SubtiWiki - User contributions [en]

SinR

2010-08-19T10:17:45Z

Swicht: /* Biological materials */

* '''Description:''' transcriptional regulator of post-exponential-phase responses genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sin, flaD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator of post-exponential-phase responses genes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of post-exponential gene expression
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 7.177
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinI]]'', ''[[tasA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14392]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinR_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:''' BSU24610

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10754]

=== Additional information===

=Categories containing this gene/protein=
[[biofilm]], [[transcription factor]], [[Spo0A regulon]]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repressor of biofilm genes, acts as co-repressor for [[SlrR]] {{PubMed|20351052}}

* '''Protein family:'''

* '''Paralogous protein(s):''' [[SlrR]]

=== Genes controlled by SinR ===

* '''Activation by SinR:''' ''[[comK]]''

* '''Repression by SinR:''' ''[[aprE]], [[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}},[[kinB]], ''[[rapG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[sigD]]'','' [[spo0A]]'',''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[spoIIE]]'', ''[[spoIIGA]]-[[sigE]]-[[sigG]]'', ''[[spoVG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[yqxM]]-[[sipW]]-[[tasA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[yvgN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[ywbD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' [[SinI]] and [[SlrA]] are antagonists to [[SinR]] {{PubMed|19788541}}, [[SlrR]] is also antagonist of [[SinR]] {{PubMed|20351052}}

* '''Interactions:''' [[SlrA]]-[[SinR]] {{PubMed|19788541}}, [[SlrR]]-[[SinR]] {{PubMed|20351052}}, [[SinR]]-[[ScoC]], [[SinR]]-[[SinI]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]])

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06533 P06533]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24610]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[sinI]]-[[sinR]]'' {{PubMed|3125149}}
** ''[[sinR]]'' {{PubMed|3125149}}

* '''[[Sigma factor]]:'''
** ''[[sinI]]'': [[SigA]] {{PubMed|3125149}}
** ''[[sinR]]'': [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** ''[[sinI]]'': repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** ''[[sinI]]'': repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** ''[[sinI]]'': repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TMB079 ''sinR::spec'', GP736 (tetR), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP960 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20395361 20541494 </pubmed>

==Original publications==
<pubmed>8955328,15661000,8878039,16923912,15104138,16430695,16430696,18047568,18430133,11751836,1906467,11751836,7635837,11751836, 19201793, 10547280, 15104138, 9799632 19788541 19898538 3125149 8932324 20351052 </pubmed>

[[Category:Protein-coding genes]]

AbrB

2010-08-19T10:13:46Z

Swicht: /* Biological materials */

* '''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/biofilm.html Biofilm], [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]]'', ''[[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''

* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[comK]], [[ftsA]]-[[ftsZ]], [[kinB]], [[pbpE]], [[sigH]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]], [[sdpA operon]], [[sunA]], [[skfA operon]], [[sinI]]-[[sinR]], [[sigW]], [[yuaB]]''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on Ser-86 {{PubMed|20509597}}

* '''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), [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]

* '''UniProt:''' [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:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''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=
==Reviews==
<pubmed>11964117 19995980 11931565 </pubmed>

==Original Publications==
<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407,19202088, 12076816,17660417,18326573,2554317,18430133,7768874,2507867,1766371,15687200,1908787,18840696,2106683,15687200,2504584,18840696 3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 19202088 7592460, 19465659 20509597 </pubmed>

[[Category:Protein-coding genes]]

SlrA

2010-08-19T10:12:34Z

Swicht: /* Biological materials */

* '''Description:''' anti-repressor, antagonist of [[SinR]] and [[SlrR]], involved in control of flagellar genes and ''[[epsA|eps]]'' and ''[[yqxM]]-[[sipW]]-[[tasA]]'' operons 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''slrA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || antagonist of [[SinR]] and [[SlrR]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of biofilm formation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, y.yy
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywcC]]'', ''[[ywcB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAX52707]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ywcC_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:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:'''

=== Additional information===

This gene was only recently identified. [http://www.ncbi.nlm.nih.gov/sites/entrez/18647168 PubMed]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binding of [[SinR]] resulting in induction of [[SinR]]-repressed genes and operons {{PubMed|19788541}}

* '''Protein family:'''

