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Select item 110770871.

RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations

Yu Bao, Xinyun Cao, Robert Landick

Nucleic Acids Res. 2024 May 8; 52(8): 4556–4574. Published online 2024 Mar 30. doi: 10.1093/nar/gkae209

PMCID:: PMC11077087

Abstract Article PDF–2.7M

Select item 81960132.

Reliable identification of protein-protein interactions by crosslinking mass spectrometry

Swantje Lenz, Ludwig R. Sinn, Francis J. O’Reilly, Lutz Fischer, Fritz Wegner, Juri Rappsilber

Nat Commun. 2021; 12: 3564. Published online 2021 Jun 11. doi: 10.1038/s41467-021-23666-z

PMCID:: PMC8196013

Abstract Article PDF–1.6M

Select item 67782013.

Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli

Xiaoli Weng, Christopher H. Bohrer, Kelsey Bettridge, Arvin Cesar Lagda, Cedric Cagliero, Ding Jun Jin, Jie Xiao

Proc Natl Acad Sci U S A. 2019 Oct 1; 116(40): 20115–20123. Published online 2019 Sep 16. doi: 10.1073/pnas.1903968116

PMCID:: PMC6778201

Abstract Article PDF–1.5M

Select item 67378934.

Maintaining Integrity Under Stress: Envelope Stress Response Regulation of Pathogenesis in Gram-Negative Bacteria

Claire L. Hews, Timothy Cho, Gary Rowley, Tracy L. Raivio

Front Cell Infect Microbiol. 2019; 9: 313. Published online 2019 Sep 4. doi: 10.3389/fcimb.2019.00313

PMCID:: PMC6737893

Abstract Article PDF–1.5M

Select item 66488965.

Structures and mechanism of transcription initiation by bacterial ECF factors

Chengli Fang, Lingting Li, Liqiang Shen, Jing Shi, Sheng Wang, Yu Feng, Yu Zhang

Nucleic Acids Res. 2019 Jul 26; 47(13): 7094–7104. Published online 2019 May 27. doi: 10.1093/nar/gkz470

PMCID:: PMC6648896

Abstract Article PDF–4.0M

Select item 59499866.

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

Abstract Article PDF–2.8M

Select item 54932967.

The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase

Tomohiro Shimada, Kan Tanaka, Akira Ishihama

PLoS One. 2017; 12(6): e0179181. Published online 2017 Jun 30. doi: 10.1371/journal.pone.0179181

PMCID:: PMC5493296

Abstract Article PDF–4.7M

Select item 54545338.

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

Abstract Article PDF–1.5M

Select item 46740769.

Regulation of Transcript Elongation

Georgiy A. Belogurov, Irina Artsimovitch

Annu Rev Microbiol. Author manuscript; available in PMC 2016 Oct 15.

Published in final edited form as: Annu Rev Microbiol. 2015 Oct 15; 69: 49–69. Published online 2015 Jun 24. doi: 10.1146/annurev-micro-091014-104047

PMCID:: PMC4674076

Abstract Article PDF–1.2M

Select item 447148110.

UvrD facilitates DNA repair by pulling RNA polymerase backwards

Vitaly Epshtein, Venu Kamarthapu, Katelyn McGary, Vladimir Svetlov, Beatrix Ueberheide, Sergey Proshkin, Alexander Mironov, Evgeny Nudler

Nature. Author manuscript; available in PMC 2015 Jun 18.

Published in final edited form as: Nature. 2014 Jan 16; 505(7483): 372–377. Published online 2014 Jan 8. doi: 10.1038/nature12928

PMCID:: PMC4471481

Abstract Article PDF–1.8M

Select item 388718211.

Antisense Oligonucleotide-stimulated Transcriptional Pausing Reveals RNA Exit Channel Specificity of RNA Polymerase and Mechanistic Contributions of NusA and RfaH

Kellie E. Kolb, Pyae P. Hein, Robert Landick

J Biol Chem. 2014 Jan 10; 289(2): 1151–1163. Published online 2013 Nov 25. doi: 10.1074/jbc.M113.521393

PMCID:: PMC3887182

Abstract Article PDF–2.3M

Select item 375475412.

