Difference between revisions of "Transcription factors and their control"

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(→‎Control of response regulators/ other)
(→‎Transcription factors/ other)
 
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Line 12: Line 12:
 
* 3.4.7. [[Phosphorelay]]
 
* 3.4.7. [[Phosphorelay]]
 
* 3.4.8. [[Quorum sensing]]
 
* 3.4.8. [[Quorum sensing]]
 +
* 3.4.9. [[Other regulators]]
 
|Related=
 
|Related=
 
* [[Transcription]]
 
* [[Transcription]]
Line 26: Line 27:
 
=DNA-binding transcription factors=
 
=DNA-binding transcription factors=
 
* [[transcription factors activating transcription at SigL-dependent promoters]]
 
* [[transcription factors activating transcription at SigL-dependent promoters]]
 +
* [[transcription factors of the AraC family]]
 +
* [[transcription factors of the ArgR family]]
 +
* [[transcription factors of the ArsR family]]
 +
* [[transcription factors of the BirA family]]
 +
* [[transcription factors of the CcpN family]]
 
* [[transcription factors of the DeoR family]]
 
* [[transcription factors of the DeoR family]]
 +
* [[transcription factors of the Fur family]]
 
* [[transcription factors of the GntR family]]
 
* [[transcription factors of the GntR family]]
 
* [[transcription factors of the LacI family]]
 
* [[transcription factors of the LacI family]]
 +
* [[transcription factors of the Lrp family]]
 
* [[transcription factors of the LysR family]]
 
* [[transcription factors of the LysR family]]
 
* [[transcription factors of the MarR/DUF24 family]]
 
* [[transcription factors of the MarR/DUF24 family]]
 
* [[transcription factors of the MerR family]]
 
* [[transcription factors of the MerR family]]
 +
* [[transcription factors of the MocR/ GabR family]]
 +
* [[transcription factors of the OmpR family]]
 +
* [[transcription factors of the PucR family]]
 +
* [[transcription factors of the SorC family]]
 +
* [[transcription factors of the TetR family]]
 +
* [[transcription factors of the Xre family]]
  
 
=RNA-binding transcription factors=
 
=RNA-binding transcription factors=
Line 43: Line 57:
  
 
=Reviews on transcription regulation=
 
=Reviews on transcription regulation=
−
<pubmed> 19721087 19632156 16772031 18599813 </pubmed>
+
<pubmed> 19721087 19632156 16772031 18599813 22210308 23504016 22728391</pubmed>
  
 
== Genes in this functional category ==
 
== Genes in this functional category ==
Line 143: Line 157:
 
* ''[[phrF]]''
 
* ''[[phrF]]''
 
* ''[[phrG]]''
 
* ''[[phrG]]''
−
* ''[[swrA]]''
+
* ''[[swrAA/1]]''
 +
* ''[[swrAA/2]]''
 
* ''[[yycH]]''
 
* ''[[yycH]]''
 
* ''[[yycI]]''
 
* ''[[yycI]]''
Line 175: Line 190:
 
* ''[[acoR]]''
 
* ''[[acoR]]''
 
* ''[[adaA]]''
 
* ''[[adaA]]''
 +
* ''[[adeR]]''
 
* ''[[adhR]]''
 
* ''[[adhR]]''
 
* ''[[ahrC]]''
 
* ''[[ahrC]]''
Line 197: Line 213:
 
* ''[[ccpN]]''
 
* ''[[ccpN]]''
 
* ''[[cggR]]''
 
* ''[[cggR]]''
 +
* ''[[chrS]]''
 
* ''[[citR]]''
 
* ''[[citR]]''
 
* ''[[codY]]''
 
* ''[[codY]]''
Line 208: Line 225:
 
* ''[[degA]]''
 
* ''[[degA]]''
 
* ''[[deoR]]''
 
* ''[[deoR]]''
 +
* ''[[dtrR]]''
 
* ''[[exuR]]''
 
* ''[[exuR]]''
 
* ''[[fadR]]''
 
* ''[[fadR]]''
Line 217: Line 235:
 
