Difference between revisions of "Transcription"

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* 3.2.4. [[RNases]]
 
* 3.2.4. [[RNases]]
 
|Related=
 
|Related=
−
none
+
* [[Transcription factors and their control]]
 +
* [[sigma factors]]
 +
* [[RNA polymerase]]
 +
* [[genome-wide analyses]]
 
|}}
 
|}}
 
__TOC__
 
__TOC__
 
<br><br><br><br><br>
 
<br><br><br><br><br>
  
−
==Reviews==
+
== [http://cellpublisher.gobics.de/subtiexpress/ SubtiExpress] - A database integrating gene expression of all genes under 104 conditions ==
−
<pubmed>18599813 14527287 12455702 12213655 12073657 7708009 </pubmed>
 
  
 
== Genes in this functional category ==
 
== Genes in this functional category ==
  
−
=== Rna polymerase ===  
+
=== [[RNA polymerase]] ===  
 
* ''[[rpoA]]''
 
* ''[[rpoA]]''
 
* ''[[rpoB]]''
 
* ''[[rpoB]]''
 
* ''[[rpoC]]''
 
* ''[[rpoC]]''
 
* ''[[rpoE]]''
 
* ''[[rpoE]]''
−
* ''[[ykzG]]''
+
* ''[[rpoY]]''
 
* ''[[yloH]]''
 
* ''[[yloH]]''
  
−
=== Sigma factors ===  
+
=== [[Sigma factors]] ===  
−
* ''[[sigA]]''
+
:*[[SigA]]: housekeeping sigma factor 
−
* ''[[sigB]]''
+
:*[[SigB]]: general stress sigma factor
−
* ''[[sigD]]''
+
:*[[SigD]]: sigma factor for chemotaxis and motility genes
−
* ''[[sigE]]''
+
:*[[SigE]]: early mother cell-specific sporulation sigma factor
−
* ''[[sigF]]''
+
:*[[SigF]]: early forespore-specific sporulation sigma factor
−
* ''[[sigG]]''
+
:*[[SigG]]: late forespore-specific sporulation sigma factor
−
* ''[[sigH]]''
+
:*[[SigH]]: sigma factor that controls genes of the transition phase
−
* ''[[sigI]]''
+
:*[[SigI]]:
−
* ''[[sigL]]''
+
:*[[SigK]]: late mother cell-specific sporulation sigma factor
−
* ''[[sigM]]''
+
:*[[SigL]]: enhancer-dependent sigma factor (Sigma-54 family)
−
* ''[[sigV]]''
+
:*[[SigM]]: ECF sigma factor, controls genes required at high salt concentrations
−
* ''[[sigW]]''
+
:*[[SigV]]: ECF sigma factor
−
* ''[[sigX]]''
+
:*[[SigW]]: ECF sigma factor, mediates the transcriptional response to cell wall stress {{PubMed|12207695}}
−
* ''[[sigY]]''
+
:*[[SigX]]: ECF sigma factor
−
* ''[[sigZ]]''
+
:*[[SigY]]: ECF sigma factor
−
* ''[[spoIIIC]]''
+
:*[[SigZ]]: ECF sigma factor
−
* ''[[spoIVCB]]''
+
:*[[Xpf]]
−
* ''[[xpf]]''
+
:*[[YlaC]]
−
* ''[[ylaC]]''
+
:*[[SigO]]-[[RsoA]]: (composite sigma factor)
−
* ''[[yvrHa]]''
 
−
* ''[[yvrI]]''
 
  
 
=== Transcription elongation/ termination ===  
 
=== Transcription elongation/ termination ===  
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* ''[[nusG]]''
 
* ''[[nusG]]''
 
* ''[[rho]]''
 
* ''[[rho]]''
 +
 +
==Important publications==
 +
<pubmed> 21350489 22087258 22383849 24789973 27195891 28723971</pubmed>
 +
 +
==Reviews==
 +
<pubmed>18599813 14527287 12455702 12213655 12073657 7708009 19489723 10329121 21478900 22210308 24237659 26132790,29856930</pubmed>
 +
 +
=Back to [[categories]]=

Latest revision as of 11:10, 4 June 2018

Parent categories
Neighbouring categories
Related categories






SubtiExpress - A database integrating gene expression of all genes under 104 conditions

Genes in this functional category

RNA polymerase

Sigma factors

  • SigA: housekeeping sigma factor
  • SigB: general stress sigma factor
  • SigD: sigma factor for chemotaxis and motility genes
  • SigE: early mother cell-specific sporulation sigma factor
  • SigF: early forespore-specific sporulation sigma factor
  • SigG: late forespore-specific sporulation sigma factor
  • SigH: sigma factor that controls genes of the transition phase
  • SigI:
  • SigK: late mother cell-specific sporulation sigma factor
  • SigL: enhancer-dependent sigma factor (Sigma-54 family)
  • SigM: ECF sigma factor, controls genes required at high salt concentrations
  • SigV: ECF sigma factor
  • SigW: ECF sigma factor, mediates the transcriptional response to cell wall stress PubMed
  • SigX: ECF sigma factor
  • SigY: ECF sigma factor
  • SigZ: ECF sigma factor
  • Xpf
  • YlaC
  • SigO-RsoA: (composite sigma factor)

Transcription elongation/ termination

Important publications

Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guerin, Francis Repoila, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis.
PLoS Genet: 2017, 13(7);e1006909
[PubMed:28723971] [WorldCat.org] [DOI] (I e)

Ivan Junier, Olivier Rivoire
Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation.
PLoS One: 2016, 11(5);e0155740
[PubMed:27195891] [WorldCat.org] [DOI] (I e)

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)

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

Evert-Jan Blom, Anja N J A Ridder, Andrzej T Lulko, Jos B T M Roerdink, Oscar P Kuipers
Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis.
PLoS One: 2011, 6(11);e27160
[PubMed:22087258] [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)


Reviews

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)

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

Julio A Freyre-González, Alejandra M Manjarrez-Casas, Enrique Merino, Mario Martinez-Nuñez, Ernesto Perez-Rueda, Rosa-María Gutiérrez-Ríos
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.
BMC Syst Biol: 2013, 7;127
[PubMed:24237659] [WorldCat.org] [DOI] (I e)

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)

Thomas J Santangelo, Irina Artsimovitch
Termination and antitermination: RNA polymerase runs a stop sign.
Nat Rev Microbiol: 2011, 9(5);319-29
[PubMed:21478900] [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)

Tanja M Gruber, Carol A Gross
Multiple sigma subunits and the partitioning of bacterial transcription space.
Annu Rev Microbiol: 2003, 57;441-66
[PubMed:14527287] [WorldCat.org] [DOI] (P p)

Sergei Borukhov, Konstantin Severinov
Role of the RNA polymerase sigma subunit in transcription initiation.
Res Microbiol: 2002, 153(9);557-62
[PubMed:12455702] [WorldCat.org] [DOI] (P p)

Paul Gollnick, Paul Babitzke
Transcription attenuation.
Biochim Biophys Acta: 2002, 1577(2);240-50
[PubMed:12213655] [WorldCat.org] [DOI] (P p)

John D Helmann
The extracytoplasmic function (ECF) sigma factors.
Adv Microb Physiol: 2002, 46;47-110
[PubMed:12073657] [WorldCat.org] [DOI] (P p)

E Nudler
Transcription elongation: structural basis and mechanisms.
J Mol Biol: 1999, 288(1);1-12
[PubMed:10329121] [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)


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