann, John D.
- Journal of Molecular Biology, Vol. 267, Issue 1
Structural Basis of Transcription: RNA Polymerase II at 2.8 Angstrom Resolution
journal, April 2001
- Cramer, P.
- Science, Vol. 292, Issue 5523
Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the -10 region of a cognate promoter.
journal, October 1990
- Daniels, D.; Zuber, P.; Losick, R.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 20
Three-Dimensional Structure of the Tn5 Synaptic Complex Transposition Intermediate
journal, July 2000
- Davies, D. R.
- Science, Vol. 289, Issue 5476
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase
journal, April 2007
- Davis, C. A.; Bingman, C. A.; Landick, R.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 19
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
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
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 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
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
Effect of DNA bases and backbone on sigma70 holoenzyme binding and isomerization using fork junction probes
journal, June 2003
- Fenton, M. S.
- Nucleic Acids Research, Vol. 31, Issue 11
Escherichia coli promoter opening and −10 recognition: mutational analysis of σ70
journal, March 2000
- Fenton, Mike S.; Lee, Shun Jin; Gralla, Jay D.
- The EMBO Journal, Vol. 19, Issue 5
Promoter recognition and discrimination by EsigmaS RNA polymerase
journal, November 2001
- Gaal, Tamas; Ross, Wilma; Estrem, Shawn T.
- Molecular Microbiology, Vol. 42, Issue 4
Direct Detection of Abortive RNA Transcripts in Vivo
journal, May 2009
- Goldman, S. R.; Ebright, R. H.; Nickels, B. E.
- Science, Vol. 324, Issue 5929
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex
journal, May 2010
- Gries, T. J.; Kontur, W. S.; Capp, M. W.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 23
Molecular systematic studies of eubacteria, using sigma70-type sigma factors of group 1 and group 2.
journal, March 1997
- Gruber, T. M.; Bryant, D. A.
- Journal of Bacteriology, Vol. 179, Issue 5
Multiple Sigma Subunits and the Partitioning of Bacterial Transcription Space
journal, October 2003
- Gruber, Tanja M.; Gross, Carol A.
- Annual Review of Microbiology, Vol. 57, Issue 1
Structural insights into transcription initiation by RNA polymerase II
journal, December 2013
- Grünberg, Sebastian; Hahn, Steven
- Trends in Biochemical Sciences, Vol. 38, Issue 12
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
Structure and Function of Bacterial Sigma Factors
journal, June 1988
- Helmann, John D.; Chamberlin, Michael J.
- Annual Review of Biochemistry, Vol. 57, Issue 1
A Consensus Adenine at Position –11 of the Nontemplate Strand of Bacterial Promoter Is Important for Nucleation of Promoter Melting
journal, March 2006
- Heyduk, Ewa; Kuznedelov, Konstantin; Severinov, Konstantin
- Journal of Biological Chemistry, Vol. 281, Issue 18
Protein family annotation in a multiple alignment viewer
journal, March 2003
- Johnson, J. M.; Mason, K.; Moallemi, C.
- Bioinformatics, Vol. 19, Issue 4
A Promoter Melting Region in the Primary σ Factor of Bacillus subtilis
journal, February 1994
- Juang, Yue-Li; Helmann, John D.
- Journal of Molecular Biology, Vol. 235, Issue 5
Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
journal, November 2006
- Kapanidis, A. N.; Margeat, E.; Ho, S. O.
- Science, Vol. 314, Issue 5802
Linking Crystallographic Model and Data Quality
journal, May 2012
- Karplus, P. A.; Diederichs, K.
- Science, Vol. 336, Issue 6084
Genetic evidence that RNA polymerase associated with sigma A factor uses a sporulation-specific promoter in Bacillus subtilis.
journal, December 1989
- Kenney, T. J.; York, K.; Youngman, P.
- Proceedings of the National Academy of Sciences, Vol. 86, Issue 23
Mechanism of ATP-Dependent Promoter Melting by Transcription Factor IIH
journal, May 2000
- Kim, T.
- Science, Vol. 288, Issue 5470
Kinetics of promoter escape by bacterial RNA polymerase: effects of promoter contacts and transcription bubble collapse
journal, September 2014
- Ko, Je; Heyduk, Tomasz
- Biochemical Journal, Vol. 463, Issue 1
Solute Probes of Conformational Changes in Open Complex (RP o ) Formation by Escherichia coli RNA Polymerase at the λP R Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RP o †
journal, February 2006
- Kontur, Wayne S.; Saecker, Ruth M.; Davis, Caroline A.
