Difference between revisions of "Transcription factors and their control"

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{{CategoryTree
 
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* 3.4.7. [[Phosphorelay]]
 
* 3.4.7. [[Phosphorelay]]
 
* 3.4.8. [[Quorum sensing]]
 
* 3.4.8. [[Quorum sensing]]
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* 3.4.9. [[Other regulators]]
 
|Related=
 
|Related=
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none
+
* [[Transcription]]
 +
* [[Regulons]]
 +
* [[Trigger enzymes]]
 +
* [[Two-component systems]]
 
|}}
 
|}}
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__TOC__
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<br><br><br><br><br>
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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=
 +
* [[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]]
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* [[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 ==
 +
 +
=== Two-component system response regulators ===
 +
* ''[[bceR]]''
 +
* ''[[cheY]]''
 +
* ''[[citT]]''
 +
* ''[[comA]]''
 +
* ''[[cssR]]''
 +
* ''[[dctR]]''
 +
* ''[[degU]]''
 +
* ''[[desR]]''
 +
* ''[[glnL]]''
 +
* ''[[liaR]]''
 +
* ''[[lytT]]''
 +
* ''[[malR]]''
 +
* ''[[natR]]''
 +
* ''[[phoP]]''
 +
* ''[[psdR]]''
 +
* ''[[resD]]''
 +
* ''[[spo0A]]''
 +
* ''[[walR]]''
 +
* ''[[ybdJ]]''
 +
* ''[[ycbL]]''
 +
* ''[[yclJ]]''
 +
* ''[[ydfI]]''
 +
* ''[[yesN]]''
 +
* ''[[yfiK]]''
 +
* ''[[yhcZ]]''
 +
* ''[[ykoG]]''
 +
* ''[[yneI]]''
 +
* ''[[yrkP]]''
 +
* ''[[yvfU]]''
 +
* ''[[yvrHb]]''
 +
* ''[[yxdJ]]''
 +
* ''[[yxjL]]''
 +
 +
=== Control of two-component response regulators ===
 +
==== Two-component sensor kinase ====
 +
* ''[[bceS]]''
 +
* ''[[cheA]]''
 +
* ''[[citS]]''
 +
* ''[[comP]]''
 +
* ''[[cssS]]''
 +
* ''[[dctS]]''
 +
* ''[[degS]]''
 +
* ''[[desK]]''
 +
* ''[[glnK]]''
 +
* ''[[kinA]]''
 +
* ''[[kinB]]''
 +
* ''[[kinC]]''
 +
* ''[[kinD]]''
 +
* ''[[kinE]]''
 +
* ''[[liaS]]''
 +
* ''[[lytS]]''
 +
* ''[[malK]]''
 +
* ''[[natK]]''
 +
* ''[[phoR]]''
 +
* ''[[psdS]]''
 +
* ''[[resE]]''
 +
* ''[[walK]]''
 +
* ''[[ybdK]]''
 +
* ''[[ycbM]]''
 +
* ''[[yclK]]''
 +
* ''[[ydfH]]''
 +
* ''[[yesM]]''
 +
* ''[[yfiJ]]''
 +
* ''[[yhcY]]''
 +
* ''[[ykoH]]''
 +
* ''[[yrkQ]]''
 +
* ''[[yvfT]]''
 +
* ''[[yvrG]]''
 +
* ''[[ywpD]]''
 +
* ''[[yxdK]]''
 +
* ''[[yxjM]]''
 +
 +
==== Response regulator aspartate phosphatase ====
 +
* ''[[phrI]]''
 +
* ''[[phrK]]''
 +
* ''[[rapA]]''
 +
* ''[[rapB]]''
 +
* ''[[rapC]]''
 +
* ''[[rapD]]''
 +
* ''[[rapE]]''
 +
* ''[[rapF]]''
 +
* ''[[rapG]]''
 +
* ''[[rapH]]''
 +
* ''[[rapI]]''
 +
* ''[[rapJ]]''
 +
* ''[[rapK]]''
 +
 +
==== Control of response regulators/ other ====
 +
* ''[[cheV]]''
 +
* ''[[degQ]]''
 +
* ''[[degR]]''
 +
* ''[[liaF]]''
 +
* ''[[phrC]]''
 +
* ''[[phrF]]''
 +
* ''[[phrG]]''
 +
* ''[[swrAA/1]]''
 +
* ''[[swrAA/2]]''
 +
* ''[[yycH]]''
 +
* ''[[yycI]]''
 +
* ''[[yydF]]''
 +
* ''[[yydG]]''
 +
* ''[[yydH]]''
 +
* ''[[yydI]]''
 +
* ''[[yydJ]]''
 +
 +
=== PRD-type regulators ===
 +
* [[GlcT]]''
 +
* [[LevR]]
 +
* [[LicR]]
 +
* [[LicT]]
 +
* [[ManR]]
 +
* [[MtlR]]
 +
* [[SacT]]
 +
* [[SacY]]
 +
 +
=== Control of PRD-type regulators ===
 +
* [[PtsG]]
 +
* [[BglP]]
 +
* [[SacP]]
 +
* [[SacX]]
 +
* [[LevE]]
 +
* [[MtlA]]
 +
* [[LicB]]
 +
* [[ManP]]
 +
 +
=== Transcription factors/ other ===
 +
* ''[[acoR]]''
 +
* ''[[adaA]]''
 +
* ''[[adeR]]''
 +
* ''[[adhR]]''
 +
* ''[[ahrC]]''
 +
* ''[[alaR]]''
 +
* ''[[alsR]]''
 +
* ''[[ansR]]''
 +
* ''[[araR]]''
 +
* ''[[arfM]]''
 +
* ''[[arsR]]''
 +
* ''[[aseR]]''
 +
* ''[[azlB]]''
 +
* ''[[birA]]''
 +
* ''[[bkdR]]''
 +
* ''[[bltR]]''
 +
* ''[[bmrR]]''
 +
* ''[[bsdA]]''
 +
* ''[[btr]]''
 +
* ''[[catR]]''
 +
* ''[[ccpA]]''
 +
* ''[[ccpB]]''
 +
* ''[[ccpC]]''
 +
* ''[[ccpN]]''
 +
* ''[[cggR]]''
 +
* ''[[chrS]]''
 +
* ''[[citR]]''
 +
* ''[[codY]]''
 +
* ''[[comK]]''
 +
* ''[[csoR]]''
 +
