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Items: 1 to 20 of 131

1.
A single rare σ70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82
Melissa Arroyo-Mendoza, Alexandra Proctor, Abraham Correa-Medina, Sarah DeWolf, Meghan Wymore Brand, Virginia Rosas, Hernan Lorenzi, Michael J Wannemuehler, Gregory J Phillips, Deborah M Hinton
Nucleic Acids Res. 2024 Oct 28; 52(19): 11552–11570. Published online 2024 Sep 11. doi: 10.1093/nar/gkae773
PMCID:
PMC11514462
ArticlePDF–1.9M
2.
Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria
Zhe Sun, Alexander V. Yakhnin, Peter C. FitzGerald, Carl E. Mclntosh, Mikhail Kashlev
Nat Commun. 2021; 12: 906. Published online 2021 Feb 10. doi: 10.1038/s41467-021-21150-2
PMCID:
PMC7876045
ArticlePDF–5.7M
3.
Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA
Wooyoung Kang, Kook Sun Ha, Heesoo Uhm, Kyuhyong Park, Ja Yil Lee, Sungchul Hohng, Changwon Kang
Nat Commun. 2020; 11: 450. Published online 2020 Jan 23. doi: 10.1038/s41467-019-14200-3
PMCID:
PMC6978380
ArticlePDF–1.2M
4.
Alternative transcription cycle for bacterial RNA polymerase
Timothy T. Harden, Karina S. Herlambang, Mathew Chamberlain, Jean-Benoît Lalanne, Christopher D. Wells, Gene-Wei Li, Robert Landick, Ann Hochschild, Jane Kondev, Jeff Gelles
Nat Commun. 2020; 11: 448. Published online 2020 Jan 23. doi: 10.1038/s41467-019-14208-9
PMCID:
PMC6978322
ArticlePDF–2.0M
5.
Cryo-EM structure of Escherichia coli σ70 RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation
Anoop Narayanan, Frank S. Vago, Kunpeng Li, M. Zuhaib Qayyum, Dinesh Yernool, Wen Jiang, Katsuhiko S. Murakami
J Biol Chem. 2018 May 11; 293(19): 7367–7375. Published online 2018 Mar 26. doi: 10.1074/jbc.RA118.002161
PMCID:
PMC5949986
ArticlePDF–2.8M
6.
Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli
Paramita Sarkar, Amy Switzer, Christine Peters, Joe Pogliano, Sivaramesh Wigneshweraraj
Nucleic Acids Res. 2017 Nov 2; 45(19): 11131–11143. Published online 2017 Aug 23. doi: 10.1093/nar/gkx733
PMCID:
PMC5737641
ArticlePDF–4.0M
7.
Regulatory network structure determines patterns of intermolecular epistasis
Mato Lagator, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, Călin C Guet
eLife. 2017; 6: e28921. Published online 2017 Nov 13. doi: 10.7554/eLife.28921
PMCID:
PMC5699867
ArticlePDF–1.8M
8.
Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor
Da Shi, Dmitri Svetlov, Ruben Abagyan, Irina Artsimovitch
Nucleic Acids Res. 2017 Sep 6; 45(15): 8835–8843. Published online 2017 Jun 10. doi: 10.1093/nar/gkx523
PMCID:
PMC5587751
ArticlePDF–2.3M
9.
Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification
Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J. R. Heck
Nat Commun. 2017; 8: 15473. Published online 2017 May 19. doi: 10.1038/ncomms15473
PMCID:
PMC5454533
ArticlePDF–1.5M
10.
Metalloregulator CueR biases RNA polymerase’s kinetic sampling of dead-end or open complex to repress or activate transcription
Danya J. Martell, Chandra P. Joshi, Ahmed Gaballa, Ace George Santiago, Tai-Yen Chen, Won Jung, John D. Helmann, Peng Chen
Proc Natl Acad Sci U S A. 2015 Nov 3; 112(44): 13467–13472. Published online 2015 Oct 19. doi: 10.1073/pnas.1515231112
PMCID:
PMC4640755
ArticlePDF–1.0M
11.
The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo
Seth R Goldman, Nikhil U Nair, Christopher D Wells, Bryce E Nickels, Ann Hochschild
eLife. 2015; 4: e10514. Published online 2015 Sep 15. doi: 10.7554/eLife.10514
PMCID:
PMC4604602
ArticlePDF–2.0M
12.