- Biochemistry, Vol. 45, Issue 7
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
Global Regulation of Promoter Melting in Naive Lymphocytes
journal, May 2013
- Kouzine, Fedor; Wojtowicz, Damian; Yamane, Arito
- Cell, Vol. 153, Issue 5
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
Molecular Evolution of Multisubunit RNA Polymerases: Sequence Analysis
journal, January 2010
- Lane, William J.; Darst, Seth A.
- Journal of Molecular Biology, Vol. 395, Issue 4
Crystal Structure of a Human Alkylbase-DNA Repair Enzyme Complexed to DNA
journal, October 1998
- Lau, Albert Y.; Schärer, Orlando D.; Samson, Leona
- Cell, Vol. 95, Issue 2
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
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
The sigma 70 family: sequence conservation and evolutionary relationships.
journal, June 1992
- Lonetto, M.; Gribskov, M.; Gross, C. A.
- Journal of Bacteriology, Vol. 174, Issue 12
Crystal Structure of a σ70 Subunit Fragment from E. coli RNA Polymerase
journal, October 1996
- Malhotra, Arun; Severinova, Elena; Darst, Seth A.
- Cell, Vol. 87, Issue 1
Rate-limiting steps in RNA chain initiation.
journal, October 1980
- McClure, W. R.
- Proceedings of the National Academy of Sciences, Vol. 77, Issue 10
Mechanism and Control of Transcription Initiation in Prokaryotes
journal, June 1985
- McClure, W. R.
- Annual Review of Biochemistry, Vol. 54, Issue 1
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Interaction of Escherichia coli RNA Polymerase σ 70 Subunit with Promoter Elements in the Context of Free σ 70 , RNA Polymerase Holoenzyme, and the β′-σ 70 Complex
journal, October 2010
- Mekler, Vladimir; Pavlova, Olga; Severinov, Konstantin
- Journal of Biological Chemistry, Vol. 286, Issue 1
Location of close contacts between Escherichia coli RNA polymerase and guanine residues at promoters either with or without consensus -35 region sequences
journal, February 1993
- Minchin, S.; Busby, S.
- Biochemical Journal, Vol. 289, Issue 3
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
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
Crystallographic Analysis of Thermus aquaticus RNA Polymerase Holoenzyme and a Holoenzyme???Promoter DNA Complex
journal, January 2003
- Murakami, Katsuhiko S.; Masuda, Shoko; Darst, Seth A.
- Methods in Enzymology, Vol. 370, p. 42-53
Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex
journal, May 2002
- Murakami, K. S.
- Science, Vol. 296, Issue 5571
The interaction between 70 and the -flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation
journal, March 2005
- Nickels, B. E.; Garrity, S. J.; Mekler, V.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 12
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complex
journal, June 2000
- Panaghie, Gianina; Aiyar, Sarah E.; Bobb, Kathryn L.
- Journal of Molecular Biology, Vol. 299, Issue 5
rRNA Transcription in Escherichia coli
journal, December 2004
- Paul, Brian J.; Ross, Wilma; Gaal, Tamas
- Annual Review of Genetics, Vol. 38, Issue 1
Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching
journal, November 2006
- Revyakin, A.; Liu, C.; Ebright, R. H.
- Science, Vol. 314, Issue 5802
BIOCHEMISTRY: RNA Polymerase, a Scrunching Machine
journal, November 2006
- Roberts, J. W.
- Science, Vol. 314, Issue 5802
Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the λPR promoter
journal, July 1984
- Roe, Jung-Hye; Burgess, Richard R.; Record, M. Thomas
- Journal of Molecular Biology, Vol. 176, Issue 4
Analysis of RNA polymerase-promoter complex formation
journal, January 2009
- Ross, Wilma; Gourse, Richard L.
- Methods, Vol. 47, Issue 1
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
Kinetic Studies and Structural Models of the Association of E.coli σ70 RNA Polymerase with the λPR Promoter: Large Scale Conformational Changes in Forming the Kinetically Significant Intermediates
journal, June 2002
- Saecker, Ruth M.; Tsodikov, Oleg V.; McQuade, Kristi L.
- Journal of Molecular Biology, Vol. 319, Issue 3
Structure and function of the initially transcribing RNA polymerase II–TFIIB complex
journal, November 2012
- Sainsbury, Sarah; Niesser, Jürgen; Cramer, Patrick
- Nature, Vol. 493, Issue 7432
Topography of intermediates in transcription initiation of E.coli.
journal, July 1990
- Schickor, P.; Metzger, W.; Werel, W.