* ''[[ctsR]]''
 +
* ''[[cueR]]''
 +
* ''[[cysL]]''
 +
* ''[[cymR]]''
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* ''[[czrA]]''
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* ''[[degA]]''
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* ''[[deoR]]''
 +
* ''[[dtrR]]''
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* ''[[exuR]]''
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* ''[[fadR]]''
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* ''[[fapR]]''
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* ''[[fatR]]''
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* ''[[fnr]]''
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* ''[[frlR]]''
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* ''[[fruR]]''
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* ''[[fur]]''
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* ''[[gabR]]''
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* ''[[gamR]]''
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* ''[[gbsR]]''
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* ''[[gerE]]''
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* ''[[gerR]]''
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* ''[[glcR]]''
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* ''[[glnR]]''
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* ''[[glpP]]''
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* ''[[gltC]]''
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* ''[[gltR]]''
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* ''[[glvR]]''
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* ''[[gmuR]]''
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* ''[[gntR]]''
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* ''[[gutR]]''
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* ''[[hrcA]]''
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* ''[[hutP]]''
 +
* ''[[hxlR]]''
 +
* ''[[hypR]]''
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* ''[[immR]]''
 +
* ''[[iolR]]''
 +
* ''[[kdgR]]''
 +
* ''[[kipR]]''
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* ''[[lacR]]''
 +
* ''[[lexA]]''
 +
* ''[[lmrA]]''
 +
* ''[[lrpA]]''
 +
* ''[[lrpB]]''
 +
* ''[[lutR]]''
 +
* ''[[mdtR]]''
 +
* ''[[mgsR]]''
 +
* ''[[mhqR]]''
 +
* ''[[mntR]]''
 +
* ''[[msmR]]''
 +
* ''[[mta]]''
 +
* ''[[mtrB]]''
 +
* ''[[murR]]''
 +
* ''[[nadR]]''
 +
* ''[[nagR]]''
 +
* ''[[nrdR]]''
 +
* ''[[nsrR]]''
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* ''[[ntdR]]''
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* ''[[ohrR]]''
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* ''[[opcR]]''
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* ''[[padR]]''
 +
* ''[[paiB]]''
 +
* ''[[perR]]''
 +
* ''[[pksA]]''
 +
* ''[[pucR]]''
 +
* ''[[purR]]''
 +
*'' [[putR]]''
 +
* ''[[pyrR]]''
 +
* ''[[qdoR]]''
 +
* ''[[rbsR]]''
 +
* ''[[remA]]''
 +
* ''[[rex]]''
 +
* ''[[rghR]]''
 +
* ''[[rhaR]]''
 +
* ''[[rhgR]]''
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* ''[[rocR]]''
 +
* ''[[rok]]''
 +
* ''[[scoC]]''
 +
* ''[[sdpR]]''
 +
* ''[[senS]]''
 +
* ''[[sinR]]''
 +
* ''[[sknR]]''
 +
* ''[[slrR]]''
 +
* ''[[splA]]''
 +
* ''[[spoIIID]]''
 +
* ''[[spoVT]]''
 +
* ''[[spx]]''
 +
* [[TilS]]-[[HprT]]
 +
* ''[[thrR]]''
 +
* ''[[tnrA]]''
 +
* ''[[treR]]''
 +
* ''[[xre]]''
 +
* ''[[xylR]]''
 +
 +
* ''[[ycbG]]''
 +
* ''[[ycnK]]''
 +
 +
* ''[[yetL]]''
 +
* ''[[yfmP]]''
 +
* ''[[ykrK]]''
 +
* ''[[yodB]]''
 +
* ''[[yofA]]''
 +
* ''[[yplP]]''
 +
* ''[[ytlI]]''
 +
* ''[[ytrA]]''
 +
* ''[[ywbI]]''
 +
* ''[[ywcC]]''
 +
* ''[[zur]]''
 +
 +
=== Transcription factor/ other/ based on similarity ===
 +
* ''[[yazB]]''
 +
* ''[[ybfI]]''
 +
* ''[[ybfP]]''
 +
* ''[[ybzH]]''
 +
* ''[[yceK]]''
 +
* ''[[ycgE]]''
 +
* ''[[ycgK]]''
 +
* ''[[ycnC]]''
 +
* ''[[ycxD]]''
 +
* ''[[yczG]]''
 +
* ''[[ydeB]]''
 +
* ''[[ydeC]]''
 +
* ''[[ydeE]]''
 +
* ''[[ydeF]]''
 +
