Difference between revisions of "SwrB"
| (53 intermediate revisions by 7 users not shown) | |||
| Line 1: | Line 1: | ||
| − | * '''Description:''' | + | * '''Description:''' control of [[SigD]] activity, required for full [[SigD]] activity, activates the flagellar type III secretion export apparatus by the membrane protein [[FliP]] <br/><br/> |
{| align="right" border="1" cellpadding="2" | {| align="right" border="1" cellpadding="2" | ||
|- | |- | ||
|style="background:#ABCDEF;" align="center"|'''Gene name''' | |style="background:#ABCDEF;" align="center"|'''Gene name''' | ||
| − | |'' | + | |''swrB '' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylxL'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Essential''' || | + | |style="background:#ABCDEF;" align="center"| '''Essential''' || no |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || unknown |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigD]] activity |
| + | |- | ||
| + | |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=BSU16480 swrB] | ||
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 4.417 | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 4.417 | ||
| Line 18: | Line 20: | ||
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 501 bp, 167 aa | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 501 bp, 167 aa | ||
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sigD]]'', ''[[rpsB]]'' |
|- | |- | ||
| − | |style="background:#FAF8CC;" align="center"|'''[http:// | + | |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16480 DNA_with_flanks] |
| − | |||
|- | |- | ||
|colspan="2" | '''Genetic context''' <br/> [[Image:ylxL_context.gif]] | |colspan="2" | '''Genetic context''' <br/> [[Image:ylxL_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=ylxL_1717286_1717789_1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:swrB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16480]] | ||
|- | |- | ||
|} | |} | ||
__TOC__ | __TOC__ | ||
| + | <br/><br/><br/><br/> | ||
| + | <br/><br/><br/><br/> | ||
| + | <br/><br/><br/><br/> | ||
| + | <br/><br/> | ||
| + | |||
| + | = [[Categories]] containing this gene/protein = | ||
| + | {{SubtiWiki category|[[sigma factors and their control]]}}, | ||
| + | {{SubtiWiki category|[[motility and chemotaxis]]}} | ||
| − | + | = This gene is a member of the following [[regulons]] = | |
| + | {{SubtiWiki regulon|[[CodY regulon]]}}, | ||
| + | {{SubtiWiki regulon|[[DegU regulon]]}}, | ||
| + | {{SubtiWiki regulon|[[SigD regulon]]}}, | ||
| + | {{SubtiWiki regulon|[[Spo0A regulon]]}} | ||
=The gene= | =The gene= | ||
| Line 35: | Line 51: | ||
=== Basic information === | === Basic information === | ||
| − | * ''' | + | * '''Locus tag:''' BSU16480 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
| + | * no swarming motility on B medium [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed] | ||
| + | * defective in the assembly of the flagellar hook {{PubMed|26244495}} | ||
=== Database entries === | === Database entries === | ||
| + | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16480&redirect=T BSU16480] | ||
| − | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ | + | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html] |
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10752] | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10752] | ||
=== Additional information=== | === Additional information=== | ||
| − | |||
=The protein= | =The protein= | ||
| Line 70: | Line 88: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
| − | * '''Interactions:''' | + | * '''[[SubtInteract|Interactions]]:''' |
| − | * '''Localization:''' | + | * '''[[Localization]]:''' |
| + | ** membrane-proximal (Spotty) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] | ||
| + | ** membrane {{PubMed|26244495}} | ||
=== Database entries === | === Database entries === | ||
| + | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16480&redirect=T BSU16480] | ||
* '''Structure:''' | * '''Structure:''' | ||
| − | * ''' | + | * '''UniProt:''' [http://www.uniprot.org/uniprot/P40405 P40405] |
| − | * '''KEGG entry:''' | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16480] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
| Line 87: | Line 108: | ||
=Expression and regulation= | =Expression and regulation= | ||
| + | * '''Operon:''' part of the [[fla-che operon]] | ||
| + | ** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}} | ||
| + | ** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}} | ||
| + | ** ''[[sigD]]-[[swrB]]'' {{PubMed|9335309}} | ||
| − | * ''' | + | * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylxL_1717286_1717789_1 swrB] {{PubMed|22383849}} |
| − | * '''Sigma factor:''' | + | * '''[[Sigma factor]]:''' |
| + | ** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}} | ||
| + | ** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}} | ||
| + | ** ''[[sigD]]'': [[SigA]] {{PubMed|9335309}} | ||
| − | * '''Regulation:''' | + | * '''Regulation:''' see [[fla-che operon]] |
| − | * '''Regulatory mechanism:''' | + | * '''Regulatory mechanism:''' see [[fla-che operon]] |
