ComK

• Description: competence transcription factor (CTF)
  
  

Gene name	comK
Synonyms
Essential	no
Product	competence transcription factor (CTF)
Function	regulation of competence and DNA uptake
Interactions involving this protein in SubtInteract: ComK
Metabolic function and regulation of this protein in SubtiPathways: Nucleotides (regulation), Protein secretion
MW, pI	22 kDa, 7.669
Gene length, protein length	576 bp, 192 aa
Immediate neighbours	yhzC, yhxD
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

genetic competence, transcription factors and their control

This gene is a member of the following regulons

AbrB regulon, CodY regulon, ComK regulon, DegU regulon, Rok regulon, Spo0A regulon

The gene

Basic information

• Locus tag: BSU10420

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

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:

• Interactions:
  • MecA-ComK PubMed

• Localization:

Database entries

• Structure:

• UniProt: P40396

• KEGG entry: [3]

• E.C. number:

Expression and regulation

• Operon: comK PubMed

• Expression browser: comK PubMed

• Sigma factor: SigA PubMed

• Regulation:
  • repressed by casamino acids PubMed
  • repressed by Rok PubMed
  • repressed during growth in the presence of branched chain amino acids (CodY) PubMed
  • repressed during logrithmic growth (AbrB) PubMed
  • induced at the entry to stationary phase (Spo0A-P) PubMed

• Regulatory mechanism:
  • Rok: transcription repression PubMed
  • CodY: transcription repression PubMed
  • AbrB: transcription repression PubMed
  • ComK: transcription activation (autoregulation) PubMed
  • DegU (non-phosphorylated form): transcription activation PubMed
  • Spo0A-P: transcription activation, acts as antagonist of Rok PubMed

• Additional information:
  • degraded by ClpC-ClpP (with MecA as adaptor protein) PubMed

Biological materials

• Mutant:

• Expression vector: for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

Labs working on this gene/protein

Oscar Kuipers, University of Groningen, The Netherlands Homepage

References

Reviews

Daniel Schultz, Peter G Wolynes, Eshel Ben Jacob, José N Onuchic
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2009, 106(50);21027-34
[PubMed:19995980] [WorldCat.org] [DOI] (I p)

Leendert W Hamoen, Gerard Venema, Oscar P Kuipers
Controlling competence in Bacillus subtilis: shared use of regulators.
Microbiology (Reading): 2003, 149(Pt 1);9-17
[PubMed:12576575] [WorldCat.org] [DOI] (P p)

The ComK regulon

Mitsuo Ogura, Hirotake Yamaguchi, Kazuo Kobayashi, Naotake Ogasawara, Yasutaro Fujita, Teruo Tanaka
Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK.
J Bacteriol: 2002, 184(9);2344-51
[PubMed:11948146] [WorldCat.org] [DOI] (P p)

Randy M Berka, Jeanette Hahn, Mark Albano, Irena Draskovic, Marjan Persuh, Xianju Cui, Alan Sloma, William Widner, David Dubnau
Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK.
Mol Microbiol: 2002, 43(5);1331-45
[PubMed:11918817] [WorldCat.org] [DOI] (P p)

Original Publications

Additional publications: PubMed

Sandra H Dandach, Mustafa Khammash
Analysis of stochastic strategies in bacterial competence: a master equation approach.
PLoS Comput Biol: 2010, 6(11);e1000985
[PubMed:21085679] [WorldCat.org] [DOI] (I e)

Reindert Nijland, J Grant Burgess, Jeff Errington, Jan-Willem Veening
Transformation of environmental Bacillus subtilis isolates by transiently inducing genetic competence.
PLoS One: 2010, 5(3);e9724
[PubMed:20300532] [WorldCat.org] [DOI] (I e)

Wiep Klaas Smits, Cristina Bongiorni, Jan-Willem Veening, Leendert W Hamoen, Oscar P Kuipers, Marta Perego
Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis.
Mol Microbiol: 2007, 65(1);103-20
[PubMed:17581123] [WorldCat.org] [DOI] (P p)

