CcpA

• Description: Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon
  
  

Gene name	ccpA
Synonyms	graR, alsA, amyR
Essential	no
Product	transcriptional regulator (LacI family)
Function	mediates carbon catabolite repression (CCR)
Metabolic function and regulation of this protein in SubtiPathways: Nucleoside catabolism, Nucleotides (regulation), Ile, Leu, Val, His, Coenzyme A, Central C-metabolism
MW, pI	36,8 kDa, 5.06
Gene length, protein length	1002 bp, 334 amino acids
Immediate neighbours	motP, aroA
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList

The gene

Basic information

• Locus tag: BSU29740

Phenotypes of a mutant

Loss of carbon catabolite repression. Loss of PTS-dependent sugar transport due to excessive phosphorylation of HPr by HprK. The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: transcriptional regulator of carbon catabolite repression (CCR)

• Protein family: LacI family

• Paralogous protein(s):

Genes controlled by CcpA

• Activation by CcpA: pta, ackA, ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD

• Repression by CcpA: abbA, amyE, bglP-bglH, bglS, cccA, citZ-icd-mdh, levD-levE-levF-levG-sacC, licB-licC-licA-licH, phoP-phoR, xylA-xylB, xynP-xynB

Extended information on the protein

• Kinetic information:

• Domains:
  • HTH lacI-type Domain (1 – 58)
  • DNA binding Domain (6 – 25)

• Modification:

• Cofactor(s): HPr-Ser46-P, Crh-Ser-46-P

• Effectors of protein activity:glucose-6-phosphate, fructose-1,6-bisphosphate Pubmed

• Interactions: CcpA-HPr PubMed, CcpA-Crh PubMed

• Localization:

Database entries

• Structure: 2JCG (Apoprotein from Bacillus megaterium), CcpA-Crh-DNA-complex NCBI, complex with P-Ser-HPr and sulphate ions NCBI

• UniProt: P25144

• KEGG entry: [3]

Expression and regulation

• Operon: ccpA-motP-motS PubMed

• Sigma factor:

• Regulation: constitutively expressed PubMed

• Additional information: there are about 3.000 molecules of CcpA per cell PubMed

Biological materials

• Mutant: QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ccpA), available in Stülke lab

• Expression vector: pGP643 (N-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP380), available in Stülke lab

• lacZ fusion:

• GFP fusion:

• Antibody: available in Hillen and Stülke labs

Labs working on this gene/protein

• • Wolfgang Hillen, Erlangen University, Germany Homepage
  • Richard Brennan, Houston, Texas, USA Homepage
  • Milton H. Saier, University of California at San Diego, USA Homepage
  • Yasutaro Fujita, University of Fukuyama, Japan
  • Jörg Stülke, University of Göttingen, Germany Homepage
  • Oscar Kuipers, University of Groningen, The Netherlands Homepage

References

Reviews

Yasutaro Fujita
Carbon catabolite control of the metabolic network in Bacillus subtilis.
Biosci Biotechnol Biochem: 2009, 73(2);245-59
[PubMed:19202299] [WorldCat.org] [DOI] (I p)

Boris Görke, Jörg Stülke
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients.
Nat Rev Microbiol: 2008, 6(8);613-24
[PubMed:18628769] [WorldCat.org] [DOI] (I p)

Josef Deutscher
The mechanisms of carbon catabolite repression in bacteria.
Curr Opin Microbiol: 2008, 11(2);87-93
[PubMed:18359269] [WorldCat.org] [DOI] (P p)

Jessica B Warner, Juke S Lolkema
CcpA-dependent carbon catabolite repression in bacteria.
Microbiol Mol Biol Rev: 2003, 67(4);475-90
[PubMed:14665673] [WorldCat.org] [DOI] (P p)

T M Henkin
The role of CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis.
FEMS Microbiol Lett: 1996, 135(1);9-15
[PubMed:8598282] [WorldCat.org] [DOI] (P p)

General and physiological studies

Kalpana D Singh, Matthias H Schmalisch, Jörg Stülke, Boris Görke
Carbon catabolite repression in Bacillus subtilis: quantitative analysis of repression exerted by different carbon sources.
J Bacteriol: 2008, 190(21);7275-84
[PubMed:18757537] [WorldCat.org] [DOI] (I p)