Coupling of downstream RNA polymerase-promoter interactions with formation of catalytically competent transcription initiation complex
Vladimir Mekler, Leonid Minakhin, Sergei Borukhov, Arkady Mustaev, Konstantin Severinov
J Mol Biol. Author manuscript; available in PMC 2015 Dec 12.
Published in final edited form as: J Mol Biol. 2014 Dec 12; 426(24): 3973–3984. Published online 2014 Oct 13. doi: 10.1016/j.jmb.2014.10.005
PMCID:
PMC4258483
ArticlePDF–1.4M
13.
The binary protein-protein interaction landscape of Escherichia coli
Seesandra V. Rajagopala, Patricia Sikorski, Ashwani Kumar, Roberto Mosca, James Vlasblom, Roland Arnold, Jonathan Franca-Koh, Suman B. Pakala, Sadhna Phanse, Arnaud Ceol, Roman Häuser, Gabriella Siszler, Stefan Wuchty, Andrew Emili, Mohan Babu, Patrick Aloy, Rembert Pieper, Peter Uetz
Nat Biotechnol. Author manuscript; available in PMC 2014 Sep 1.
Published in final edited form as: Nat Biotechnol. 2014 Mar; 32(3): 285–290. Published online 2014 Feb 23. doi: 10.1038/nbt.2831
PMCID:
PMC4123855
ArticlePDF–1.1M
14.
In vitro characterization of 6S RNA release-defective mutants uncovers features of pRNA-dependent release from RNA polymerase in E. coli
Mariana Oviedo Ovando, Lindsay Shephard, Peter J. Unrau
RNA. 2014 May; 20(5): 670–680. doi: 10.1261/rna.036343.112
PMCID:
PMC3988568
ArticlePDF–364K
15.
Transcription Activation by Escherichia coli Rob at Class II Promoters: Protein–Protein Interactions between Rob’s N-Terminal Domain and the σ70 Subunit of RNA Polymerase
Lanyn P. Taliaferro, Edward F. Keen, III, Neus Sanchez-Alberola, Richard E. Wolf, Jr
J Mol Biol. Author manuscript; available in PMC 2013 Jun 8.
Published in final edited form as: J Mol Biol. 2012 Jun 8; 419(0): 139–157. Published online 2012 Mar 28. doi: 10.1016/j.jmb.2012.03.019
PMCID:
PMC3640845
ArticlePDF–1.8M
16.
X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme
Katsuhiko S. Murakami
J Biol Chem. 2013 Mar 29; 288(13): 9126–9134. Published online 2013 Feb 6. doi: 10.1074/jbc.M112.430900
PMCID:
PMC3610985
ArticlePDF–2.3M
17.
E. coli 6S RNA release from RNA polymerase requires σ70 ejection by scrunching and is orchestrated by a conserved RNA hairpin
Shanker Shyam S. Panchapakesan, Peter J. Unrau
RNA. 2012 Dec; 18(12): 2251–2259. doi: 10.1261/rna.034785.112
PMCID:
PMC3504675
ArticlePDF–1.5M
18.
Distinct Functions of Regions 1.1 and 1.2 of RNA Polymerase σ Subunits from Escherichia coli and Thermus aquaticus in Transcription Initiation
Nataliya Miropolskaya, Artem Ignatov, Irina Bass, Ekaterina Zhilina, Danil Pupov, Andrey Kulbachinskiy
J Biol Chem. 2012 Jul 6; 287(28): 23779–23789. Published online 2012 May 17. doi: 10.1074/jbc.M112.363242
PMCID:
PMC3390652
ArticlePDF–2.9M
19.
Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the β-subunit flap domain of Escherichia coli RNA polymerase
Kelly-Anne F. Twist, Elizabeth A. Campbell, Padraig Deighan, Sergei Nechaev, Vikas Jain, E. Peter Geiduschek, Ann Hochschild, Seth A. Darst
Proc Natl Acad Sci U S A. 2011 Dec 13; 108(50): 19961-19966. Published online 2011 Dec 1. doi: 10.1073/pnas.1113328108
PMCID:
PMC3250119
ArticlePDF–1.9M
20.
Redefining Escherichia coli σ70 Promoter Elements: −15 Motif as a Complement of the −10 Motif
Marko Djordjevic
J Bacteriol. 2011 Nov; 193(22): 6305–6314. doi: 10.1128/JB.05947-11
PMCID:
PMC3209215
ArticlePDF–797K

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