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 | + | * [[Transcription]] |
| + | * [[Regulons]] | ||
* [[Trigger enzymes]] | * [[Trigger enzymes]] | ||
* [[Two-component systems]] | * [[Two-component systems]] | ||
| Line 19: | Line 21: | ||
__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 121: | Line 157: | ||
* ''[[phrF]]'' | * ''[[phrF]]'' | ||
* ''[[phrG]]'' | * ''[[phrG]]'' | ||
| + | * ''[[swrAA/1]]'' | ||
| + | * ''[[swrAA/2]]'' | ||
* ''[[yycH]]'' | * ''[[yycH]]'' | ||
* ''[[yycI]]'' | * ''[[yycI]]'' | ||
| Line 152: | Line 190: | ||
* ''[[acoR]]'' | * ''[[acoR]]'' | ||
* ''[[adaA]]'' | * ''[[adaA]]'' | ||
| + | * ''[[adeR]]'' | ||
* ''[[adhR]]'' | * ''[[adhR]]'' | ||
* ''[[ahrC]]'' | * ''[[ahrC]]'' | ||
| Line 174: | Line 213: | ||
* ''[[ccpN]]'' | * ''[[ccpN]]'' | ||
* ''[[cggR]]'' | * ''[[cggR]]'' | ||
| + | * ''[[chrS]]'' | ||
* ''[[citR]]'' | * ''[[citR]]'' | ||
* ''[[codY]]'' | * ''[[codY]]'' | ||
| Line 185: | Line 225: | ||
* ''[[degA]]'' | * ''[[degA]]'' | ||
* ''[[deoR]]'' | * ''[[deoR]]'' | ||
| + | * ''[[dtrR]]'' | ||
* ''[[exuR]]'' | * ''[[exuR]]'' | ||
* ''[[fadR]]'' | * ''[[fadR]]'' | ||
| Line 194: | Line 235: | ||
* ''[[fur]]'' | * ''[[fur]]'' | ||
* ''[[gabR]]'' | * ''[[gabR]]'' | ||
| + | * ''[[gamR]]'' | ||
| + | * ''[[gbsR]]'' | ||
* ''[[gerE]]'' | * ''[[gerE]]'' | ||
* ''[[gerR]]'' | * ''[[gerR]]'' | ||
| Line 208: | Line 251: | ||
* ''[[hutP]]'' | * ''[[hutP]]'' | ||
* ''[[hxlR]]'' | * ''[[hxlR]]'' | ||
| + | * ''[[hypR]]'' | ||
* ''[[immR]]'' | * ''[[immR]]'' | ||
* ''[[iolR]]'' | * ''[[iolR]]'' | ||
| Line 218: | Line 262: | ||
* ''[[lrpB]]'' | * ''[[lrpB]]'' | ||
* ''[[lutR]]'' | * ''[[lutR]]'' | ||
| − | |||
* ''[[mdtR]]'' | * ''[[mdtR]]'' | ||
* ''[[mgsR]]'' | * ''[[mgsR]]'' | ||
| Line 229: | Line 272: | ||
* ''[[nadR]]'' | * ''[[nadR]]'' | ||
* ''[[nagR]]'' | * ''[[nagR]]'' | ||
| + | * ''[[nrdR]]'' | ||
* ''[[nsrR]]'' | * ''[[nsrR]]'' | ||
* ''[[ntdR]]'' | * ''[[ntdR]]'' | ||
* ''[[ohrR]]'' | * ''[[ohrR]]'' | ||
| + | * ''[[opcR]]'' | ||
* ''[[padR]]'' | * ''[[padR]]'' | ||
* ''[[paiB]]'' | * ''[[paiB]]'' | ||
| Line 238: | Line 283: | ||
* ''[[pucR]]'' | * ''[[pucR]]'' | ||
* ''[[purR]]'' | * ''[[purR]]'' | ||
| + | *'' [[putR]]'' | ||
* ''[[pyrR]]'' | * ''[[pyrR]]'' | ||
| + | * ''[[qdoR]]'' | ||
* ''[[rbsR]]'' | * ''[[rbsR]]'' | ||
| + | * ''[[remA]]'' | ||
* ''[[rex]]'' | * ''[[rex]]'' | ||
* ''[[rghR]]'' | * ''[[rghR]]'' | ||
| + | * ''[[rhaR]]'' | ||
| + | * ''[[rhgR]]'' | ||
* ''[[rocR]]'' | * ''[[rocR]]'' | ||
* ''[[rok]]'' | * ''[[rok]]'' | ||
| Line 254: | Line 304: | ||
* ''[[spoVT]]'' | * ''[[spoVT]]'' | ||
* ''[[spx]]'' | * ''[[spx]]'' | ||
| − | * ''[[ | + | * [[TilS]]-[[HprT]] |
| + | * ''[[thrR]]'' | ||
* ''[[tnrA]]'' | * ''[[tnrA]]'' | ||
* ''[[treR]]'' | * ''[[treR]]'' | ||
* ''[[xre]]'' | * ''[[xre]]'' | ||
* ''[[xylR]]'' | * ''[[xylR]]'' | ||
| − | + | ||
* ''[[ycbG]]'' | * ''[[ycbG]]'' | ||
* ''[[ycnK]]'' | * ''[[ycnK]]'' | ||
| − | + | ||
* ''[[yetL]]'' | * ''[[yetL]]'' | ||
* ''[[yfmP]]'' | * ''[[yfmP]]'' | ||
| + | * ''[[ykrK]]'' | ||
* ''[[yodB]]'' | * ''[[yodB]]'' | ||
* ''[[yofA]]'' | * ''[[yofA]]'' | ||
| Line 270: | Line 322: | ||
* ''[[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]]'' | ||
| Line 289: | Line 342: | ||
* ''[[ydeF]]'' | * ''[[ydeF]]'' | ||
* ''[[ydeL]]'' | * ''[[ydeL]]'' | ||
| + | * ''[[ydeP]]'' | ||
* ''[[ydeS]]'' | * ''[[ydeS]]'' | ||
* ''[[ydfD]]'' | * ''[[ydfD]]'' | ||
| Line 301: | Line 355: | ||
