SubtiWiki - User contributions [en]

AbrB

2009-06-26T13:52:29Z

Mstrauch: /* Genes/ operons controlled by AbrB */

* '''Description:''' transcriptional regulator of transition state genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''abrB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX, tolB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition from growth to stationary phase
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/aspartate_asparagine.html Asp, Asn], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 282 bp, 94 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11813]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:abrB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00370

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)

=== Genes/ operons controlled by AbrB ===

* '''Activated by AbrB:''' ''[[citB]]'', ''[[comK]], [[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''

* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]], [[sdpA operon]], [[sunA operon]], [[skfA operon]], [[abh]], [[pbpE]], [[ggt]], [[sinI]]-[[sinR]], [[sigW]], [[yuaB]]''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]

* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), 1Z0R (N-terminal DNA recognition domain) [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00370]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]

* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]

* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TT731 (aphA3)

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]

=Your additional remarks=

=References=

<pubmed>3145384,2437099,8878039,2504584,11377867,1850083,2106683,11931565,12586407,19202088,12076816,17660417,18326573,2554317,18430133,7768874,2507867,1766371,15687200,1908787,18840696,2106683,15687200,2504584,18840696 3145384 8821944 8576231 11101897 11395475 11583849 11964117 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 19202088 7592460, 19465659 </pubmed>

AbrB

2009-06-23T13:49:08Z

Mstrauch: corrected size of gene & protein: AbrB protein starts at 2nd Met in seq = met-phe-met...

* '''Description:''' transcriptional regulator of transition state genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''abrB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX, tolB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition from growth to stationary phase
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/aspartate_asparagine.html Asp, Asn], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 282 bp, 94 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11813]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:abrB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00370

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)

=== Genes/ operons controlled by AbrB ===

* '''Activated by AbrB:''' ''[[citB]]'', ''[[comK]], [[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''

* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]]''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]

* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), 1Z0R (N-terminal DNA recognition domain) [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00370]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]

* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]

* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TT731 (aphA3)

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]

=Your additional remarks=

=References=

<pubmed>3145384,2437099,8878039,2504584,11377867,1850083,2106683,11931565,12586407,19202088,12076816,17660417,18326573,2554317,18430133,7768874,2507867,1766371,15687200,1908787,18840696,2106683,15687200,2504584,18840696 3145384 8821944 8576231 11101897 11395475 11583849 11964117 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 19202088 7592460, 19465659 </pubmed>

AbrB

2009-06-23T13:44:10Z

Mstrauch: added other synonym for abrB

* '''Description:''' transcriptional regulator of transition state genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''abrB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX, tolB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition from growth to stationary phase
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/aspartate_asparagine.html Asp, Asn], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11813]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:abrB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00370

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)

=== Genes/ operons controlled by AbrB ===

* '''Activated by AbrB:''' ''[[citB]]'', ''[[comK]], [[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''

* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]]''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]

* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), 1Z0R (N-terminal DNA recognition domain) [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00370]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]

* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]

* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TT731 (aphA3)

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]

=Your additional remarks=

=References=

<pubmed>3145384,2437099,8878039,2504584,11377867,1850083,2106683,11931565,12586407,19202088,12076816,17660417,18326573,2554317,18430133,7768874,2507867,1766371,15687200,1908787,18840696,2106683,15687200,2504584,18840696 3145384 8821944 8576231 11101897 11395475 11583849 11964117 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 19202088 7592460, 19465659 </pubmed>

Labs working on Bacillus

2009-06-23T13:39:18Z

Mstrauch: Added Mark A. Strauch to labs working on subtilis

This is a partial list of groups working with ''Bacillus subtilis'':

* [[Alessandra Albertini]]
* [[Arthur Aronson]]
* [[Stephane Aymerich]]
* [[Imrich Barak]]
* [[David Bechhofer]]
* [[Sabine Brantl]]
* [[Erhard Bremer]]
* [[Richard Brennan]]
* [[Ciaran Condon]]
* [[Simon Cutting]]
* [[Isabel de Sa-Nogueira]]
* [[Nathalie Declerck]]
* [[Kevin Devine]]
* [[Josef Deutscher]]
* [[Jeff Errington]]
* [[Jan Maarten van Dijl]]
* [[Susan Fisher]]
* [[Yasutaro Fujita]]
* [[Anne Galinier]]
* [[Boris Görke]]
* [[Peter Graumann]]
* [[Bill Haldenwang]]
* [[Leendert Hamoen]]
* [[Elisabeth Härtig]]
* [[Roland Hartmann]]
* [[Colin Harwood]]
* [[Michael Hecker]]
* [[Lars Hederstedt]]
* [[John Helmann]]
* [[Tina Henkin]]
* [[Adriano Henriques]]
* [[Wolfgang Hillen]]
* [[Jim Hoch]]
* [[Marion Hulett]]
* [[Laurent Janniere]]
* [[Hanne Jarmer]]
* [[Mark J. Jedrzejas]]
* [[Oscar Kuipers]]
* [[Rick Lewis]]
* [[Isabelle Martin-Verstraete]]
* [[Thorsten Mascher]]
* [[Ivan Mijakovic]]
* [[Anne Moir]]
* [[Charles Moran]]
* [[Philippe Noirot]]
* [[Naotake Ogasawara]]
* [[Chet Price]]
* [[Harald Putzer]]
* [[Milton H. Saier]]
* [[Margarita Salas]]
* [[Uwe Sauer]]
* [[Wolfgang Schumann]]
* [[Linc Sonenshein]]
* [[Jörg Stülke]]
* [[Hendrik Szurmant]]
* [[User:Jwveening |Jan-Willem Veening]]
* [[Uwe Völker]]
* [[Claes von Wachenfeldt]]
* [[Thomas Wiegert]]
* [[Tony Wilkinson]]
* [[Wade Winkler]]
* [[Ken-ichi Yoshida]]
* [[Daniel R. Zeigler]]
* [[Peter Zuber]]
* [[Mark A. Strauch]]