Detailed information    

experimental Experimentally validated

Overview

Name   comK   Type   Regulator
Locus tag   BSU_10420 Genome accession   NC_000964
Coordinates   1117109..1117687 (+) Length   192 a.a.
NCBI ID   NP_388923.1    Uniprot ID   P40396
Organism   Bacillus subtilis subsp. subtilis str. 168     
Function   activate transcription of late competence genes   
Competence regulation

Function

In the natural transformation process of Bacillus subtilis, the comK gene encodes a competence transcription factor that serves as the master regulator of competence development. ComK is essential for the transcription of late competence genes, including those involved in DNA binding, uptake, and recombination (e.g., comC, comE, comF, comG, addAB, and recA). It also positively regulates its own expression through an autoregulatory loop. ComK acts as a key regulatory protein that integrates various signaling pathways and controls the transition to the competence state, enabling cells to bind and internalize transforming DNA. It binds specifically to the promoter regions of competence-related genes, activating their transcription and facilitating the assembly of the DNA uptake machinery.


Genomic Context

Location: 1112109..1122687
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  BSU_10380 (BSU10380) hemAT 1112620..1113918 (-) 1299 NP_388919.1 heme-based dioxygen sensor -
  BSU_10390 (BSU10390) yhfW 1114057..1115586 (-) 1530 NP_388920.1 putative oxidoreductase with Rieske [2Fe-2S] center Unclear
  BSU_10400 (BSU10400) yhxC 1115698..1116555 (+) 858 NP_388921.1 putative oxidoreductase Unclear
  BSU_10410 (BSU10410) yhzC 1116583..1116816 (-) 234 NP_388922.1 hypothetical protein -
  BSU_10420 (BSU10420) comK 1117109..1117687 (+) 579 NP_388923.1 competence transcription factor (CTF) Regulator
  BSU_10430 (BSU10430) yhxD 1117734..1118633 (-) 900 NP_388924.1 putative oxidoreductase -
  BSU_10440 (BSU10440) yhjA 1118850..1119119 (+) 270 NP_388925.1 hypothetical protein -
  BSU_10450 (BSU10450) yhjB 1119162..1120631 (-) 1470 NP_388926.1 putative Na+/metabolite cotransporter -
  BSU_10460 (BSU10460) yhjC 1120628..1120828 (-) 201 NP_388927.1 hypothetical protein -
  BSU_10470 (BSU10470) yhjD 1121036..1121398 (-) 363 NP_388928.1 hypothetical protein -
  BSU_10480 (BSU10480) yhjE 1121550..1122173 (+) 624 NP_388929.1 putative integral membrane protein -
  BSU_10490 (BSU10490) sipV 1122175..1122681 (+) 507 NP_388930.1 type I signal peptidase -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  comK comK positive effect
  comK late competence genes positive effect
  codY comK negative effect
  clpP comK negative effect
  mecA comK negative effect
  kre comK negative effect
  abrB comK negative effect
  comS comK positive effect
  spo0A comK positive effect
  rok comK negative effect
  degU comK positive effect
  clpC comK negative effect
  med comK positive effect
  spo0A comK negative effect
  comK late competence genes positive effect
  clpP degU negative effect
  abrB rok negative effect
  spo0A abrB negative effect
  comA comS positive effect
  spo0A rok negative effect
  sinR spo0A negative effect
  sinR rok negative effect
  sinR degU negative effect
  degQ degU positive effect
  clpC degU negative effect
  degS degU positive effect
  rapC comA negative effect
  rapF comA negative effect
  comP comA positive effect
  sinI sinR negative effect
  phrC rapC negative effect
  phrF rapF negative effect
  comX comP positive effect
  comQ comX positive effect

Sequence

Protein


Download         Length: 192 a.a.        Molecular weight: 22429.68 Da        Isoelectric Point: 7.7153

>NTDB_id=78 BSU_10420 NP_388923.1 1117109..1117687(+) (comK) [Bacillus subtilis subsp. subtilis str. 168]
MSQKTDAPLESYEVNGATIAVLPEEIDGKICSKIIEKDCVFYVNMKPLQIVDRSCRFFGSSYAGRKAGTYEVTKISHKPP
IMVDPSNQIFLFPTLSSTRPQCGWISHVHVKEFKATEFDDTEVTFSNGKTMELPISYNSFENQVYRTAWLRTKFQDRIDH
RVPKRQEFMLYPKEERTKMIYDFILRELGERY

