Difference between revisions of "CitB"

From SubtiWiki
Jump to: navigation, search
(Original publications)
Line 47: Line 47:
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[CcpA regulon]]}},
 
{{SubtiWiki regulon|[[CcpC regulon]]}},
 
{{SubtiWiki regulon|[[CcpC regulon]]}},
 
{{SubtiWiki regulon|[[CodY regulon]]}},
 
{{SubtiWiki regulon|[[CodY regulon]]}},
Line 76: Line 77:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:'''  
 +
** Citrate = isocitrate (according to Swiss-Prot)  
 
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
 
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
  
Line 116: Line 118:
  
 
=Expression and regulation=
 
=Expression and regulation=
 
 
* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])
 
* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])
  
Line 148: Line 149:
  
 
* '''Expression vector:
 
* '''Expression vector:
**GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
+
**GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab  
**pGP1810 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
+
**pGP1810 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab  
 
        
 
        
 
* '''lacZ fusion:'''  
 
* '''lacZ fusion:'''  
 
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab
 
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab
  
* '''GFP fusion:''' GP1434 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab
+
* '''GFP fusion:''' GP1434 (spc, based on [[pGP1870]]), available in [[Jörg Stülke]]'s lab  
  
 
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
Line 165: Line 166:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 
+
* [[Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
+
* [[Jörg Stülke]], University of Göttingen, Germany
 
 
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
 
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
  
Line 177: Line 176:
 
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
 
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
 
==Original publications==
 
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480 23139400</pubmed>
+
'''Additional publications:''' {{PubMed|20817675}}
 
+
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 </pubmed>
 +
----
 +
<pubmed>21099137 21446632 21821766 22389480 23139400</pubmed>
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 18:06, 9 December 2012

Gene name citB
Synonyms
Essential no
Product trigger enzyme: aconitate hydratase (aconitase)
Function TCA cycle
Gene expression levels in SubtiExpress: citB
Interactions involving this protein in SubtInteract: CitB
Metabolic function and regulation of this protein in SubtiPathways:
Central C-metabolism
MW, pI 99 kDa, 4.903
Gene length, protein length 2727 bp, 909 aa
Immediate neighbours sspO, yneN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CitB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
CitB expression.png















Categories containing this gene/protein

carbon core metabolism, trigger enzyme, RNA binding regulators

This gene is a member of the following regulons

CcpA regulon, CcpC regulon, CodY regulon, FsrA regulon

The CitB regulon: feuA-feuB-feuC-ybbA

The gene

Basic information

  • Locus tag: BSU18000

Phenotypes of a mutant

glutamate auxotrophy and a defect in sporulation PubMed

Database entries

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

Additional information

  • A mutation was found in this gene after evolution under relaxed selection for sporulation PubMed


The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • Citrate = isocitrate (according to Swiss-Prot)
    • Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s): FeS cluster
  • Effectors of protein activity:

Database entries

  • Structure: 1L5J (E. coli)
  • KEGG entry: [3]

Additional information

  • B. subtilis aconitase is both an enzyme and an RNA binding protein (moonlighting protein) PubMed
  • extensive information on the structure and enzymatic properties of CitB can be found at Proteopedia

Expression and regulation

  • Regulation:
    • repressed during growth in the presence of branched chain amino acids (CodY) PubMed
    • repressed in the presence of glucose and glutamate (CcpC) PubMed
    • expressed upon transition into the stationary phase (AbrB) PubMed, indirect negative regulation by AbrB PubMed
    • repressed by glucose (3.7-fold) (CcpA) PubMed
    • repression by glucose + arginine (CcpC) PubMed
    • less expressed under conditions of extreme iron limitation (FsrA) PubMed
    • part of the iron sparing response (FsrA) PubMed
  • Additional information:

Biological materials

  • Expression vector:
    • GP1439 (citB-Strep (spc)), purification from B. subtilis, for SPINE, available in Jörg Stülke's lab
    • pGP1810 (for expression, purification in E. coli with N-terminal Strep-tag, in pGP172, available in Jörg Stülke's lab
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab

Labs working on this gene/protein

Homepage

Your additional remarks

References

Reviews

Karl Volz
The functional duality of iron regulatory protein 1.
Curr. Opin. Struct. Biol.: 2008, 18(1);106-11
[PubMed:18261896] [WorldCat.org] [DOI] (P p)

Fabian M Commichau, Jörg Stülke
Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression.
Mol. Microbiol.: 2008, 67(4);692-702
[PubMed:18086213] [WorldCat.org] [DOI] (P p)

Patricia J Kiley, Helmut Beinert
The role of Fe-S proteins in sensing and regulation in bacteria.
Curr. Opin. Microbiol.: 2003, 6(2);181-5
[PubMed:12732309] [WorldCat.org] (P p)

R L Switzer
Non-redox roles for iron-sulfur clusters in enzymes.
Biofactors: 1989, 2(2);77-86
[PubMed:2696478] [WorldCat.org] (P p)

Original publications

Additional publications: PubMed

Frederik M Meyer, Jan Gerwig, Elke Hammer, Christina Herzberg, Fabian M Commichau, Uwe Völker, Jörg Stülke
Physical interactions between tricarboxylic acid cycle enzymes in Bacillus subtilis: evidence for a metabolon.
Metab. Eng.: 2011, 13(1);18-27
[PubMed:20933603] [WorldCat.org] [DOI] (I p)