Hédia Maamar, Arjun Raj, David Dubnau
Noise in gene expression determines cell fate in Bacillus subtilis.
Science: 2007, 317(5837);526-9
[PubMed:17569828] [WorldCat.org] [DOI] (I p)

Peter Prepiak, David Dubnau
A peptide signal for adapter protein-mediated degradation by the AAA+ protease ClpCP.
Mol Cell: 2007, 26(5);639-47
[PubMed:17560370] [WorldCat.org] [DOI] (P p)

Wiep Klaas Smits, Tran Thu Hoa, Leendert W Hamoen, Oscar P Kuipers, David Dubnau
Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein.
Mol Microbiol: 2007, 64(2);368-81
[PubMed:17493123] [WorldCat.org] [DOI] (P p)

Kim A Susanna, Fabrizia Fusetti, Andy-Mark W H Thunnissen, Leendert W Hamoen, Oscar P Kuipers
Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants.
Microbiology (Reading): 2006, 152(Pt 2);473-483
[PubMed:16436435] [WorldCat.org] [DOI] (P p)

Kim A Susanna, Chris D den Hengst, Leendert W Hamoen, Oscar P Kuipers
Expression of transcription activator ComK of Bacillus subtilis in the heterologous host Lactococcus lactis leads to a genome-wide repression pattern: a case study of horizontal gene transfer.
Appl Environ Microbiol: 2006, 72(1);404-11
[PubMed:16391071] [WorldCat.org] [DOI] (P p)

Hédia Maamar, David Dubnau
Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop.
Mol Microbiol: 2005, 56(3);615-24
[PubMed:15819619] [WorldCat.org] [DOI] (P p)

Kana Shimane, Mitsuo Ogura
Mutational analysis of the helix-turn-helix region of Bacillus subtilis response regulator DegU, and identification of cis-acting sequences for DegU in the aprE and comK promoters.
J Biochem: 2004, 136(3);387-97
[PubMed:15598897] [WorldCat.org] [DOI] (P p)

Hideaki Nanamiya, Emiko Shiomi, Mitsuo Ogura, Teruo Tanaka, Kei Asai, Fujio Kawamura
Involvement of ClpX protein in the post-transcriptional regulation of a competence specific transcription factor, ComK protein, of Bacillus subtilis.
J Biochem: 2003, 133(3);295-302
[PubMed:12761164] [WorldCat.org] [DOI] (P p)

Leendert W Hamoen, Daisy Kausche, Mohamed A Marahiel, Douwe van Sinderen, Gerard Venema, Pascale Serror
The Bacillus subtilis transition state regulator AbrB binds to the -35 promoter region of comK.
FEMS Microbiol Lett: 2003, 218(2);299-304
[PubMed:12586407] [WorldCat.org] [DOI] (P p)

Huang-Mo Sung, Ronald E Yasbin
Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis.
J Bacteriol: 2002, 184(20);5641-53
[PubMed:12270822] [WorldCat.org] [DOI] (P p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

Mitsuo Ogura, Hitoshi Hashimoto, Teruo Tanaka
Med, a cell-surface localized protein regulating a competence transcription factor gene, comK, in Bacillus subtilis.
Biosci Biotechnol Biochem: 2002, 66(4);892-6
[PubMed:12036071] [WorldCat.org] [DOI] (P p)

Michiko M Nakano, Shunji Nakano, Peter Zuber
Spx (YjbD), a negative effector of competence in Bacillus subtilis, enhances ClpC-MecA-ComK interaction.
Mol Microbiol: 2002, 44(5);1341-9
[PubMed:12028382] [WorldCat.org] [DOI] (P p)

Tran Thu Hoa, Pablo Tortosa, Mark Albano, David Dubnau
Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK.
Mol Microbiol: 2002, 43(1);15-26
[PubMed:11849533] [WorldCat.org] [DOI] (P p)