Nucleotide


Download         Length: 579 bp        

>NTDB_id=78 BSU_10420 NP_388923.1 1117109..1117687(+) (comK) [Bacillus subtilis subsp. subtilis str. 168]
ATGAGTCAGAAAACAGACGCACCTTTAGAATCGTATGAAGTGAACGGCGCAACAATTGCCGTGCTGCCAGAAGAAATAGA
CGGCAAAATCTGTTCCAAAATTATTGAAAAAGATTGCGTGTTTTATGTAAACATGAAGCCGCTGCAAATTGTCGACAGAA
GCTGCCGATTTTTTGGATCAAGCTATGCGGGAAGAAAAGCAGGAACTTATGAAGTGACAAAAATTTCACACAAGCCGCCG
ATCATGGTGGACCCTTCGAACCAAATCTTTTTATTCCCTACACTTTCTTCGACAAGACCCCAATGCGGCTGGATTTCCCA
TGTGCATGTAAAAGAATTCAAAGCGACTGAATTCGACGATACGGAAGTGACGTTTTCCAATGGGAAAACGATGGAGCTGC
CGATCTCTTATAATTCGTTCGAGAACCAGGTATACCGAACAGCGTGGCTCAGAACCAAATTCCAAGACAGAATCGACCAC
CGCGTGCCGAAAAGACAGGAATTTATGCTGTACCCGAAAGAAGAGCGGACGAAGATGATTTATGATTTTATTTTGCGTGA
GCTCGGGGAACGGTATTAG

Domains

Predicted by InterproScan.

ComK protein (ComK)

(10-158)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB P40396

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value

References

[1] Eugenie J Dubnau et al. (2016) A protein complex supports the production of Spo0A-P and plays additional roles for biofilms and the K-state in Bacillus subtilis. Molecular Microbiology 101(4):606-24. [PMID: 27501195]
[2] Mathieu Miras et al. (2016) A DegU-P and DegQ-Dependent Regulatory Pathway for the K-state in Bacillus subtilis. Frontiers in Microbiology 7:1868. [PMID: 27920766]
[3] Regine Rahmer et al. (2015) Construction of a Super-Competent Bacillus subtilis 168 Using the P mtlA -comKS Inducible Cassette. Frontiers in Microbiology 6:1431. [PMID: 26732353]
[4] Madeleine Leisner et al. (2007) Basal expression rate of comK sets a 'switching-window' into the K-state of Bacillus subtilis. Molecular Microbiology 63(6):1806-16. [PMID: 17367397]
[5] Kim A Susanna et al. (2007) A single, specific thymine mutation in the ComK-binding site severely decreases binding and transcription activation by the competence transcription factor ComK of Bacillus subtilis. Journal of Bacteriology 189(13):4718-28. [PMID: 17468244]
[6] Kim A Susanna et al. (2006) Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants. Microbiology (Reading, England) 152(Pt 2):473-483. [PMID: 16436435]
[7] Gürol M Süel et al. (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440(7083):545-50. [PMID: 16554821]
[8] J-W Veening et al. (2006) Single cell analysis of gene expression patterns of competence development and initiation of sporulation in Bacillus subtilis grown on chemically defined media. Journal of Applied Microbiology 101(3):531-41. [PMID: 16907804]
[9] Mark Albano et al. (2005) The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions. Journal of Bacteriology 187(6):2010-9. [PMID: 15743949]
[10] Hédia Maamar et al. (2005) Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Molecular Microbiology 56(3):615-24. [PMID: 15819619]
[11] K A Susanna et al. (2004) Mechanism of transcription activation at the comG promoter by the competence transcription factor ComK of Bacillus subtilis. Journal of Bacteriology 186(4):1120-8. [PMID: 14762007]
[12] Leendert W Hamoen et al. (2003) The Bacillus subtilis transition state regulator AbrB binds to the -35 promoter region of comK. FEMS Microbiology Letters 218(2):299-304. [PMID: 12586407]
[13] Randy M Berka et al. (2002) Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Molecular Microbiology 43(5):1331-45. [PMID: 11918817]
[14] Mitsuo Ogura et al. (2002) Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. Journal of Bacteriology 184(9):2344-51. [PMID: 11948146]
[15] Leendert W Hamoen et al. (2002) Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Research 30(24):5517-28. [PMID: 12490720]
[16] J Liu et al. (1998) A molecular switch controlling competence and motility: competence regulatory factors ComS, MecA, and ComK control sigmaD-dependent gene expression in Bacillus subtilis. Journal of Bacteriology 180(16):4243-51. [PMID: 9696775]
[17] K Turgay et al. (1998) Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. The EMBO Journal 17(22):6730-8. [PMID: 9890793]
[18] M Ogura et al. (1996) Bacillus subtilis DegU acts as a positive regulator for comK expression. FEBS Letters 397(2-3):173-6. [PMID: 8955341]
[19] D van Sinderen et al. (1995) comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Molecular Microbiology 15(3):455-62. [PMID: 7783616]
[20] D van Sinderen et al. (1994) comK acts as an autoregulatory control switch in the signal transduction route to competence in Bacillus subtilis. Journal of Bacteriology 176(18):5762-70. [PMID: 8083168]
[21] D van Sinderen et al. (1994) Molecular cloning and sequence of comK, a gene required for genetic competence in Bacillus subtilis. Molecular Microbiology 11(4):695-703. [PMID: 8196543]