Naoya Terahara, Makoto Fujisawa, Benjamin Powers, Tina M Henkin, Terry A Krulwich, Masahiro Ito
An intergenic stem-loop mutation in the Bacillus subtilis ccpA-motPS operon increases motPS transcription and the MotPS contribution to motility.
J Bacteriol: 2006, 188(7);2701-5
[PubMed:16547058] [WorldCat.org] [DOI] (P p)

Ingrid Wacker, Holger Ludwig, Irene Reif, Hans-Matti Blencke, Christian Detsch, Jörg Stülke
The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA.
Microbiology (Reading): 2003, 149(Pt 10);3001-3009
[PubMed:14523131] [WorldCat.org] [DOI] (P p)

Holger Ludwig, Nicole Rebhan, Hans-Matti Blencke, Matthias Merzbacher, Jörg Stülke
Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation.
Mol Microbiol: 2002, 45(2);543-53
[PubMed:12123463] [WorldCat.org] [DOI] (P p)

N Faires, S Tobisch, S Bachem, I Martin-Verstraete, M Hecker, J Stülke
The catabolite control protein CcpA controls ammonium assimilation in Bacillus subtilis.
J Mol Microbiol Biotechnol: 1999, 1(1);141-8
[PubMed:10941796] [WorldCat.org] (P p)

Y Miwa, M Saikawa, Y Fujita
Possible function and some properties of the CcpA protein of Bacillus subtilis.
Microbiology (Reading): 1994, 140 ( Pt 10);2567-75
[PubMed:8000527] [WorldCat.org] [DOI] (P p)

T M Henkin, F J Grundy, W L Nicholson, G H Chambliss
Catabolite repression of alpha-amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacl and galR repressors.
Mol Microbiol: 1991, 5(3);575-84
[PubMed:1904524] [WorldCat.org] [DOI] (P p)

Global analyses (proteome, transcriptome)

Andrzej T Lulko, Girbe Buist, Jan Kok, Oscar P Kuipers
Transcriptome analysis of temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals additional target genes.
J Mol Microbiol Biotechnol: 2007, 12(1-2);82-95
[PubMed:17183215] [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] [DOI] (P p)

M S Moreno, B L Schneider, R R Maile, W Weyler, M H Saier
Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses.
Mol Microbiol: 2001, 39(5);1366-81
[PubMed:11251851] [WorldCat.org] [DOI] (P p)

K Yoshida, K Kobayashi, Y Miwa, C M Kang, M Matsunaga, H Yamaguchi, S Tojo, M Yamamoto, R Nishi, N Ogasawara, T Nakayama, Y Fujita
Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis.
Nucleic Acids Res: 2001, 29(3);683-92
[PubMed:11160890] [WorldCat.org] [DOI] (I p)

S Tobisch, D Zühlke, J Bernhardt, J Stülke, M Hecker
Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis.
J Bacteriol: 1999, 181(22);6996-7004
[PubMed:10559165] [WorldCat.org] [DOI] (P p)

Repression of target genes by CcpA

José Manuel Inácio, Isabel de Sá-Nogueira
trans-Acting factors and cis elements involved in glucose repression of arabinan degradation in Bacillus subtilis.
J Bacteriol: 2007, 189(22);8371-6
[PubMed:17827291] [WorldCat.org] [DOI] (I p)

Soo-Keun Choi, Milton H Saier
Mechanism of CcpA-mediated glucose repression of the resABCDE operon of Bacillus subtilis.
J Mol Microbiol Biotechnol: 2006, 11(1-2);104-10
[PubMed:16825793] [WorldCat.org] [DOI] (P p)

Soo-Keun Choi, Milton H Saier
Regulation of pho regulon gene expression by the carbon control protein A, CcpA, in Bacillus subtilis.
J Mol Microbiol Biotechnol: 2005, 10(1);40-50
[PubMed:16491025] [WorldCat.org] [DOI] (P p)

Soo-Keun Choi, Milton H Saier
Regulation of sigL expression by the catabolite control protein CcpA involves a roadblock mechanism in Bacillus subtilis: potential connection between carbon and nitrogen metabolism.
J Bacteriol: 2005, 187(19);6856-61
[PubMed:16166551] [WorldCat.org] [DOI] (P p)

Boris R Belitsky, Hyun-Jin Kim, Abraham L Sonenshein
CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression.
J Bacteriol: 2004, 186(11);3392-8
[PubMed:15150224] [WorldCat.org] [DOI] (P p)