- The EMBO Journal, Vol. 9, Issue 7
Evidence for a Tyrosine–Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA
journal, January 2009
- Schroeder, Lisa A.; Gries, Theodore J.; Saecker, Ruth M.
- Journal of Molecular Biology, Vol. 385, Issue 2
Super-resolution biomolecular crystallography with low-resolution data
journal, April 2010
- Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.
- Nature, Vol. 464, Issue 7292
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
Escherichia coli σ 70 senses sequence and conformation of the promoter spacer region
journal, March 2011
- Singh, Shivani S.; Typas, Athanasios; Hengge, Regine
- Nucleic Acids Research, Vol. 39, Issue 12
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
Different Roles for Basic and Aromatic Amino Acids in Conserved Region 2 of Escherichia coli ς 70 in the Nucleation and Maintenance of the Single-stranded DNA Bubble in Open RNA Polymerase-Promoter Complexes
journal, July 2001
- Tomsic, Mark; Tsujikawa, Laura; Panaghie, Gianina
- Journal of Biological Chemistry, Vol. 276, Issue 34
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
Structural basis for transcription elongation by bacterial RNA polymerase
journal, June 2007
- Vassylyev, Dmitry G.; Vassylyeva, Marina N.; Perederina, Anna
- Nature, Vol. 448, Issue 7150
Changes in conserved region 2 of Escherichia coli σ70 affecting promoter recognition
journal, September 1990
- Waldburger, Carey; Gardella, Thomas; Wong, Rex
- Journal of Molecular Biology, Vol. 215, Issue 2
Damage Detection and Base Flipping in Direct DNA Alkylation Repair
journal, February 2009
- Yang, Cai-Guang; Garcia, Kristel; He, Chuan
- ChemBioChem, Vol. 10, Issue 3
Duplex interrogation by a direct DNA repair protein in search of base damage
journal, June 2012
- Yi, Chengqi; Chen, Baoen; Qi, Bo
- Nature Structural & Molecular Biology, Vol. 19, Issue 7
A new basal promoter element recognized by RNA polymerase core enzyme: Novel class of bacterial promoters
journal, July 2011
- Yuzenkova, Yulia; Tadigotla, Vasisht R.; Severinov, Konstantin
- The EMBO Journal, Vol. 30, Issue 18
Structural Basis of Transcription Initiation
journal, October 2012
- Zhang, Y.; Feng, Y.; Chatterjee, S.
- Science, Vol. 338, Issue 6110
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
Conformational exchange in the potassium channel blocker ShK
journal, December 2019
- Iwakawa, Naoto; Baxter, Nicola J.; Wai, Dorothy C. C.
- Scientific Reports, Vol. 9, Issue 1
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
Works referencing / citing this record:
Transcription initiation complex structures elucidate DNA opening
journal, May 2016
- Plaschka, C.; Hantsche, M.; Dienemann, C.
- Nature, Vol. 533, Issue 7603
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
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
Structural basis of ECF-σ-factor-dependent transcription initiation
journal, February 2019
- Lin, Wei; Mandal, Sukhendu; Degen, David
- Nature Communications, Vol. 10, Issue 1
Structural basis for transcription initiation by bacterial ECF σ factors
journal, March 2019
- Li, Lingting; Fang, Chengli; Zhuang, Ningning
- Nature Communications, Vol. 10, Issue 1
Target preference of Type III-A CRISPR-Cas complexes at the transcription bubble
journal, July 2019
- Liu, Tina Y.; Liu, Jun-Jie; Aditham, Abhishek J.
- Nature Communications, Vol. 10, Issue 1
Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation
journal, January 2018
- Roy, Neeladri Sekhar; Debnath, Subrata; Chakraborty, Abhijit
- Physical Chemistry Chemical Physics, Vol. 20, Issue 14
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
Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin
journal, January 2019
- Braffman, Nathaniel R.; Piscotta, Frank J.; Hauver, Jesse
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 4
RbpA relaxes promoter selectivity of M. tuberculosis RNA polymerase
journal, August 2018
- Sudalaiyadum Perumal, Ayyappasamy; Vishwakarma, Rishi Kishore; Hu, Yangbo
- Nucleic Acids Research
Active site closure stabilizes the backtracked state of RNA polymerase
journal, September 2018
- Turtola, Matti; Mäkinen, Janne J.; Belogurov, Georgiy A.
