Difference between revisions of "SigD"

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|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of flagella, motility, chemotaxis and autolysis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of flagella, motility, chemotaxis and autolysis
 
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|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16470 sigD]
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|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=BSU16470 sigD]
 
|-
 
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigD SigD]
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigD SigD]
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheD]]'', ''[[swrB]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheD]]'', ''[[swrB]]''
 
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13520&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16470 Advanced_DNA]
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:sigD_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:sigD_context.gif]]

Revision as of 12:51, 13 May 2013

Gene name sigD
Synonyms flaB
Essential no
Product RNA polymerase sigma factor SigD
Function regulation of flagella, motility, chemotaxis and autolysis
Gene expression levels in SubtiExpress: sigD
Interactions involving this protein in SubtInteract: SigD
MW, pI 29 kDa, 5.167
Gene length, protein length 762 bp, 254 aa
Immediate neighbours cheD, swrB
Sequences Protein DNA Advanced_DNA
Genetic context
SigD context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
SigD expression.png















Categories containing this gene/protein

transcription, sigma factors and their control, motility and chemotaxis

This gene is a member of the following regulons

CodY regulon, SigD regulon, Spo0A regulon

The SigD regulon

The gene

Basic information

  • Locus tag: BSU16470

Phenotypes of a mutant

  • Inactivation of alsR, sigD and sigW increases competitive fitness of Bacillus subtilis under non-sporulating conditions PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: sigma-70 factor family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: interaction with FlgM inhibits SigD activity PubMed

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • flgB promoter: repressed under conditions that trigger sporulation (Spo0A) PubMed
  • Regulatory mechanism:
  • 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
  • FLAG-tag construct: GP948 (ermC, based on pGP1087), available in the Stülke lab
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Reviews

Jan-Willem Veening, Oscar P Kuipers
Gene position within a long transcript as a determinant for stochastic switching in bacteria.
Mol Microbiol: 2010, 76(2);269-72
[PubMed:20233302] [WorldCat.org] [DOI] (I p)


The SigD regulon

Masakuni Serizawa, Hiroki Yamamoto, Hirotake Yamaguchi, Yasutaro Fujita, Kazuo Kobayashi, Naotake Ogasawara, Junichi Sekiguchi
Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses.
Gene: 2004, 329;125-36
[PubMed:15033535] [WorldCat.org] [DOI] (P p)

L M Márquez, J D Helmann, E Ferrari, H M Parker, G W Ordal, M J Chamberlin
Studies of sigma D-dependent functions in Bacillus subtilis.
J Bacteriol: 1990, 172(6);3435-43
[PubMed:2111808] [WorldCat.org] [DOI] (P p)


Original publications

Additional publications: PubMed

Wayne L Nicholson
Increased competitive fitness of Bacillus subtilis under nonsporulating conditions via inactivation of pleiotropic regulators AlsR, SigD, and SigW.
Appl Environ Microbiol: 2012, 78(9);3500-3
[PubMed:22344650] [WorldCat.org] [DOI] (I p) 

Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J  
A Novel Factor Controlling Bistability in Bacillus subtilis: The YmdB Protein Affects
Flagellin Expression and Biofilm Formation. 
J Bacteriol.: 2011, 193(21):5997-6007. 
PubMed:21856853

Loralyn M Cozy, Daniel B Kearns
Gene position in a long operon governs motility development in Bacillus subtilis.
Mol Microbiol: 2010, 76(2);273-85
[PubMed:20233303] [WorldCat.org] [DOI] (I p)

Letal I Salzberg, John D Helmann
Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition.
J Bacteriol: 2008, 190(23);7797-807
[PubMed:18820022] [WorldCat.org] [DOI] (I 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)

Ana R Perez, Angelica Abanes-De Mello, Kit Pogliano
Suppression of engulfment defects in bacillus subtilis by elevated expression of the motility regulon.
J Bacteriol: 2006, 188(3);1159-64
[PubMed:16428420] [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)

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)

Haike Antelmann, Hiroki Yamamoto, Junichi Sekiguchi, Michael Hecker
Stabilization of cell wall proteins in Bacillus subtilis: a proteomic approach.
Proteomics: 2002, 2(5);591-602
[PubMed:11987133] [WorldCat.org] [DOI] (P p)

D B Mirel, W F Estacio, M Mathieu, E Olmsted, J Ramirez, L M Márquez-Magaña
Environmental regulation of Bacillus subtilis sigma(D)-dependent gene expression.
J Bacteriol: 2000, 182(11);3055-62
[PubMed:10809682] [WorldCat.org] [DOI] (P p)

M G Bertero, B Gonzales, C Tarricone, F Ceciliani, A Galizzi
Overproduction and characterization of the Bacillus subtilis anti-sigma factor FlgM.
J Biol Chem: 1999, 274(17);12103-7
[PubMed:10207036] [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)

T Caramori, A Galizzi
The UP element of the promoter for the flagellin gene, hag, stimulates transcription from both SigD- and SigA-dependent promoters in Bacillus subtilis.
Mol Gen Genet: 1998, 258(4);385-8
[PubMed:9648743] [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)

K Fredrick, J D Helmann
RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates.
Proc Natl Acad Sci U S A: 1997, 94(10);4982-7
[PubMed:9144176] [WorldCat.org] [DOI] (P p)

Y F Chen, J D Helmann
DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally.
J Mol Biol: 1997, 267(1);47-59
[PubMed:9096206] [WorldCat.org] [DOI] (P p)

K Fredrick, J D Helmann
FlgM is a primary regulator of sigmaD activity, and its absence restores motility to a sinR mutant.
J Bacteriol: 1996, 178(23);7010-3
[PubMed:8955328] [WorldCat.org] [DOI] (P p)

M H Rashid, J Sekiguchi
flaD (sinR) mutations affect SigD-dependent functions at multiple points in Bacillus subtilis.
J Bacteriol: 1996, 178(22);6640-3
[PubMed:8932324] [WorldCat.org] [DOI] (P p)

Y F Chen, J D Helmann
The Bacillus subtilis flagellar regulatory protein sigma D: overproduction, domain analysis and DNA-binding properties.
J Mol Biol: 1995, 249(4);743-53
[PubMed:7602586] [WorldCat.org] [DOI] (P p)

K Fredrick, T Caramori, Y F Chen, A Galizzi, J D Helmann
Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element.
Proc Natl Acad Sci U S A: 1995, 92(7);2582-6
[PubMed:7708689] [WorldCat.org] [DOI] (P p)

L Chen, J D Helmann
The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT.
J Bacteriol: 1994, 176(11);3093-101
[PubMed:8195064] [WorldCat.org] [DOI] (P p)

K L Fredrick, J D Helmann
Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains.
J Bacteriol: 1994, 176(9);2727-35
[PubMed:8169223] [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)

D B Mirel, M J Chamberlin
The Bacillus subtilis flagellin gene (hag) is transcribed by the sigma 28 form of RNA polymerase.
J Bacteriol: 1989, 171(6);3095-101
[PubMed:2498284] [WorldCat.org] [DOI] (P p)

J D Helmann, F R Masiarz, M J Chamberlin
Isolation and characterization of the Bacillus subtilis sigma 28 factor.
J Bacteriol: 1988, 170(4);1560-7
[PubMed:3127378] [WorldCat.org] [DOI] (P p)

J D Helmann, L M Márquez, M J Chamberlin
Cloning, sequencing, and disruption of the Bacillus subtilis sigma 28 gene.
J Bacteriol: 1988, 170(4);1568-74
[PubMed:2832368] [WorldCat.org] [DOI] (P p)

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