Difference between revisions of "Transcription factors and their control"

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* 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 factors]]
+
* [[Transcription]]
 +
* [[Regulons]]
 +
* [[Trigger enzymes]]
 
* [[Two-component systems]]  
 
* [[Two-component systems]]  
 
|}}
 
|}}
 
__TOC__
 
__TOC__
 
<br><br><br><br><br>
 
<br><br><br><br><br>
 +
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).
  
−
==Reviews==
+
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.
−
<pubmed>18599813 </pubmed>
+
 
 +
=DNA-binding transcription factors=
 +
* [[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 Fur family]]
 +
* [[transcription factors of the GntR family]]
 +
* [[transcription factors of the LacI family]]
 +
* [[transcription factors of the Lrp family]]
 +
* [[transcription factors of the LysR family]]
 +
* [[transcription factors of the MarR/DUF24 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=
 +
* [[transcription antiterminators]]
 +
* [[transcription termination proteins]]
 +
 
 +
=Transcription factors according to signal perception=
 +
* [[PRD-containing transcription factors]]
 +
* [[transcription factors modulated by trigger enzymes]]
 +
* [[two-component systems]]
 +
 
 +
=Reviews on transcription regulation=
 +
<pubmed> 19721087 19632156 16772031 18599813 22210308 23504016 22728391</pubmed>
  
 
== Genes in this functional category ==
 
== Genes in this functional category ==
Line 91: Line 128:
 
* ''[[ykoH]]''
 
* ''[[ykoH]]''
 
* ''[[yrkQ]]''
 
* ''[[yrkQ]]''
−
* ''[[ytrP]]''
 
 
* ''[[yvfT]]''
 
* ''[[yvfT]]''
 
* ''[[yvrG]]''
 
* ''[[yvrG]]''
Line 121: Line 157:
 
* ''[[phrF]]''
 
* ''[[phrF]]''
 
* ''[[phrG]]''
 
* ''[[phrG]]''
 +
* ''[[swrAA/1]]''
 +
* ''[[swrAA/2]]''
 
* ''[[yycH]]''
 
* ''[[yycH]]''
 
* ''[[yycI]]''
 
* ''[[yycI]]''
Line 130: Line 168:
  
 
=== PRD-type regulators ===  
 
=== PRD-type regulators ===  
−
* ''[[glcT]]''
+
* [[GlcT]]''
−
* ''[[levR]]''
+
* [[LevR]]
−
* ''[[licR]]''
+
* [[LicR]]
−
* ''[[licT]]''
+
* [[LicT]]
−
* ''[[manR]]''
+
* [[ManR]]
−
* ''[[mtlR]]''
+
* [[MtlR]]
−
* ''[[sacT]]''
+
* [[SacT]]
−
* ''[[sacY]]''
+
* [[SacY]]
 +
 
 +
=== Control of PRD-type regulators ===
 +
* [[PtsG]]
 +
* [[BglP]]
 +
* [[SacP]]
 +
* [[SacX]]
 +
* [[LevE]]
 +
* [[MtlA]]
 +
* [[LicB]]
 +
* [[ManP]]
  
 
=== Transcription factors/ other ===  
 
=== Transcription factors/ other ===  
 
* ''[[acoR]]''
 
* ''[[acoR]]''
 +
* ''[[adaA]]''
 +
* ''[[adeR]]''
 
* ''[[adhR]]''
 
* ''[[adhR]]''
 
* ''[[ahrC]]''
 
* ''[[ahrC]]''
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* ''[[btr]]''
 
* ''[[btr]]''
 
* ''[[catR]]''
 
* ''[[catR]]''
 +
* ''[[ccpA]]''
 
* ''[[ccpB]]''
 
* ''[[ccpB]]''
 +
* ''[[ccpC]]''
 +
* ''[[ccpN]]''
 +
* ''[[cggR]]''
 +
* ''[[chrS]]''
 
* ''[[citR]]''
 
* ''[[citR]]''
 +
* ''[[codY]]''
 
* ''[[comK]]''
 
* ''[[comK]]''
 
* ''[[csoR]]''
 
* ''[[csoR]]''
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* ''[[cueR]]''
 