- Nucleic Acids Research
Structural basis of σ appropriation
journal, August 2019
- Shi, Jing; Wen, Aijia; Zhao, Minxing
- Nucleic Acids Research, Vol. 47, Issue 17
Active site closure stabilizes the backtracked state of RNA polymerase
journal, September 2018
- Turtola, Matti; Mäkinen, Janne J.; Belogurov, Georgiy A.
- Nucleic Acids Research
Reaction mechanisms of Pol IV, RDR2 and DCL3 drive RNA channeling in the siRNA-directed DNA methylation pathway
journal, June 2019
- Singh, Jasleen; Mishra, Vibhor; Wang, Feng
- Molecular Cell
Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7
journal, October 2019
- Ye, Fuzhou; Kotta-Loizou, Ioly; Jovanovic, Milija
- eLife
Where to begin? Sigma factors and the selectivity of transcription initiation in bacteria
journal, June 2019
- Helmann, John D.
- Molecular Microbiology, Vol. 112, Issue 2
Single-molecule analysis reveals the mechanism of transcription activation in M. tuberculosis
journal, May 2018
- Vishwakarma, Rishi Kishore; Cao, Anne-Marinette; Morichaud, Zakia
- Science Advances, Vol. 4, Issue 5
Structural basis of transcription activation
journal, June 2016
- Feng, Y.; Zhang, Y.; Ebright, R. H.
- Science, Vol. 352, Issue 6291
RNA polymerase motions during promoter melting
journal, May 2017
- Feklistov, Andrey; Bae, Brian; Hauver, Jesse
- Science, Vol. 356, Issue 6340
Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer
journal, January 2018
- Lerner, Eitan; Cordes, Thorben; Ingargiola, Antonino
- Science, Vol. 359, Issue 6373
Ancient Transcription Factors in the News
journal, February 2019
- Artsimovitch, Irina; Knauer, Stefan H.
- mBio, Vol. 10, Issue 1
High-throughput detection of RNA processing in bacteria
journal, March 2018
- Gill, Erin E.; Chan, Luisa S.; Winsor, Geoffrey L.
- BMC Genomics, Vol. 19, Issue 1
Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts
journal, February 2018
- Boyaci, Hande; Chen, James; Lilic, Mirjana
- eLife, Vol. 7
The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand
journal, May 2018
- Zuber, Philipp K.; Artsimovitch, Irina; NandyMazumdar, Monali
- eLife, Vol. 7
E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation
journal, December 2019
- Chen, James; Gopalkrishnan, Saumya; Chiu, Courtney
- eLife, Vol. 8
Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway
journal, August 2019
- Singh, Jasleen; Mishra, Vibhor; Wang, Feng
- Molecular Cell, Vol. 75, Issue 3
Molecular insight into RNA polymerase I promoter recognition and promoter melting
journal, December 2019
- Sadian, Yashar; Baudin, Florence; Tafur, Lucas
- Nature Communications, Vol. 10, Issue 1
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
Exploitation of the Escherichia coli lac operon promoter for controlled recombinant protein production
journal, April 2019
- Browning, Douglas F.; Godfrey, Rita E.; Richards, Kirsty L.
- Biochemical Society Transactions, Vol. 47, Issue 2
Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example
journal, March 2018
- Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon
- The Journal of Chemical Physics, Vol. 148, Issue 12
Transcription initiation in mycobacteria: a biophysical perspective
journal, December 2019
- Boyaci, Hande; Saecker, Ruth M.; Campbell, Elizabeth A.
- Transcription, Vol. 11, Issue 2
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
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
Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7
journal, February 2020
- Ye, Fuzhou; Kotta-Loizou, Ioly; Jovanovic, Milija
- eLife, Vol. 9
Characterizing highly dynamic conformational states: the transcription bubble in RNAP-promoter open complex as an example
journal, December 2017
- Lerner, Eitan; Ingargiola, Antonino; Weiss12/, Shimon
- The Journal of Chemical Physics
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
The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand
journal, April 2018
- Zuber, Philipp K.; Artsimovitch, Irina; Mazumdar, Monali Nandy
- eLife
Structural basis of Q-dependent transcription antitermination
journal, July 2019
- Shi, Jing; Gao, Xiang; Tian, Tongguan
- Nature Communications, Vol. 10, Issue 1
High-throughput detection of RNA processing in bacteria
text, January 2018
- Gill, Erin E.; Chan, Luisa S.; Winsor, Geoffrey L.
- BioMed Central