* '''Paralogous protein(s):''' [[SinI]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' [[SlrR]] inhibits activity of [[SlrA]] (i. e. binding to [[SinR]]) {{PubMed|19788541}}

* '''Interactions:''' [[SlrA]]-[[SinR]] {{PubMed|19788541}}, [[SlrA]]-[[SlrR]] {{PubMed|19788541}}

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P0C8M5 P0C8M5]

* '''KEGG entry:''' no entry

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[slrA]]-[[ywcB]]-[[ywcA]]''
** ''[[slrA]]-[[ywcB]]''
** ''[[slrA]]''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[YwcC]]: transcription repression {{PubMed|18647168,19788541}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18647168, 19788541, </pubmed>

[[Category:Protein-coding genes]]

SlrR

2010-08-19T10:10:06Z

Swicht: /* Biological materials */

* '''Description:''' transcriptional activator of competence development and sporulation genes, represses [[SigD]]-dependent flagellar genes, antagonist of [[SlrA]] and [[SinR]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''slrR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveJ, slr''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription regulator, [[SlrA]] antagonist
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of initiation of biofilm formation and of autolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.63
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 456 bp, 152 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsA]]'', ''[[pnbA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15443]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:slr_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:''' BSU34380

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11858]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binding and concomintant inactivation of [[SlrA]] results in release of [[SinR]] from the [[SinR]]-[[SlrA]] complex and subsequent induction of [[SinR]]-controlled genes and operons for biofilm formation {{PubMed|19788541}}, repression of transcription of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'' {{PubMed|20351052}}

* '''Protein family:'''

* '''Paralogous protein(s):''' [[SinR]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' interaction with [[SinR]] triggers binding of SlrR to the promoters of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'', resulting in their repression {{PubMed|20351052}}

* '''Interactions:''' [[SlrA]]-[[SlrR]] {{PubMed|19788541}}, [[SinR]]-[[SlrR]] {{PubMed|20351052}}

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71049 P71049]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34380]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[Abh]]: transcription activation {{PubMed|19767430}}
** [[SinR]]: transcription repression {{PubMed|19788541}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]], [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR itself {{PubMed|20351052}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Original publications==
<pubmed>18430133,18647168, 19767430, 19788541 20351052 </pubmed>

[[Category:Protein-coding genes]]

SinI

2010-08-19T10:08:51Z

Swicht: /* Biological materials */

* '''Description:''' antagonist of [[SinR]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || antagonist of [[SinR]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SinR]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 6.333
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 171 bp, 57 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqhG]]'', ''[[sinR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14391]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinI_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:''' BSU24600

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10753]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

* '''Paralogous protein(s):''' [[SlrA]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''

* '''Interactions:''' [[SinR]]-[[SinI]]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23308 P23308]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24600]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' [[sinI]]-[[sinR]] {{PubMed|3125149}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** activated under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation, in a portion of cells [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP959 (spc), available in [[Stülke]] lab
** DS91 (spc) NCIB3610 derivate, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Original publications==
<pubmed>3125149 15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 </pubmed>

[[Category:Protein-coding genes]]

SinR

2010-08-19T10:07:03Z

Swicht: /* Biological materials */

* '''Description:''' transcriptional regulator of post-exponential-phase responses genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sin, flaD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator of post-exponential-phase responses genes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of post-exponential gene expression
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 7.177
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinI]]'', ''[[tasA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14392]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinR_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:''' BSU24610

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10754]

=== Additional information===

=Categories containing this gene/protein=
[[biofilm]], [[transcription factor]], [[Spo0A regulon]]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repressor of biofilm genes, acts as co-repressor for [[SlrR]] {{PubMed|20351052}}

* '''Protein family:'''

* '''Paralogous protein(s):''' [[SlrR]]

=== Genes controlled by SinR ===

* '''Activation by SinR:''' ''[[comK]]''

* '''Repression by SinR:''' ''[[aprE]], [[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}},[[kinB]], ''[[rapG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[sigD]]'','' [[spo0A]]'',''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[spoIIE]]'', ''[[spoIIGA]]-[[sigE]]-[[sigG]]'', ''[[spoVG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[yqxM]]-[[sipW]]-[[tasA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[yvgN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed], ''[[ywbD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' [[SinI]] and [[SlrA]] are antagonists to [[SinR]] {{PubMed|19788541}}, [[SlrR]] is also antagonist of [[SinR]] {{PubMed|20351052}}