* ''[[cueR]]''
 
* ''[[cysL]]''
 
* ''[[cysL]]''
 +
* ''[[cymR]]''
 
* ''[[czrA]]''
 
* ''[[czrA]]''
 
* ''[[degA]]''
 
* ''[[degA]]''
 
* ''[[deoR]]''
 
* ''[[deoR]]''
 +
* ''[[dtrR]]''
 
* ''[[exuR]]''
 
* ''[[exuR]]''
 
* ''[[fadR]]''
 
* ''[[fadR]]''
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* ''[[fur]]''
 
* ''[[fur]]''
 
* ''[[gabR]]''
 
* ''[[gabR]]''
 +
* ''[[gamR]]''
 +
* ''[[gbsR]]''
 
* ''[[gerE]]''
 
* ''[[gerE]]''
 
* ''[[gerR]]''
 
* ''[[gerR]]''
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* ''[[hutP]]''
 
* ''[[hutP]]''
 
* ''[[hxlR]]''
 
* ''[[hxlR]]''
 +
* ''[[hypR]]''
 
* ''[[immR]]''
 
* ''[[immR]]''
 
* ''[[iolR]]''
 
* ''[[iolR]]''
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* ''[[lrpB]]''
 
* ''[[lrpB]]''
 
* ''[[lutR]]''
 
* ''[[lutR]]''
−
* ''[[lytR]]''
 
 
* ''[[mdtR]]''
 
* ''[[mdtR]]''
 
* ''[[mgsR]]''
 
* ''[[mgsR]]''
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* ''[[murR]]''
 
* ''[[murR]]''
 
* ''[[nadR]]''
 
* ''[[nadR]]''
 +
* ''[[nagR]]''
 +
* ''[[nrdR]]''
 
* ''[[nsrR]]''
 
* ''[[nsrR]]''
 
* ''[[ntdR]]''
 
* ''[[ntdR]]''
 
* ''[[ohrR]]''
 
* ''[[ohrR]]''
 +
* ''[[opcR]]''
 
* ''[[padR]]''
 
* ''[[padR]]''
 
* ''[[paiB]]''
 
* ''[[paiB]]''
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* ''[[pucR]]''
 
* ''[[pucR]]''
 
* ''[[purR]]''
 
* ''[[purR]]''
 +
*'' [[putR]]''
 
* ''[[pyrR]]''
 
* ''[[pyrR]]''
 +
* ''[[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]]''
 
* ''[[treR]]''
 
* ''[[treR]]''
 
* ''[[xre]]''
 
* ''[[xre]]''
 
* ''[[xylR]]''
 
* ''[[xylR]]''
−
* ''[[ybgA]]''
+
 
 
* ''[[ycbG]]''
 
* ''[[ycbG]]''
 
* ''[[ycnK]]''
 
* ''[[ycnK]]''
−
* ''[[yesS]]''
+
 
 
* ''[[yetL]]''
 
* ''[[yetL]]''
 
* ''[[yfmP]]''
 
* ''[[yfmP]]''
 +
* ''[[ykrK]]''
 
* ''[[yodB]]''
 
* ''[[yodB]]''
 
* ''[[yofA]]''
 
* ''[[yofA]]''
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* ''[[ytlI]]''
 
* ''[[ytlI]]''
 
* ''[[ytrA]]''
 
* ''[[ytrA]]''
−
* ''[[yuaC]]''
+
* ''[[ywbI]]''
−
* ''[[yvoA]]''
 
 
* ''[[ywcC]]''
 
* ''[[ywcC]]''
−
* ''[[yxaF]]''
 
 
* ''[[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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* ''[[ydeF]]''
 
* ''[[ydeF]]''
 
* ''[[ydeL]]''
 
* ''[[ydeL]]''
 +
* ''[[ydeP]]''
 
* ''[[ydeS]]''
 
* ''[[ydeS]]''
 
* ''[[ydfD]]''
 
* ''[[ydfD]]''
Line 283: Line 355:
 
* ''[[yfiR]]''
 
* ''[[yfiR]]''
 
* ''[[yfiV]]''
 
