RNA polymerase

Parent categories	3. Information processing 3.2. RNA synthesis and degradation 3.2.1. Transcription
Neighbouring categories	Sigma factors
Related categories	protein-protein interactions transcription
Overview on the categories (Excel file) All genes and their categories (Excel file)

The enzyme responsible for transcription

• As an important difference as compared to the E. coli enzyme, the B. subtilis RNA polymerase has a strong preference for G as first nucleotides in transcripts PubMed

Components of the RNA polymerase

Core subunits

• RpoA: alpha subunit
• RpoB: beta subunit
• RpoC: beta' subunit

• The stoichiometry of the enzyme is RpoA(2)-RpoB-RpoC

Sigma factors

• In addition to the housekeeping sigma factor, SigA, there are several other sigma factors with different promoter recognition specifiity that are active under specific conditions (such as stress or sporulation)

Small accessory subunits

• RpoE: delta subunit
• RpoY: epsilon subunit
• YloH: omega subunit

Other interaction partners

• NusA: essential elongation factor
• NusG: transcription elongation factor PubMed
• GreA: resolves promoter proximal pausing of RNA polymerase PubMed
• CshA: DEAD-box RNA helicase PubMed
• PcrA: ATP-dependent DNA helicase PubMed

Temporary interaction partners

• Spx: transcription regulator, interacts with RpoA
• MgsR: transcription regulator orthologous to Spx, interacts with RpoA
• Btr: transcription activator PubMed
• YlyA: modulates SigG-dependent transcription PubMed

• Additional interaction partners of the RNA polymerase (no specific subunit specified)
  • HelD, TopA, CssR, RnhC, YpsC, Mfd, YpiA, YdjO, ResD PubMed

References

The structure of RNA polymerase

Katsuhiko S Murakami, Yeonoh Shin, Charles L Turnbough, Vadim Molodtsov
X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway.
Proc Natl Acad Sci U S A: 2017, 114(31);8211-8216
[PubMed:28652344] [WorldCat.org] [DOI] (I p)

Yun Yang, Vidya C Darbari, Nan Zhang, Duo Lu, Robert Glyde, Yi-Ping Wang, Jared T Winkelman, Richard L Gourse, Katsuhiko S Murakami, Martin Buck, Xiaodong Zhang
TRANSCRIPTION. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies.
Science: 2015, 349(6250);882-5
[PubMed:26293966] [WorldCat.org] [DOI] (I p)

Elecia B Johnston, Peter J Lewis, Renate Griffith
The interaction of Bacillus subtilis sigmaA with RNA polymerase.
Protein Sci: 2009, 18(11);2287-97
[PubMed:19735077] [WorldCat.org] [DOI] (I p)

Sergei Borukhov, Evgeny Nudler
RNA polymerase holoenzyme: structure, function and biological implications.
Curr Opin Microbiol: 2003, 6(2);93-100
[PubMed:12732296] [WorldCat.org] [DOI] (P p)

Katsuhiko S Murakami, Seth A Darst
Bacterial RNA polymerases: the wholo story.
Curr Opin Struct Biol: 2003, 13(1);31-9
[PubMed:12581657] [WorldCat.org] [DOI] (P p)

S A Darst
Bacterial RNA polymerase.
Curr Opin Struct Biol: 2001, 11(2);155-62
[PubMed:11297923] [WorldCat.org] [DOI] (P p)

Important original publications

Nelly Said, Tarek Hilal, Nicholas D Sunday, Ajay Khatri, Jörg Bürger, Thorsten Mielke, Georgiy A Belogurov, Bernhard Loll, Ranjan Sen, Irina Artsimovitch, Markus C Wahl
Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ.
Science: 2021, 371(6524);
[PubMed:33243850] [WorldCat.org] [DOI] (I p)

Grace E Johnson, Jean-Benoît Lalanne, Michelle L Peters, Gene-Wei Li
Functionally uncoupled transcription-translation in Bacillus subtilis.
Nature: 2020, 585(7823);124-128
[PubMed:32848247] [WorldCat.org] [DOI] (I p)

Hugo B Brandão, Payel Paul, Aafke A van den Berg, David Z Rudner, Xindan Wang, Leonid A Mirny
RNA polymerases as moving barriers to condensin loop extrusion.
Proc Natl Acad Sci U S A: 2019, 116(41);20489-20499
[PubMed:31548377] [WorldCat.org] [DOI] (I p)

Jin Park, Marta Dies, Yihan Lin, Sahand Hormoz, Stephanie E Smith-Unna, Sofia Quinodoz, María Jesús Hernández-Jiménez, Jordi Garcia-Ojalvo, James C W Locke, Michael B Elowitz
Molecular Time Sharing through Dynamic Pulsing in Single Cells.
Cell Syst: 2018, 6(2);216-229.e15
[PubMed:29454936] [WorldCat.org] [DOI] (P p)