* '''Interactions:''' [[SlrA]]-[[SinR]] {{PubMed|19788541}}, [[SlrR]]-[[SinR]] {{PubMed|20351052}}, [[SinR]]-[[ScoC]], [[SinR]]-[[SinI]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]])

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06533 P06533]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24610]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[sinI]]-[[sinR]]'' {{PubMed|3125149}}
** ''[[sinR]]'' {{PubMed|3125149}}

* '''[[Sigma factor]]:'''
** ''[[sinI]]'': [[SigA]] {{PubMed|3125149}}
** ''[[sinR]]'': [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** ''[[sinI]]'': repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** ''[[sinI]]'': repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** ''[[sinI]]'': repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TMB079 ''sinR::spec'', GP736 (tetR), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20395361 20541494 </pubmed>

==Original publications==
<pubmed>8955328,15661000,8878039,16923912,15104138,16430695,16430696,18047568,18430133,11751836,1906467,11751836,7635837,11751836, 19201793, 10547280, 15104138, 9799632 19788541 19898538 3125149 8932324 20351052 </pubmed>

[[Category:Protein-coding genes]]

Talk:SubtiPathways

2010-06-04T14:08:52Z

Swicht: /* Biofilm formation */

<big>'''Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!'''</big>

__TOC__

== General comments about all diagrams ==
* There seem to be some compatibility problems using Google Chrome. Nonetheless, Mozilla Firefox, Netscape, Microsoft Explorer, Safari, and Opera are working properly.
* write comments here

 

== Carbon metabolism ==

=== Central carbon metabolism ===

* write comments here

=== Utilization of different carbon sources ===

* write comments here

 

== Nitrogen and amino acid metabolism ==

=== Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine) ===

*write comments here

=== Alanine, glycine, serine ===

*write comments here

=== Aspartate, asparagine ===

* write comments here

=== Cysteine, methionine ===

* Repel: Eventuell Einbindung von Extramarkern für die S-Box (bzw. alle riboswitches)???? Es gibt ja dafür extra Seiten im Subtiwiki. Sollte man aber erst mal mit Lope und Arne diskutieren (Jörg)
* Cystin-Aufnahme-Systeme mit aufnehmen: TcyP, TcyABC, TcyJKLMN (Jörg)

=== Histidine ===

*write comments here

=== Isoleucine, valine, leucine ===

* Isoleucin-Abbau: Bcd und YwaA sind zwei unterschiedliche Reaktionen, Bcd geht mit NAD, nicht mit 2-KG (Jörg)

=== Lysine, threonine ===

* write comments here

=== Phenylalanine, tyrosine, tryptophan ===

* write comments here

=== Proline ===

*write comments here

 
== Lipid metabolism ==

=== Fatty acid and phospholipid biosynthesis ===

* The structure of PDGP is wrong (although the name, CDP-diacylglycerol, seems right). Wrong PubChem ID?
* The same applies for phosphatidylglycerol, L-serine, and others.

=== Fatty acid degradation ===

* write comments here

== Nucleotides ==

=== Gene regulation of nucleotides ===

* write comments here

=== Nucleosides catabolism ===

*write comments here

=== Purine metabolism ===

*write comments here

=== Purine catabolism ===

*write comments here

=== Purine salvage pathways ===

* write comments here

=== Pyrimidine metabolism ===

*write comments here

 

== Metabolism of cofactors ==

=== CoA synthesis ===

*write comments here

=== Folate biosynthesis ===

*write comments here

=== Menaquinone ===

*write comments here

=== Riboflavin and FAD synthesis ===

* write comments here

=== Thiamin synthesis ===

* write comments here
 

== Other pathways ==

=== Cellwall ===

*write comments here

=== Stress response ===

* write comments here

=== Phosphorelay ===
* In the interaction between KipI and KipA, that prevents the complex between KinA and KipI, KinA should be released from the complex. This has to be added to the diagram.

=== Sulfate assimilation ===

*write comments here

=== tRNA charging ===

* write comments here

=== Biofilm formation ===

* SlrR bind SinR, according to Losick {{PubMed|20351052}}