TranscriptionalRegulation_gntR_TU_063 – Transcriptional regulation of TU_063 by gntR

Name
WID TranscriptionalRegulation_gntR_TU_063
Name Transcriptional regulation of TU_063 by gntR
 
Regulation
Transcription unit TU_063 View in model
Transcripton factor MG_101_MONOMER View in model
Binding site 128140129158 MG_100 MG_101
Chromosome: Mgenitalium_Chr_1, Coordinate: 128640 (nt), Length: 18 (nt), Direction: Forward, Sequence:
1
TCGAGCAAACCCCCAACA
18
View in model
Fold‑change activity
0.02 (dimensionless)
View in model
 
Comments
Comments GntR transcription factor is an HTH-type transcriptional regulator [PUB_0096] which represses its own transcription and that of genes involved in gluconate metabolism [PUB_0110, PUB_0196]. GntR transcriptional regulatory activity was inferred from B. subtilis [PUB_0433, PUB_0419]. GntR is repressed by gluconate [PUB_0110]. Consensus sequence ATACTTGTATACAAGTAT is 18 bp [PUB_0419]. In M. genitalium the upstream region doesn't contain the consensus binding sequence. Consequently, we wanted set the transcription factor binding site by setting its distance from the start codon to be the mean of that of observed transcription factors (56 nt). However, this would have overlapped with the LuxR binding site which is further upstream, so we set the GntR binding site to be just immediately downstream of the LuxR binding site. Binding site has motif ATACTTGTATACAAGTAT. Site responds to the condition: absence of 10 mM gluconate.
References
  1. Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res 31, 474-7 (2003). WholeCell: PUB_0110, PubMed: 12520055, URL: http://www.ncbi.nlm.nih.gov/Structure/

  2. Peekhaus N, Conway T. Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex. J Bacteriol 180, 1777-85 (1998). WholeCell: PUB_0196, PubMed: 9537375

  3. Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36, D93-6 (2008). WholeCell: PUB_0419, PubMed: 17962296, URL: http://dbtbs.hgc.jp/

  4. UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37, D169-74 (2009). WholeCell: PUB_0096, PubMed: 18836194, URL: http://www.uniprot.org/uniprot/

  5. Zuber U, Schumann W. CIRCE, a novel heat shock element involved in regulation of heat shock operon dnaK of Bacillus subtilis. J Bacteriol 176, 1359-63 (1994). WholeCell: PUB_0433, PubMed: 8113175

 
Metadata
Created 2012-10-01 15:09:28
Last updated 2012-10-01 15:18:56