Hyun-Jin Kim, Agnes Roux, Abraham L Sonenshein
Direct and indirect roles of CcpA in regulation of Bacillus subtilis Krebs cycle genes.
Mol Microbiol: 2002, 45(1);179-90
[PubMed:12100558] [WorldCat.org] [DOI] (P p)

Hyun-Jin Kim, Cécile Jourlin-Castelli, Sam-In Kim, Abraham L Sonenshein
Regulation of the bacillus subtilis ccpC gene by ccpA and ccpC.
Mol Microbiol: 2002, 43(2);399-410
[PubMed:11985717] [WorldCat.org] [DOI] (P p)

Emmanuelle Darbon, Pascale Servant, Sandrine Poncet, Josef Deutscher
Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P-GlpK dephosphorylation control Bacillus subtilis glpFK expression.
Mol Microbiol: 2002, 43(4);1039-52
[PubMed:11929549] [WorldCat.org] [DOI] (P p)

I Martin-Verstraete, J Stülke, A Klier, G Rapoport
Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon.
J Bacteriol: 1995, 177(23);6919-27
[PubMed:7592486] [WorldCat.org] [DOI] (P p)

F J Grundy, A J Turinsky, T M Henkin
Catabolite regulation of Bacillus subtilis acetate and acetoin utilization genes by CcpA.
J Bacteriol: 1994, 176(15);4527-33
[PubMed:7913927] [WorldCat.org] [DOI] (P p)

Positive regulation of gene expression by CcpA

Robert P Shivers, Abraham L Sonenshein
Bacillus subtilis ilvB operon: an intersection of global regulons.
Mol Microbiol: 2005, 56(6);1549-59
[PubMed:15916605] [WorldCat.org] [DOI] (P p)

Holger Ludwig, Christoph Meinken, Anastasija Matin, Jörg Stülke
Insufficient expression of the ilv-leu operon encoding enzymes of branched-chain amino acid biosynthesis limits growth of a Bacillus subtilis ccpA mutant.
J Bacteriol: 2002, 184(18);5174-8
[PubMed:12193635] [WorldCat.org] [DOI] (P p)

A J Turinsky, T R Moir-Blais, F J Grundy, T M Henkin
Bacillus subtilis ccpA gene mutants specifically defective in activation of acetoin biosynthesis.
J Bacteriol: 2000, 182(19);5611-4
[PubMed:10986270] [WorldCat.org] [DOI] (P p)

E Presecan-Siedel, A Galinier, R Longin, J Deutscher, A Danchin, P Glaser, I Martin-Verstraete
Catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis.
J Bacteriol: 1999, 181(22);6889-97
[PubMed:10559153] [WorldCat.org] [DOI] (P p)

A J Turinsky, F J Grundy, J H Kim, G H Chambliss, T M Henkin
Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter.
J Bacteriol: 1998, 180(22);5961-7
[PubMed:9811655] [WorldCat.org] [DOI] (P p)

F J Grundy, D A Waters, S H Allen, T M Henkin
Regulation of the Bacillus subtilis acetate kinase gene by CcpA.
J Bacteriol: 1993, 175(22);7348-55
[PubMed:8226682] [WorldCat.org] [DOI] (P p)

Control of CcpA activity

Lwin Mar Aung-Hilbrich, Gerald Seidel, Andrea Wagner, Wolfgang Hillen
Quantification of the influence of HPrSer46P on CcpA-cre interaction.
J Mol Biol: 2002, 319(1);77-85
[PubMed:12051938] [WorldCat.org] [DOI] (P p)

A Galinier, J Deutscher, I Martin-Verstraete
Phosphorylation of either crh or HPr mediates binding of CcpA to the bacillus subtilis xyn cre and catabolite repression of the xyn operon.
J Mol Biol: 1999, 286(2);307-14
[PubMed:9973552] [WorldCat.org] [DOI] (P p)

J H Kim, M I Voskuil, G H Chambliss
NADP, corepressor for the Bacillus catabolite control protein CcpA.
Proc Natl Acad Sci U S A: 1998, 95(16);9590-5
[PubMed:9689125] [WorldCat.org] [DOI] (P p)

B E Jones, V Dossonnet, E Küster, W Hillen, J Deutscher, R E Klevit
Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr.
J Biol Chem: 1997, 272(42);26530-5
[PubMed:9334231] [WorldCat.org] [DOI] (P p)