* ''[[ydeL]]''
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* ''[[ydeP]]''
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* ''[[ydeS]]''
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* ''[[ydfD]]''
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* ''[[ydfL]]''
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* ''[[ydgG]]''
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* ''[[ydgJ]]''
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* ''[[ydhC]]''
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* ''[[yerO]]''
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* ''[[yezC]]''
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* ''[[yezE]]''
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* ''[[yfiF]]''
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* ''[[yfiR]]''
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* ''[[yfiV]]''
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* ''[[ygzD]]''
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* ''[[yhbI]]''
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* ''[[yhcB]]''
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* ''[[yhcF]]''
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* ''[[yhdI]]''
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* ''[[yhgD]]''
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* ''[[yisR]]''
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* ''[[yisV]]''
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* ''[[ykoM]]''
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* ''[[ykvN]]''
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* ''[[ykvZ]]''
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* ''[[ymfC]]''
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* ''[[yoaU]]''
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* ''[[yobD]]''
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* ''[[yobQ]]''
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* ''[[yonR]]''
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* ''[[yopO]]''
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* ''[[yopS]]''
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* ''[[yotL]]''
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* ''[[yozG]]''
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* ''[[ypoP]]''
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* ''[[yqaF]]''
 +
* ''[[yqaG]]''
 +
* ''[[yraN]]''
 +
* ''[[yrdQ]]''
 +
* ''[[ysmB]]''
 +
* ''[[ytcD]]''
 +
* ''[[ytdP]]''
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* ''[[ytoI]]''
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* ''[[ytzE]]''
 +
 +
* ''[[yusT]]''
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* ''[[yvaO]]''
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* ''[[yvaV]]''
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* ''[[yvbU]]''
 +
* ''[[yvcL]]''
 +
* ''[[yvzC]]''
 +
* ''[[yvdE]]''
 +
* ''[[yvdT]]''
 +
* ''[[yvkB]]''
 +
 +
* ''[[ywhA]]''
 +
* ''[[ywoH]]''
 +
* ''[[ywqM]]''
 +
 +
* ''[[yxaD]]''
 +
* ''[[yxjO]]''
 +
* ''[[yyaN]]''
 +
* ''[[yybA]]''
 +
* ''[[yybE]]''
 +
* ''[[yydK]]''
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 +
=== Control of transcription factor (other than two-component system) ===
 +
* [[AbbA]]
 +
* [[Crh]]
 +
* [[CysK]]
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* [[GlnA]]
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* [[GudB]]
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* [[HprK]]
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* [[ImmA]]
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* [[McsA]]
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* [[McsB]]
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* [[NrgB]]
 +
* [[PtsH]]
 +
* [[RocG]]
 +
* [[RtpA]]
 +
* [[SalA]]
 +
* [[SinI]]
 +
* [[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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