Jatin Narula, Abhinav Tiwari, Oleg A Igoshin
Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks.
PLoS Comput Biol: 2016, 12(12);e1005267
[PubMed:27977677] [WorldCat.org] [DOI] (I e)

Cong Ma, Xiao Yang, Peter J Lewis
Bacterial Transcription Inhibitor of RNA Polymerase Holoenzyme Formation by Structure-Based Drug Design: From in Silico Screening to Validation.
ACS Infect Dis: 2016, 2(1);39-46
[PubMed:27622946] [WorldCat.org] [DOI] (I p)

Shreya Sengupta, Ranjit Kumar Prajapati, Jayanta Mukhopadhyay
Promoter Escape with Bacterial Two-component σ Factor Suggests Retention of σ Region Two in the Elongation Complex.
J Biol Chem: 2015, 290(47);28575-28583
[PubMed:26400263] [WorldCat.org] [DOI] (I p)

Evan T Graves, Camille Duboc, Jun Fan, François Stransky, Mathieu Leroux-Coyau, Terence R Strick
A dynamic DNA-repair complex observed by correlative single-molecule nanomanipulation and fluorescence.
Nat Struct Mol Biol: 2015, 22(6);452-7
[PubMed:25961799] [WorldCat.org] [DOI] (I p)

Matthew H Larson, Rachel A Mooney, Jason M Peters, Tricia Windgassen, Dhananjaya Nayak, Carol A Gross, Steven M Block, William J Greenleaf, Robert Landick, Jonathan S Weissman
A pause sequence enriched at translation start sites drives transcription dynamics in vivo.
Science: 2014, 344(6187);1042-7
[PubMed:24789973] [WorldCat.org] [DOI] (I p)

Hsin-Yi Yeh, Hsiu-Ting Hsu, Tsung-Ching Chen, Kuei-Min Chung, Kung-Ming Liou, Ban-Yang Chang
The reduction in σ-promoter recognition flexibility as induced by core RNAP is required for σ to discern the optimal promoter spacing.
Biochem J: 2013, 455(2);185-93
[PubMed:23875654] [WorldCat.org] [DOI] (I p)

Vladimir Mekler, Konstantin Severinov
Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase.
Nucleic Acids Res: 2013, 41(15);7276-85
[PubMed:23771146] [WorldCat.org] [DOI] (I p)

Ignacio J Cabrera-Ostertag, Amy T Cavanagh, Karen M Wassarman
Initiating nucleotide identity determines efficiency of RNA synthesis from 6S RNA templates in Bacillus subtilis but not Escherichia coli.
Nucleic Acids Res: 2013, 41(15);7501-11
[PubMed:23761441] [WorldCat.org] [DOI] (I p)

Benedikt M Beckmann, Philipp G Hoch, Manja Marz, Dagmar K Willkomm, Margarita Salas, Roland K Hartmann
A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.
EMBO J: 2012, 31(7);1727-38
[PubMed:22333917] [WorldCat.org] [DOI] (I p)

Olivier Delumeau, François Lecointe, Jan Muntel, Alain Guillot, Eric Guédon, Véronique Monnet, Michael Hecker, Dörte Becher, Patrice Polard, Philippe Noirot
The dynamic protein partnership of RNA polymerase in Bacillus subtilis.
Proteomics: 2011, 11(15);2992-3001
[PubMed:21710567] [WorldCat.org] [DOI] (I p)

Yoko Kusuya, Ken Kurokawa, Shu Ishikawa, Naotake Ogasawara, Taku Oshima
Transcription factor GreA contributes to resolving promoter-proximal pausing of RNA polymerase in Bacillus subtilis cells.
J Bacteriol: 2011, 193(12);3090-9
[PubMed:21515770] [WorldCat.org] [DOI] (I p)

Houra Merrikh, Cristina Machón, William H Grainger, Alan D Grossman, Panos Soultanas
Co-directional replication-transcription conflicts lead to replication restart.
Nature: 2011, 470(7335);554-7
[PubMed:21350489] [WorldCat.org] [DOI] (I p)

Shu Ishikawa, Taku Oshima, Ken Kurokawa, Yoko Kusuya, Naotake Ogasawara
RNA polymerase trafficking in Bacillus subtilis cells.
J Bacteriol: 2010, 192(21);5778-87
[PubMed:20817769] [WorldCat.org] [DOI] (I p)

Geoff P Doherty, Mark J Fogg, Anthony J Wilkinson, Peter J Lewis
Small subunits of RNA polymerase: localization, levels and implications for core enzyme composition.
Microbiology (Reading): 2010, 156(Pt 12);3532-3543
[PubMed:20724389] [WorldCat.org] [DOI] (I p)