Hanne Jarmer, Randy Berka, Steen Knudsen, Hans H Saxild
Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions.
FEMS Microbiol Lett: 2002, 206(2);197-200
[PubMed:11814663] [WorldCat.org] [DOI] (P p)

M M Nakano, F Hajarizadeh, Y Zhu, P Zuber
Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis.
Mol Microbiol: 2001, 42(2);383-94
[PubMed:11703662] [WorldCat.org] [DOI] (P p)

L W Hamoen, A F Van Werkhoven, G Venema, D Dubnau
The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2000, 97(16);9246-51
[PubMed:10908654] [WorldCat.org] [DOI] (P p)

M Persuh, K Turgay, I Mandic-Mulec, D Dubnau
The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch.
Mol Microbiol: 1999, 33(4);886-94
[PubMed:10447896] [WorldCat.org] [DOI] (P p)

M Ogura, L Liu, M Lacelle, M M Nakano, P Zuber
Mutational analysis of ComS: evidence for the interaction of ComS and MecA in the regulation of competence development in Bacillus subtilis.
Mol Microbiol: 1999, 32(4);799-812
[PubMed:10361283] [WorldCat.org] [DOI] (P p)

K Turgay, J Hahn, J Burghoorn, D Dubnau
Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor.
EMBO J: 1998, 17(22);6730-8
[PubMed:9890793] [WorldCat.org] [DOI] (P p)

L W Hamoen, A F Van Werkhoven, J J Bijlsma, D Dubnau, G Venema
The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix.
Genes Dev: 1998, 12(10);1539-50
[PubMed:9585513] [WorldCat.org] [DOI] (P p)

M Ogura, Y Ohshiro, S Hirao, T Tanaka
A new Bacillus subtilis gene, med, encodes a positive regulator of comK.
J Bacteriol: 1997, 179(20);6244-53
[PubMed:9335269] [WorldCat.org] [DOI] (P p)

M Ogura, T Tanaka
Bacillus subtilis ComK negatively regulates degR gene expression.
Mol Gen Genet: 1997, 254(2);157-65
[PubMed:9108277] [WorldCat.org] [DOI] (P p)

K Turgay, L W Hamoen, G Venema, D Dubnau
Biochemical characterization of a molecular switch involving the heat shock protein ClpC, which controls the activity of ComK, the competence transcription factor of Bacillus subtilis.
Genes Dev: 1997, 11(1);119-28
[PubMed:9000055] [WorldCat.org] [DOI] (P p)

P Serror, A L Sonenshein
CodY is required for nutritional repression of Bacillus subtilis genetic competence.
J Bacteriol: 1996, 178(20);5910-5
[PubMed:8830686] [WorldCat.org] [DOI] (P p)

J Hahn, A Luttinger, D Dubnau
Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis.
Mol Microbiol: 1996, 21(4);763-75
[PubMed:8878039] [WorldCat.org] [DOI] (P p)

D van Sinderen, A Luttinger, L Kong, D Dubnau, G Venema, L Hamoen
comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis.
Mol Microbiol: 1995, 15(3);455-62
[PubMed:7783616] [WorldCat.org] [DOI] (P p)

B J Haijema, L W Hamoen, J Kooistra, G Venema, D van Sinderen
Expression of the ATP-dependent deoxyribonuclease of Bacillus subtilis is under competence-mediated control.
Mol Microbiol: 1995, 15(2);203-11
[PubMed:7746142] [WorldCat.org] [DOI] (P p)

L Kong, D Dubnau
Regulation of competence-specific gene expression by Mec-mediated protein-protein interaction in Bacillus subtilis.
Proc Natl Acad Sci U S A: 1994, 91(13);5793-7
[PubMed:8016067] [WorldCat.org] [DOI] (P p)

T Msadek, F Kunst, G Rapoport
MecB of Bacillus subtilis, a member of the ClpC ATPase family, is a pleiotropic regulator controlling competence gene expression and growth at high temperature.
Proc Natl Acad Sci U S A: 1994, 91(13);5788-92
[PubMed:8016066] [WorldCat.org] [DOI] (P p)