Characterization of a Novel RNA Polymerase Mutant That Alters DksA Activity

Dominik Satory, Jennifer A. Halliday, Priya Sivaramakrishnan, Rhonald C. Lua, Christophe Herman

J Bacteriol. 2013 Sep; 195(18): 4187–4194. doi: 10.1128/JB.00382-13

PMCID:: PMC3754754

Abstract Article PDF–816K

Select item 361913113.

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation

Yuri A. Nedialkov, Kristopher Opron, Fadi Assaf, Irina Artsimovitch, Maria L. Kireeva, Mikhail Kashlev, Robert I. Cukier, Evgeny Nudler, Zachary F. Burton

Biochim Biophys Acta. Author manuscript; available in PMC 2014 Feb 1.

Published in final edited form as: Biochim Biophys Acta. 2013 Feb; 1829(2): 187–198. Published online 2012 Nov 30. doi: 10.1016/j.bbagrm.2012.11.005

PMCID:: PMC3619131

Abstract Article PDF–5.9M

Select item 361098514.

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

Abstract Article PDF–2.3M

Select item 318738615.

Spatial Distribution and Diffusive Motion of RNA Polymerase in Live Escherichia coli

Benjamin P. Bratton, Rachel A. Mooney, James C. Weisshaar

J Bacteriol. 2011 Oct; 193(19): 5138–5146. doi: 10.1128/JB.00198-11

PMCID:: PMC3187386

Abstract Article PDF–1.3M

Select item 316293416.

Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Christof Francke, Tom Groot Kormelink, Yanick Hagemeijer, Lex Overmars, Vincent Sluijter, Roy Moezelaar, Roland J Siezen

BMC Genomics. 2011; 12: 385. Published online 2011 Aug 1. doi: 10.1186/1471-2164-12-385

PMCID:: PMC3162934

Abstract Article PDF–1.6M

Select item 299668217.

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

Tom M. Conrad, Michael Frazier, Andrew R. Joyce, Byung-Kwan Cho, Eric M. Knight, Nathan E. Lewis, Robert Landick, Bernhard Ø. Palsson

Proc Natl Acad Sci U S A. 2010 Nov 23; 107(47): 20500–20505. Published online 2010 Nov 5. doi: 10.1073/pnas.0911253107

PMCID:: PMC2996682

Abstract Article PDF–753K

Select item 290496318.

Role of the RNA polymerase trigger loop in nucleotidyl transfer, transcript cleavage, and transcriptional pausing

Jinwei Zhang, Murali Palangat, Robert Landick

Nat Struct Mol Biol. Author manuscript; available in PMC 2010 Jul 16.

Published in final edited form as: Nat Struct Mol Biol. 2010 Jan; 17(1): 99–104. Published online 2009 Dec 6. doi: 10.1038/nsmb.1732

PMCID:: PMC2904963

Abstract Article PDF–3.9M

Select item 278433319.

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

Tom M Conrad, Andrew R Joyce, M Kenyon Applebee, Christian L Barrett, Bin Xie, Yuan Gao, Bernhard Ø Palsson

Genome Biol. 2009; 10(10): R118. Published online 2009 Oct 22. doi: 10.1186/gb-2009-10-10-r118

PMCID:: PMC2784333

Abstract Article PDF–263K

Select item 277570220.

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Brian P. Hudson, Joel Quispe, Samuel Lara-González, Younggyu Kim, Helen M. Berman, Eddy Arnold, Richard H. Ebright, Catherine L. Lawson

Proc Natl Acad Sci U S A. 2009 Nov 24; 106(47): 19830–19835. Published online 2009 Nov 10. doi: 10.1073/pnas.0908782106

PMCID:: PMC2775702

Abstract Article PDF–2.3M

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