Latest revision as of 13:35, 2 April 2014

Description: inhibitor of AbrB activity

Gene name	abbA
Synonyms	ykzF
Essential	no
Product	anti-repressor
Function	inhibition of AbrB
*Gene expression levels in SubtiExpress*: abbA
*Interactions involving this protein in SubtInteract*: AbbA
MW, pI	7 kDa, 4.642
Gene length, protein length	195 bp, 65 aa
Immediate neighbours	ykuK, ykuL
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance PubMed

Categories containing this gene/protein

transcription factors and their control

This gene is a member of the following regulons

CcpA regulon, Spo0A regulon

The gene

Basic information

Locus tag: BSU14120

Phenotypes of a mutant

Database entries

BsubCyc: BSU14120

DBTBS entry: [1]

SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

Catalyzed reaction/ biological activity: inhibition of AbrB activity PubMed

Protein family:

Paralogous protein(s):

Extended information on the protein

Kinetic information:

Domains:

Modification:

Cofactors:

Effectors of protein activity:

Interactions:
- forms dimers PubMed
- AbbA-AbrB, AbbA binds the N-terminal DNA-binding domain of AbrB PubMed

Localization:

Database entries

BsubCyc: BSU14120

Structure: 2LZF PubMed

UniProt: O31697

KEGG entry: [3]

E.C. number:

Additional information

Expression and regulation

Operon: ykuJ-ykuK-abbA-ykuL-ccpC PubMed

Expression browser: abbA PubMed

Sigma factor:

Regulation:
- repressed by glucose (4.3-fold) (CcpA) PubMed
- expressed under conditions that trigger sporulation (Spo0A) PubMed

Regulatory mechanism:
- CcpA: transcription repression PubMed
- Spo0A: transcription activation by Spo0A~P PubMed

Additional information:

Biological materials

Mutant: GP214 (deletion of ykuJ-ykuK-abbA-ykuL, replaced by aphA3), available in the Stülke lab

Expression vector:

lacZ fusion: pGP708 (in pAC5), available in Stülke lab, pGP712 (in pAC6), available in Stülke lab

GFP fusion:

two-hybrid system:

Antibody:

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Your additional remarks

References

Ashley T Tucker, Benjamin G Bobay, Allison V Banse, Andrew L Olson, Erik J Soderblom, M Arthur Moseley, Richele J Thompson, Kristen M Varney, Richard Losick, John Cavanagh
A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA.
J Mol Biol: 2014, 426(9);1911-24
[PubMed:24534728] [WorldCat.org] [DOI] (I p)

Allison V Banse, Arnaud Chastanet, Lilah Rahn-Lee, Errett C Hobbs, Richard Losick
Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2008, 105(40);15547-52
[PubMed:18840696] [WorldCat.org] [DOI] (I p)

Hans-Matti Blencke, Irene Reif, Fabian M Commichau, Christian Detsch, Ingrid Wacker, Holger Ludwig, Jörg Stülke
Regulation of citB expression in Bacillus subtilis: integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system.
Arch Microbiol: 2006, 185(2);136-46
[PubMed:16395550] [WorldCat.org] [DOI] (P p)

Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647] [WorldCat.org] [DOI] (P p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

@@ Line 1: / Line 1: @@
-* '''Description:''' inhibitor of AbrB activity<br/><br/>
+* '''Description:''' inhibitor of [[AbrB]] activity<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of AbrB
+|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of [[AbrB]]
+|-
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14120 abbA]
+|-
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=AbbA AbbA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642
@@ Line 20: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13285&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14120 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
+|-
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykzF_1485118_1485315_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:abbA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14120]]
 |-
 |}
 __TOC__
+<br/><br/><br/><br/>
+<br/><br/><br/><br/>
+<br/><br/><br/><br/>
+<br/><br/>
-<br/><br/>
+= [[Categories]] containing this gene/protein =
+{{SubtiWiki category|[[transcription factors and their control]]}}
+= This gene is a member of the following [[regulons]] =
+{{SubtiWiki regulon|[[CcpA regulon]]}},
+{{SubtiWiki regulon|[[Spo0A regulon]]}}
 =The gene=
@@ Line 35: / Line 50: @@
 === Basic information ===
-* '''Coordinates:'''
+* '''Locus tag:''' BSU14120
 ===Phenotypes of a mutant ===
 === Database entries ===
+* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14120&redirect=T BSU14120]
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
@@ Line 46: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 62: / Line 77: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
-* '''Interactions:''' AbbA-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+* '''[[SubtInteract|Interactions]]:'''
+** forms dimers {{PubMed|24534728}}
+** [[AbbA]]-[[AbrB]], [[AbbA]] binds the N-terminal DNA-binding domain of [[AbrB]] {{PubMed|24534728,18840696}}
-* '''Localization:'''
+* '''[[Localization]]:'''
 === Database entries ===
+* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14120&redirect=T BSU14120]
-* '''Structure:'''
+* '''Structure:'''	[http://pdb.org/pdb/explore/explore.do?structureId=2LZF 2LZF] {{PubMed|24534728}}
-* '''Swiss prot entry:'''
+* '''UniProt:''' [http://www.uniprot.org/uniprot/O31697 O31697]
-* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14120]
+* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14120]
 * '''E.C. number:'''
@@ Line 88: / Line 106: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]-[[ccpC]]'' {{PubMed|16395550}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykzF_1485118_1485315_1 abbA] {{PubMed|22383849}}
 * '''Sigma factor:'''
-* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  subject to carbon catabolite repression (4-fold: [[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], expressed at onset of stationary phase ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+* '''Regulation:'''
+** repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+** expressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|18840696,14651647}}
-* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], [[Spo0A]]: transcription activation by Spo0A~P [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+* '''Regulatory mechanism:'''
+** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
+** [[Spo0A]]: transcription activation by [[Spo0A]]~P {{PubMed|18840696,14651647}}
 * '''Additional information:'''
@@ Line 100: / Line 124: @@
 =Biological materials =
-* '''Mutant:'''
+* '''Mutant:''' GP214 (deletion of ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]'', replaced by ''aphA3''), available in the [[Stülke]] lab
 * '''Expression vector:'''
-* '''lacZ fusion:'''
+* '''lacZ fusion:''' pGP708 (in [[pAC5]]), available in [[Stülke]] lab, pGP712 (in [[pAC6]]), available in [[Stülke]] lab
 * '''GFP fusion:'''
@@ Line 120: / Line 144: @@
 =References=
-# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+<pubmed> 24534728,18840696,14651647,12850135 18840696 12850135,16395550 </pubmed>
-# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
-# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
+[[Category:Protein-coding genes]]
-# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Difference between revisions of "AbbA"

Latest revision as of 13:35, 2 April 2014

Contents

Categories containing this gene/protein

This gene is a member of the following regulons

The gene

Basic information

Phenotypes of a mutant

Database entries

Additional information

The protein

Basic information/ Evolution

Extended information on the protein

Database entries

Additional information

Expression and regulation

Biological materials

Labs working on this gene/protein

Your additional remarks

References

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