| − | * '''Additional information:''' | + | * '''Additional information:''' |
=Biological materials = | =Biological materials = | ||
| Line 117: | Line 145: | ||
=References= | =References= | ||
| + | <pubmed>15175317,19202088,16357223,15066026,9335309,14651647, 16479537, 19202088 9657996,8157612, 17850253 24386445 22329926 26244495</pubmed> | ||
| − | + | [[Category:Protein-coding genes]] | |
Latest revision as of 11:48, 6 August 2015
- Description: control of SigD activity, required for full SigD activity, activates the flagellar type III secretion export apparatus by the membrane protein FliP
| Gene name | swrB |
| Synonyms | ylxL |
| Essential | no |
| Product | unknown |
| Function | control of SigD activity |
| Gene expression levels in SubtiExpress: swrB | |
| MW, pI | 18 kDa, 4.417 |
| Gene length, protein length | 501 bp, 167 aa |
| Immediate neighbours | sigD, rpsB |
| Sequences | Protein DNA DNA_with_flanks |
Genetic context 
This image was kindly provided by SubtiList
| |
Expression at a glance PubMed
| |
Contents
Categories containing this gene/protein
sigma factors and their control, motility and chemotaxis
This gene is a member of the following regulons
CodY regulon, DegU regulon, SigD regulon, Spo0A regulon
The gene
Basic information
- Locus tag: BSU16480
Phenotypes of a mutant
Database entries
- BsubCyc: BSU16480
- DBTBS entry: [1]
- SubtiList entry: [2]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity:
- Protein family:
- Paralogous protein(s):
Extended information on the protein
- Kinetic information:
- Domains:
- Modification:
- Cofactor(s):
- Effectors of protein activity:
Database entries
- BsubCyc: BSU16480
- Structure:
- UniProt: P40405
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- Operon: part of the fla-che operon
- flgB-flgC-fliE-fliF-fliG-fliH-fliI-fliJ-ylxF-fliK-flgD-flgE-fliL-fliM-fliY-cheY-fliZ-fliP-fliQ-fliR-flhB-flhA-flhF-flhG-cheB-cheA-cheW-cheC-cheD-sigD-swrB PubMed
- ylxF-fliK-flgD-flgE-fliL-fliM-fliY-cheY-fliZ-fliP-fliQ-fliR-flhB-flhA-flhF-flhG-cheB-cheA-cheW-cheC-cheD-sigD-swrB PubMed
- sigD-swrB PubMed
- Regulation: see fla-che operon
- Regulatory mechanism: see fla-che operon
- Additional information:
Biological materials
- Mutant:
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system:
- Antibody:
Labs working on this gene/protein
Your additional remarks
References
Andrew M Phillips, Rebecca A Calvo, Daniel B Kearns
Functional Activation of the Flagellar Type III Secretion Export Apparatus.
PLoS Genet: 2015, 11(8);e1005443
[PubMed:26244495]
[WorldCat.org]
[DOI]
(I e)
Serena Mordini, Cecilia Osera, Simone Marini, Francesco Scavone, Riccardo Bellazzi, Alessandro Galizzi, Cinzia Calvio
The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis.
PLoS One: 2013, 8(12);e85065
[PubMed:24386445]
[WorldCat.org]
[DOI]
(I e)
Loralyn M Cozy, Andrew M Phillips, Rebecca A Calvo, Ashley R Bate, Yi-Huang Hsueh, Richard Bonneau, Patrick Eichenberger, Daniel B Kearns
SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σ(D) in Bacillus subtilis.
Mol Microbiol: 2012, 83(6);1210-28
[PubMed:22329926]
[WorldCat.org]
[DOI]
(I p)
Kassem Hamze, Daria Julkowska, Sabine Autret, Krzysztof Hinc, Krzysztofa Nagorska, Agnieszka Sekowska, I Barry Holland, Simone J Séror
Identification of genes required for different stages of dendritic swarming in Bacillus subtilis, with a novel role for phrC.
Microbiology (Reading): 2009, 155(Pt 2);398-412
[PubMed:19202088]
[WorldCat.org]
[DOI]
(P p)
Kazuo Kobayashi
Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis.
Mol Microbiol: 2007, 66(2);395-409
[PubMed:17850253]
[WorldCat.org]
[DOI]
(P p)
Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537]
[WorldCat.org]
[DOI]
(P p)
Daniel B Kearns, Richard Losick
Cell population heterogeneity during growth of Bacillus subtilis.
Genes Dev: 2005, 19(24);3083-94
[PubMed:16357223]
[WorldCat.org]
[DOI]
(P p)
H Werhane, P Lopez, M Mendel, M Zimmer, G W Ordal, L M Márquez-Magaña
The last gene of the fla/che operon in Bacillus subtilis, ylxL, is required for maximal sigmaD function.
J Bacteriol: 2004, 186(12);4025-9
[PubMed:15175317]
[WorldCat.org]
[DOI]
(P p)
Daniel B Kearns, Frances Chu, Rivka Rudner, Richard Losick
Genes governing swarming in Bacillus subtilis and evidence for a phase variation mechanism controlling surface motility.
Mol Microbiol: 2004, 52(2);357-69
[PubMed:15066026]
[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)
W Estacio, S S Anna-Arriola, M Adedipe, L M Márquez-Magaña
Dual promoters are responsible for transcription initiation of the fla/che operon in Bacillus subtilis.
J Bacteriol: 1998, 180(14);3548-55
[PubMed:9657996]
[WorldCat.org]
[DOI]
(P p)
R Allmansberger
Temporal regulation of sigD from Bacillus subtilis depends on a minor promoter in front of the gene.
J Bacteriol: 1997, 179(20);6531-5
[PubMed:9335309]
[WorldCat.org]
[DOI]
(P p)
L M Márquez-Magaña, M J Chamberlin
Characterization of the sigD transcription unit of Bacillus subtilis.
J Bacteriol: 1994, 176(8);2427-34
[PubMed:8157612]
[WorldCat.org]
[DOI]
(P p)