* ''[[yfiV]]''
 +
* ''[[ygzD]]''
 
* ''[[yhbI]]''
 
* ''[[yhbI]]''
 
* ''[[yhcB]]''
 
* ''[[yhcB]]''
Line 291: Line 364:
 
* ''[[yisV]]''
 
* ''[[yisV]]''
 
* ''[[ykoM]]''
 
* ''[[ykoM]]''
 +
* ''[[ykvN]]''
 
* ''[[ykvZ]]''
 
* ''[[ykvZ]]''
 
* ''[[ymfC]]''
 
* ''[[ymfC]]''
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* ''[[yobQ]]''
 
* ''[[yobQ]]''
 
* ''[[yonR]]''
 
* ''[[yonR]]''
 +
* ''[[yopO]]''
 +
* ''[[yopS]]''
 +
* ''[[yotL]]''
 
* ''[[yozG]]''
 
* ''[[yozG]]''
 
* ''[[ypoP]]''
 
* ''[[ypoP]]''
 +
* ''[[yqaF]]''
 +
* ''[[yqaG]]''
 
* ''[[yraN]]''
 
* ''[[yraN]]''
 
* ''[[yrdQ]]''
 
* ''[[yrdQ]]''
 
* ''[[ysmB]]''
 
* ''[[ysmB]]''
 +
* ''[[ytcD]]''
 
* ''[[ytdP]]''
 
* ''[[ytdP]]''
 +
* ''[[ytoI]]''
 
* ''[[ytzE]]''
 
* ''[[ytzE]]''
−
* ''[[yulB]]''
+
 
 
* ''[[yusT]]''
 
* ''[[yusT]]''
 
* ''[[yvaO]]''
 
* ''[[yvaO]]''
 +
* ''[[yvaV]]''
 
* ''[[yvbU]]''
 
* ''[[yvbU]]''
 
* ''[[yvcL]]''
 
* ''[[yvcL]]''
 +
* ''[[yvzC]]''
 
* ''[[yvdE]]''
 
* ''[[yvdE]]''
 
* ''[[yvdT]]''
 
* ''[[yvdT]]''
−
* ''[[yvhJ]]''
 
 
* ''[[yvkB]]''
 
* ''[[yvkB]]''
−
* ''[[ywaE]]''
+
 
−
* ''[[ywbI]]''
 
 
* ''[[ywhA]]''
 
* ''[[ywhA]]''
 
* ''[[ywoH]]''
 
* ''[[ywoH]]''
 
* ''[[ywqM]]''
 
* ''[[ywqM]]''
−
* ''[[ywrC]]''
+
 
 
* ''[[yxaD]]''
 
* ''[[yxaD]]''
 
* ''[[yxjO]]''
 
* ''[[yxjO]]''
Line 327: Line 408:
  
 
=== Control of transcription factor (other than two-component system) ===  
 
=== Control of transcription factor (other than two-component system) ===  
−
* ''[[abbA]]''
+
* [[AbbA]]
−
* ''[[crh]]''
+
* [[Crh]]
−
* ''[[hprK]]''
+
* [[CysK]]
−
* ''[[immA]]''
+
* [[GlnA]]
−
* ''[[mcsA]]''
+
* [[GudB]]
−
* ''[[mcsB]]''
+
* [[HprK]]
−
* ''[[nrgB]]''
+
* [[ImmA]]
−
* ''[[ptsH]]''
+
* [[McsA]]
−
* ''[[rtpA]]''
+
* [[McsB]]
−
* ''[[salA]]''
+
* [[NrgB]]
−
* ''[[sinI]]''
+
* [[PtsH]]
−
* ''[[slrA]]''
+
* [[RocG]]
−
* ''[[yabJ]]''
+
* [[RtpA]]
−
* ''[[ylbF]]''
+
* [[SalA]]
−
* ''[[ymcA]]''
+
* [[SinI]]
−
* ''[[yqfL]]''
+
* [[SlrA]]
 +
* [[YabJ]]
 +
* [[YlbF]]
 +
* [[YmcA]]
 +
* [[YqfL]]
 +
 
 +
=Back to [[categories]]=

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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