Difference between revisions of "RNA polymerase"

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|Related=
 
|Related=
 
* [[protein-protein interactions]]
 
* [[protein-protein interactions]]
 +
* [[transcription]]
 
}}
 
}}
 
__TOC__
 
__TOC__
 
<br><br><br><br><br>
 
<br><br><br><br><br>
−
 
  
 
=='''The enzyme responsible for [[transcription]]'''==
 
=='''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|23761441}}
  
 
==Components of the RNA polymerase==
 
==Components of the RNA polymerase==
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===Small accessory subunits===
 
===Small accessory subunits===
 
* [[RpoE]]: delta subunit
 
* [[RpoE]]: delta subunit
 +
* [[RpoY]]: epsilon subunit
 
* [[YloH]]: omega subunit
 
* [[YloH]]: omega subunit
  
−
===Other temporary components===
+
===Other interaction partners===
 
* [[NusA]]: essential elongation factor
 
* [[NusA]]: essential elongation factor
 +
* [[NusG]]: transcription elongation factor {{PubMed|36745813}}
 +
* [[GreA]]: resolves promoter proximal pausing of RNA polymerase {{PubMed|21515770}}
 +
* [[CshA]]: [[DEAD-box RNA helicases|DEAD-box RNA helicase]] {{PubMed|21710567}}
 +
* [[PcrA]]: ATP-dependent DNA helicase {{PubMed|24147116,21710567}}
 +
 +
===Temporary interaction partners===
 +
* [[Spx]]: transcription regulator, interacts with [[RpoA]]
 +
* [[MgsR]]: transcription regulator orthologous to [[Spx]], interacts with [[RpoA]]
 +
* [[Btr]]: transcription activator {{PubMed|22210890}}
 +
* [[YlyA]]: modulates [[SigG]]-dependent transcription {{PubMed|23678950}}
 +
 +
* '''Additional interaction partners of the RNA polymerase (no specific subunit specified)'''
 +
** [[HelD]], [[TopA]], [[CssR]], [[RnhC]], [[YpsC]], [[Mfd]], [[YpiA]], [[YdjO]], [[ResD]] {{PubMed|21710567}}
 +
 +
==Back to [[protein-protein interactions]]==
  
 
==References==
 
==References==
 
===Reviews===
 
===Reviews===
−
<pubmed> 18599813 7708009 18410247 19889534 19489723 18280161 21233849 </pubmed>
+
<pubmed> 18599813 7708009 18410247 19889534 19489723 18280161 21233849 22210308 23433801 23768203 24763425 25878038 26132790 26010401 16524917,28657884,29856930 32920946</pubmed>
  
 
===The structure of RNA polymerase===
 
===The structure of RNA polymerase===
−
<pubmed> 12732296 12581657 11297923 19735077 </pubmed>
+
<pubmed> 12732296 12581657 11297923 19735077 26293966  28652344 36745813
−
===Important original publications: {{PubMed|20817769,20724389}} ===
+
</pubmed>
 +
 
 +
=== Important original publications ===
 +
<pubmed> 21350489 21515770 22333917,20817769,20724389,21710567 23761441 23875654 23771146 24789973 25961799 26400263  27622946  27977677 29454936 31548377 32848247 33243850,36972428, 37949068 </pubmed>

Latest revision as of 17:54, 20 November 2023

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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

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

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

Back to protein-protein interactions

References

Reviews

Juha Kurkela, Julia Fredman, Tiina A Salminen, Taina Tyystjärvi
Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase.
Mol Microbiol: 2021, 115(1);1-11
[PubMed:32920946] [WorldCat.org] [DOI] (I p)

Kevin S Lang, Houra Merrikh
The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria.
Annu Rev Microbiol: 2018, 72;71-88
[PubMed:29856930] [WorldCat.org] [DOI] (I p)