Alexander G Albrecht, Daili J A Netz, Marcus Miethke, Antonio J Pierik, Olaf Burghaus, Florian Peuckert, Roland Lill, Mohamed A Marahiel
SufU is an essential iron-sulfur cluster scaffold protein in Bacillus subtilis.
J. Bacteriol.: 2010, 192(6);1643-51
[PubMed:20097860] [WorldCat.org] [DOI] (I p)

Ahmed Gaballa, Haike Antelmann, Claudio Aguilar, Sukhjit K Khakh, Kyung-Bok Song, Gregory T Smaldone, John D Helmann
The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins.
Proc. Natl. Acad. Sci. U.S.A.: 2008, 105(33);11927-32
[PubMed:18697947] [WorldCat.org] [DOI] (I p)

Alisa W Serio, Kieran B Pechter, Abraham L Sonenshein
Bacillus subtilis aconitase is required for efficient late-sporulation gene expression.
J. Bacteriol.: 2006, 188(17);6396-405
[PubMed:16923907] [WorldCat.org] [DOI] (P 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)

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] (P p)

Hyun-Jin Kim, Sam-In Kim, Manoja Ratnayake-Lecamwasam, Kiyoshi Tachikawa, Abraham L Sonenshein, Mark Strauch
Complex regulation of the Bacillus subtilis aconitase gene.
J. Bacteriol.: 2003, 185(5);1672-80
[PubMed:12591885] [WorldCat.org] [DOI] (P p)

C Jourlin-Castelli, N Mani, M M Nakano, A L Sonenshein
CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis.
J. Mol. Biol.: 2000, 295(4);865-78
[PubMed:10656796] [WorldCat.org] [DOI] (P p)

C Alén, A L Sonenshein
Bacillus subtilis aconitase is an RNA-binding protein.
Proc. Natl. Acad. Sci. U.S.A.: 1999, 96(18);10412-7
[PubMed:10468622] [WorldCat.org] [DOI] (P p)

M M Nakano, P Zuber, A L Sonenshein
Anaerobic regulation of Bacillus subtilis Krebs cycle genes.
J. Bacteriol.: 1998, 180(13);3304-11
[PubMed:9642180] [WorldCat.org] (P p)

J E Craig, M J Ford, D C Blaydon, A L Sonenshein
A null mutation in the Bacillus subtilis aconitase gene causes a block in Spo0A-phosphate-dependent gene expression.
J. Bacteriol.: 1997, 179(23);7351-9
[PubMed:9393699] [WorldCat.org] [DOI] (P p)

A Fouet, S F Jin, G Raffel, A L Sonenshein
Multiple regulatory sites in the Bacillus subtilis citB promoter region.
J. Bacteriol.: 1990, 172(9);5408-15
[PubMed:2118511] [WorldCat.org] [DOI] (P p)

A Fouet, A L Sonenshein
A target for carbon source-dependent negative regulation of the citB promoter of Bacillus subtilis.
J. Bacteriol.: 1990, 172(2);835-44
[PubMed:2105305] [WorldCat.org] [DOI] (P p)

M S Rosenkrantz, D W Dingman, A L Sonenshein
Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine.
J. Bacteriol.: 1985, 164(1);155-64
[PubMed:2413006] [WorldCat.org] (P p)

S H Fisher, B Magasanik
2-Ketoglutarate and the regulation of aconitase and histidase formation in Bacillus subtilis.
J. Bacteriol.: 1984, 158(1);379-82
[PubMed:6143742] [WorldCat.org] (P p)


Meghna Mittal, Kieran B Pechter, Silvia Picossi, Hyun-Jin Kim, Kathryn O Kerstein, Abraham L Sonenshein
Dual role of CcpC protein in regulation of aconitase gene expression in Listeria monocytogenes and Bacillus subtilis.
Microbiology (Reading, Engl.): 2013, 159(Pt 1);68-76
[PubMed:23139400] [WorldCat.org] [DOI] (I p)

Gregory T Smaldone, Olga Revelles, Ahmed Gaballa, Uwe Sauer, Haike Antelmann, John D Helmann
A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism.
J. Bacteriol.: 2012, 194(10);2594-605
[PubMed:22389480] [WorldCat.org] [DOI] (I p)

Christopher T Brown, Laura K Fishwick, Binna M Chokshi, Marissa A Cuff, Jay M Jackson, Travis Oglesby, Alison T Rioux, Enrique Rodriguez, Gregory S Stupp, Austin H Trupp, James S Woollcombe-Clarke, Tracy N Wright, William J Zaragoza, Jennifer C Drew, Eric W Triplett, Wayne L Nicholson
Whole-genome sequencing and phenotypic analysis of Bacillus subtilis mutants following evolution under conditions of relaxed selection for sporulation.
Appl. Environ. Microbiol.: 2011, 77(19);6867-77
[PubMed:21821766] [WorldCat.org] [DOI] (I p)

Weihua Gao, Sen Dai, Quanli Liu, Haijin Xu, Yanlin Bai, Mingqiang Qiao
Effect of site-directed mutagenesis of citB on the expression and activity of Bacillus subtilis aconitase.
Mikrobiologiia: 2011, 79(6);774-8
[PubMed:21446632] [WorldCat.org] (P p)

Weihua Gao, Sen Dai, Quanli Liu, Haijin Xu, Mingqiang Qiao
CitB mutation increases the alkaline protease productivity in Bacillus subtilis.
J. Gen. Appl. Microbiol.: 2010, 56(5);403-7
[PubMed:21099137] [WorldCat.org] (P p)