J Deutscher, E Küster, U Bergstedt, V Charrier, W Hillen
Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in gram-positive bacteria.
Mol Microbiol: 1995, 15(6);1049-53
[PubMed:7623661] [WorldCat.org] [DOI] (P p)

CcpA-DNA interaction

Gerald Seidel, Marco Diel, Norbert Fuchsbauer, Wolfgang Hillen
Quantitative interdependence of coeffectors, CcpA and cre in carbon catabolite regulation of Bacillus subtilis.
FEBS J: 2005, 272(10);2566-77
[PubMed:15885105] [WorldCat.org] [DOI] (P p)

Y Miwa, A Nakata, A Ogiwara, M Yamamoto, Y Fujita
Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis.
Nucleic Acids Res: 2000, 28(5);1206-10
[PubMed:10666464] [WorldCat.org] [DOI] (I p)

J H Kim, G H Chambliss
Contacts between Bacillus subtilis catabolite regulatory protein CcpA and amyO target site.
Nucleic Acids Res: 1997, 25(17);3490-6
[PubMed:9254709] [WorldCat.org] [DOI] (P p)

Y Fujita, Y Miwa, A Galinier, J Deutscher
Specific recognition of the Bacillus subtilis gnt cis-acting catabolite-responsive element by a protein complex formed between CcpA and seryl-phosphorylated HPr.
Mol Microbiol: 1995, 17(5);953-60
[PubMed:8596444] [WorldCat.org] [DOI] (P p)

J H Kim, Z T Guvener, J Y Cho, K C Chung, G H Chambliss
Specificity of DNA binding activity of the Bacillus subtilis catabolite control protein CcpA.
J Bacteriol: 1995, 177(17);5129-34
[PubMed:7665492] [WorldCat.org] [DOI] (P p)

Functional analysis of CcpA

H Ludwig, J Stülke
The Bacillus subtilis catabolite control protein CcpA exerts all its regulatory functions by DNA-binding.
FEMS Microbiol Lett: 2001, 203(1);125-9
[PubMed:11557150] [WorldCat.org] [DOI] (P p)

E Küster-Schöck, A Wagner, U Völker, W Hillen
Mutations in catabolite control protein CcpA showing glucose-independent regulation in Bacillus megaterium.
J Bacteriol: 1999, 181(24);7634-8
[PubMed:10601226] [WorldCat.org] [DOI] (P p)

E Küster, T Hilbich, M K Dahl, W Hillen
Mutations in catabolite control protein CcpA separating growth effects from catabolite repression.
J Bacteriol: 1999, 181(13);4125-8
[PubMed:10383986] [WorldCat.org] [DOI] (P p)

A Kraus, E Küster, A Wagner, K Hoffmann, W Hillen
Identification of a co-repressor binding site in catabolite control protein CcpA.
Mol Microbiol: 1998, 30(5);955-63
[PubMed:9988473] [WorldCat.org] [DOI] (P p)

A Kraus, W Hillen
Analysis of CcpA mutations defective in carbon catabolite repression in Bacillus megaterium.
FEMS Microbiol Lett: 1997, 153(1);221-6
[PubMed:9252590] [WorldCat.org] [DOI] (P p)

Structural analyses

Maria A Schumacher, Gerald Seidel, Wolfgang Hillen, Richard G Brennan
Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate.
J Mol Biol: 2007, 368(4);1042-50
[PubMed:17376479] [WorldCat.org] [DOI] (P p)

Vincent Chaptal, Virginie Gueguen-Chaignon, Sandrine Poncet, Cécile Lecampion, Philippe Meyer, Josef Deutscher, Anne Galinier, Sylvie Nessler, Solange Moréra
Structural analysis of B. subtilis CcpA effector binding site.
Proteins: 2006, 64(3);814-6
[PubMed:16755587] [WorldCat.org] [DOI] (I p)

Maria A Schumacher, Gerald Seidel, Wolfgang Hillen, Richard G Brennan
Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation.
J Biol Chem: 2006, 281(10);6793-800
[PubMed:16316990] [WorldCat.org] [DOI] (P p)

Maria A Schumacher, Gregory S Allen, Marco Diel, Gerald Seidel, Wolfgang Hillen, Richard G Brennan
Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.
Cell: 2004, 118(6);731-41
[PubMed:15369672] [WorldCat.org] [DOI] (P p)