Thomas Fouqueau, Fabian Blombach, Finn Werner
Evolutionary Origins of Two-Barrel RNA Polymerases and Site-Specific Transcription Initiation.
Annu Rev Microbiol: 2017, 71;331-348
[PubMed:28657884] [WorldCat.org] [DOI] (I p)

Georgiy A Belogurov, Irina Artsimovitch
Regulation of Transcript Elongation.
Annu Rev Microbiol: 2015, 69;49-69
[PubMed:26132790] [WorldCat.org] [DOI] (I p)

Nan Zhang, Martin Buck
A perspective on the enhancer dependent bacterial RNA polymerase.
Biomolecules: 2015, 5(2);1012-9
[PubMed:26010401] [WorldCat.org] [DOI] (I e)

Andy Weiss, Lindsey N Shaw
Small things considered: the small accessory subunits of RNA polymerase in Gram-positive bacteria.
FEMS Microbiol Rev: 2015, 39(4);541-54
[PubMed:25878038] [WorldCat.org] [DOI] (I p)

Nikolay Zenkin
Multiple personalities of the RNA polymerase active centre.
Microbiology (Reading): 2014, 160(Pt 7);1316-1320
[PubMed:24763425] [WorldCat.org] [DOI] (I p)

Kimberly B Decker, Deborah M Hinton
Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases.
Annu Rev Microbiol: 2013, 67;113-39
[PubMed:23768203] [WorldCat.org] [DOI] (I p)

Katelyn McGary, Evgeny Nudler
RNA polymerase and the ribosome: the close relationship.
Curr Opin Microbiol: 2013, 16(2);112-7
[PubMed:23433801] [WorldCat.org] [DOI] (I p)

Lakshminarayan M Iyer, L Aravind
Insights from the architecture of the bacterial transcription apparatus.
J Struct Biol: 2012, 179(3);299-319
[PubMed:22210308] [WorldCat.org] [DOI] (I p)

Finn Werner, Dina Grohmann
Evolution of multisubunit RNA polymerases in the three domains of life.
Nat Rev Microbiol: 2011, 9(2);85-98
[PubMed:21233849] [WorldCat.org] [DOI] (I p)

Vladimir Svetlov, Evgeny Nudler
Macromolecular micromovements: how RNA polymerase translocates.
Curr Opin Struct Biol: 2009, 19(6);701-7
[PubMed:19889534] [WorldCat.org] [DOI] (I p)

Evgeny Nudler
RNA polymerase active center: the molecular engine of transcription.
Annu Rev Biochem: 2009, 78;335-61
[PubMed:19489723] [WorldCat.org] [DOI] (I p)

P J Lewis, G P Doherty, J Clarke
Transcription factor dynamics.
Microbiology (Reading): 2008, 154(Pt 7);1837-1844
[PubMed:18599813] [WorldCat.org] [DOI] (P p)

Kristina M Herbert, William J Greenleaf, Steven M Block
Single-molecule studies of RNA polymerase: motoring along.
Annu Rev Biochem: 2008, 77;149-76
[PubMed:18410247] [WorldCat.org] [DOI] (P p)

Sergei Borukhov, Evgeny Nudler
RNA polymerase: the vehicle of transcription.
Trends Microbiol: 2008, 16(3);126-34
[PubMed:18280161] [WorldCat.org] [DOI] (P p)

Vincent Trinh, Marie-France Langelier, Jacques Archambault, Benoit Coulombe
Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
Microbiol Mol Biol Rev: 2006, 70(1);12-36
[PubMed:16524917] [WorldCat.org] [DOI] (P p)

W G Haldenwang
The sigma factors of Bacillus subtilis.
Microbiol Rev: 1995, 59(1);1-30
[PubMed:7708009] [WorldCat.org] [DOI] (P p)


The structure of RNA polymerase

Rishi K Vishwakarma, M Zuhaib Qayyum, Paul Babitzke, Katsuhiko S Murakami
Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase.
Proc Natl Acad Sci U S A: 2023, 120(7);e2218516120
[PubMed:36745813] [WorldCat.org] [DOI] (I p)

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

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