* ''[[fur]]''
 
* ''[[fur]]''
 
* ''[[gabR]]''
 
* ''[[gabR]]''
 +
* ''[[gamR]]''
 
* ''[[gbsR]]''
 
* ''[[gbsR]]''
 
* ''[[gerE]]''
 
* ''[[gerE]]''
Line 253: Line 272:
 
* ''[[nadR]]''
 
* ''[[nadR]]''
 
* ''[[nagR]]''
 
* ''[[nagR]]''
 +
* ''[[nrdR]]''
 
* ''[[nsrR]]''
 
* ''[[nsrR]]''
 
* ''[[ntdR]]''
 
* ''[[ntdR]]''
 
* ''[[ohrR]]''
 
* ''[[ohrR]]''
 +
* ''[[opcR]]''
 
* ''[[padR]]''
 
* ''[[padR]]''
 
* ''[[paiB]]''
 
* ''[[paiB]]''
Line 266: Line 287:
 
* ''[[qdoR]]''
 
* ''[[qdoR]]''
 
* ''[[rbsR]]''
 
* ''[[rbsR]]''
 +
* ''[[remA]]''
 
* ''[[rex]]''
 
* ''[[rex]]''
 
* ''[[rghR]]''
 
* ''[[rghR]]''
 +
* ''[[rhaR]]''
 +
* ''[[rhgR]]''
 
* ''[[rocR]]''
 
* ''[[rocR]]''
 
* ''[[rok]]''
 
* ''[[rok]]''
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* ''[[spoVT]]''
 
* ''[[spoVT]]''
 
* ''[[spx]]''
 
* ''[[spx]]''
−
* ''[[tenI]]''
+
* [[TilS]]-[[HprT]]
 +
* ''[[thrR]]''
 
* ''[[tnrA]]''
 
* ''[[tnrA]]''
 
* ''[[treR]]''
 
* ''[[treR]]''
 
* ''[[xre]]''
 
* ''[[xre]]''
 
* ''[[xylR]]''
 
* ''[[xylR]]''
−
* ''[[ybgA]]''
+
 
 
* ''[[ycbG]]''
 
* ''[[ycbG]]''
 
* ''[[ycnK]]''
 
* ''[[ycnK]]''
−
* ''[[yesS]]''
+
 
 
* ''[[yetL]]''
 
* ''[[yetL]]''
 
* ''[[yfmP]]''
 
* ''[[yfmP]]''
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* ''[[ytlI]]''
 
* ''[[ytlI]]''
 
* ''[[ytrA]]''
 
* ''[[ytrA]]''
 +
* ''[[ywbI]]''
 
* ''[[ywcC]]''
 
* ''[[ywcC]]''
 
* ''[[zur]]''
 
* ''[[zur]]''
  
 
=== Transcription factor/ other/ based on similarity ===  
 
=== Transcription factor/ other/ based on similarity ===  
 +
* ''[[yazB]]''
 
* ''[[ybfI]]''
 
* ''[[ybfI]]''
 
* ''[[ybfP]]''
 
* ''[[ybfP]]''
 +
* ''[[ybzH]]''
 
* ''[[yceK]]''
 
* ''[[yceK]]''
 
* ''[[ycgE]]''
 
* ''[[ycgE]]''
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* ''[[yfiR]]''
 
* ''[[yfiR]]''
 
* ''[[yfiV]]''
 
* ''[[yfiV]]''
 +
* ''[[ygzD]]''
 
* ''[[yhbI]]''
 
* ''[[yhbI]]''
 
* ''[[yhcB]]''
 
* ''[[yhcB]]''
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* ''[[yobQ]]''
 
* ''[[yobQ]]''
 
* ''[[yonR]]''
 
* ''[[yonR]]''
 +
* ''[[yopO]]''
 +
* ''[[yopS]]''
 +
* ''[[yotL]]''
 
* ''[[yozG]]''
 
* ''[[yozG]]''
 
* ''[[ypoP]]''
 
* ''[[ypoP]]''
 +
* ''[[yqaF]]''
 +
* ''[[yqaG]]''
 