* ''[[yfiR]]'' | * ''[[yfiR]]'' | ||
* ''[[yfiV]]'' | * ''[[yfiV]]'' | ||
| + | * ''[[ygzD]]'' | ||
* ''[[yhbI]]'' | * ''[[yhbI]]'' | ||
* ''[[yhcB]]'' | * ''[[yhcB]]'' | ||
| Line 309: | Line 364: | ||
* ''[[yisV]]'' | * ''[[yisV]]'' | ||
* ''[[ykoM]]'' | * ''[[ykoM]]'' | ||
| + | * ''[[ykvN]]'' | ||
* ''[[ykvZ]]'' | * ''[[ykvZ]]'' | ||
* ''[[ymfC]]'' | * ''[[ymfC]]'' | ||
| Line 315: | Line 371: | ||
* ''[[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]]'' | ||
| − | + | ||
* ''[[yusT]]'' | * ''[[yusT]]'' | ||
* ''[[yvaO]]'' | * ''[[yvaO]]'' | ||
| + | * ''[[yvaV]]'' | ||
* ''[[yvbU]]'' | * ''[[yvbU]]'' | ||
* ''[[yvcL]]'' | * ''[[yvcL]]'' | ||
| + | * ''[[yvzC]]'' | ||
* ''[[yvdE]]'' | * ''[[yvdE]]'' | ||
* ''[[yvdT]]'' | * ''[[yvdT]]'' | ||
| − | |||
* ''[[yvkB]]'' | * ''[[yvkB]]'' | ||
| − | + | ||
| − | |||
* ''[[ywhA]]'' | * ''[[ywhA]]'' | ||
* ''[[ywoH]]'' | * ''[[ywoH]]'' | ||
* ''[[ywqM]]'' | * ''[[ywqM]]'' | ||
| − | + | ||
* ''[[yxaD]]'' | * ''[[yxaD]]'' | ||
* ''[[yxjO]]'' | * ''[[yxjO]]'' | ||
| Line 365: | Line 428: | ||
* [[YmcA]] | * [[YmcA]] | ||
* [[YqfL]] | * [[YqfL]] | ||
| + | |||
=Back to [[categories]]= | =Back to [[categories]]= | ||
Latest revision as of 17:37, 5 June 2016
| Parent categories | |
| Neighbouring categories |
|
| Related categories | |
Contents
- 1 DNA-binding transcription factors
- 2 RNA-binding transcription factors
- 3 Transcription factors according to signal perception
- 4 Reviews on transcription regulation
- 4.1 Genes in this functional category
- 4.1.1 Two-component system response regulators
- 4.1.2 Control of two-component response regulators
- 4.1.3 PRD-type regulators
- 4.1.4 Control of PRD-type regulators
- 4.1.5 Transcription factors/ other
- 4.1.6 Transcription factor/ other/ based on similarity
- 4.1.7 Control of transcription factor (other than two-component system)
- 4.1 Genes in this functional category
- 5 Back to 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
- 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 factors according to signal perception
- PRD-containing transcription factors
- transcription factors modulated by trigger enzymes
- two-component systems
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
- 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
Control of response regulators/ other
PRD-type regulators
Control of PRD-type regulators
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
- czrA
- degA
- deoR
- dtrR
- exuR
- fadR
- fapR
- fatR
- fnr
- frlR
- fruR
- fur
- gabR
- gamR
- gbsR
- gerE
- gerR
- glcR
- glnR
- glpP
- gltC
- gltR
- glvR
- gmuR
- gntR
- gutR
- hrcA
- hutP
- hxlR
- hypR
- immR
- iolR
- kdgR
- kipR
- lacR
- lexA
- lmrA
- lrpA
- lrpB
- lutR
- mdtR
- mgsR
- mhqR
- mntR
- msmR
- mta
- mtrB
- murR
- nadR
- nagR
- nrdR
- nsrR
- ntdR
- ohrR
- opcR
- padR
- paiB
- perR
- pksA
- pucR
- purR
- putR
- pyrR
- qdoR
- rbsR
- remA
- rex
- rghR
- rhaR
- rhgR
- rocR
- rok
- scoC
- sdpR
- senS
- sinR
- sknR
- slrR
- splA
- spoIIID
- spoVT
- spx
- TilS-HprT
- thrR
- tnrA
- treR
- xre
- xylR
Transcription factor/ other/ based on similarity
- yazB
- ybfI
- ybfP
- ybzH
- yceK
- ycgE
- ycgK
- ycnC
- ycxD
- yczG
- ydeB
- ydeC
- ydeE
- ydeF
- ydeL
- ydeP
- ydeS
- ydfD
- ydfL
- ydgG
- ydgJ
- ydhC
- yerO
- yezC
- yezE
- yfiF
- yfiR
- yfiV
- ygzD
- yhbI
- yhcB
- yhcF
- yhdI
- yhgD
- yisR
- yisV
- ykoM
- ykvN
- ykvZ
- ymfC
- yoaU
- yobD
- yobQ
- yonR
- yopO
- yopS
- yotL
- yozG
- ypoP
- yqaF
- yqaG
- yraN
- yrdQ
- ysmB
- ytcD
- ytdP
- ytoI
- ytzE