* ''[[yraN]]''
 
* ''[[yraN]]''
 
* ''[[yrdQ]]''
 
* ''[[yrdQ]]''
Line 349: Line 383:
 
* ''[[ytcD]]''
 
* ''[[ytcD]]''
 
* ''[[ytdP]]''
 
* ''[[ytdP]]''
 +
* ''[[ytoI]]''
 
* ''[[ytzE]]''
 
* ''[[ytzE]]''
−
* ''[[yulB]]''
+
 
 
* ''[[yusT]]''
 
* ''[[yusT]]''
 
* ''[[yvaO]]''
 
* ''[[yvaO]]''
 +
* ''[[yvaV]]''
 
* ''[[yvbU]]''
 
* ''[[yvbU]]''
 
* ''[[yvcL]]''
 
* ''[[yvcL]]''
 +
* ''[[yvzC]]''
 
* ''[[yvdE]]''
 
* ''[[yvdE]]''
 
* ''[[yvdT]]''
 
* ''[[yvdT]]''
 
* ''[[yvkB]]''
 
* ''[[yvkB]]''
−
* ''[[ywaE]]''
+
 
−
* ''[[ywbI]]''
 
 
* ''[[ywhA]]''
 
* ''[[ywhA]]''
 
* ''[[ywoH]]''
 
* ''[[ywoH]]''
 
* ''[[ywqM]]''
 
* ''[[ywqM]]''
−
* ''[[ywrC]]''
+
 
 
* ''[[yxaD]]''
 
* ''[[yxaD]]''
 
* ''[[yxjO]]''
 
* ''[[yxjO]]''

Latest revision as of 17:37, 5 June 2016

Parent categories
Neighbouring categories
Related categories






Transcription factors control gene expression by regulating transcription initiation or transcription elongation. Transcription initiation is regulated by DNA-binding proteins, whereas transcription elongation can be controlled by DNA-binding proteins ("transcriptional roadblocks") or RNA-binding proteins (transcription termination/ antitermination).

Transcription factors can be grouped according to their mode of interaction with nucleic acids (DNA-or RNA-binding proteins) and also according to the mechanism by which they perceive the signal.

DNA-binding transcription factors

RNA-binding transcription factors

Transcription factors according to signal perception

Reviews on transcription regulation

Semen A Leyn, Marat D Kazanov, Natalia V Sernova, Ekaterina O Ermakova, Pavel S Novichkov, Dmitry A Rodionov
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.
J Bacteriol: 2013, 195(11);2463-73
[PubMed:23504016] [WorldCat.org] [DOI] (I p)

Julio A Freyre-González, Luis G Treviño-Quintanilla, Ilse A Valtierra-Gutiérrez, Rosa María Gutiérrez-Ríos, José A Alonso-Pavón
Prokaryotic regulatory systems biology: Common principles governing the functional architectures of Bacillus subtilis and Escherichia coli unveiled by the natural decomposition approach.
J Biotechnol: 2012, 161(3);278-86
[PubMed:22728391] [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)

Sacha A F T van Hijum, Marnix H Medema, Oscar P Kuipers
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.
Microbiol Mol Biol Rev: 2009, 73(3);481-509, Table of Contents
[PubMed:19721087] [WorldCat.org] [DOI] (I p)

Sarath Chandra Janga, Ernesto Pérez-Rueda
Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.
Comput Biol Chem: 2009, 33(4);261-8
[PubMed:19632156] [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)

Samadhi Moreno-Campuzano, Sarath Chandra Janga, Ernesto Pérez-Rueda
Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach.
BMC Genomics: 2006, 7;147
[PubMed:16772031] [WorldCat.org] [DOI] (I e)


Genes in this functional category

Two-component system response regulators

Control of two-component response regulators

Two-component sensor kinase

Response regulator aspartate phosphatase

Control of response regulators/ other

PRD-type regulators

Control of PRD-type regulators

Transcription factors/ other

Transcription factor/ other/ based on similarity

Control of transcription factor (other than two-component system)

Back to categories

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