Note_TranscriptionalRegulation – TranscriptionalRegulation

WID Note_TranscriptionalRegulation
Name TranscriptionalRegulation
Comments M. genitalium transcriptional regulatory network was reconstructed from the primary literature [PUB_0006, PUB_0112, PUB_0186, PUB_0411, PUB_0418, PUB_0419, PUB_0420, PUB_0433, PUB_0434, PUB_0435, PUB_0436, PUB_0437, PUB_0438, PUB_0459, PUB_0460, PUB_0505], and the B. subtilis transcriptional regulation database DBTBS [PUB_0419]. We also searched EcoCyc [PUB_0006] and RegulonDB [PUB_0568] for the M. genitalium transcriptional regulators with little success. M. genitalium was determined to contain the transcriptional regulators: Fur (MG_236_MONOMER) – activated by iron stress and negatively regulates expression of siderophore biosynthesis and ferri-siderophore uptake genes [PUB_0418, PUB_0419, PUB_0438] GntR (MG_101_MONOMER) – repressed by gluconate and negatively represses its own expression [PUB_0110, PUB_0196] HrcA (MG_205_DIMER) – repressed by heat and negatively regulates the heat shock proteins including chaperones and chaperonins [PUB_0186, PUB_0418, PUB_0419, PUB_0433]. LuxR (MG_428_DIMER) – in other bacteria N-acyl-L-homoserine lactone is produced by LuxI and activates LuxR which in turn enhances luxI transcription. Spx (MG_127_MONOMER) – activated by thiol-specific oxidative stress, and enhances the expression of reductases [PUB_0434, PUB_0435, PUB_0436]. For each transcription factor we attempted to identify the regulated genes, the strength of the regulation (typically measured by microarray or PCR), the consensus regulatory element, and the affinity of the regulatory for the regulatory element.
  1. Antunes LC, Ferreira RB, Lostroh CP, Greenberg EP. A mutational analysis defines Vibrio fischeri LuxR binding sites. J Bacteriol 190, 4392-7 (2008). WholeCell: PUB_0505, PubMed: 18083819

  2. Baichoo N, Wang T, Ye R, Helmann JD. Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. Mol Microbiol 45, 1613-29 (2002). WholeCell: PUB_0438, PubMed: 12354229

  3. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R. Transcriptional regulation by the numbers: applications. Curr Opin Genet Dev 15, 125-35 (2005). WholeCell: PUB_0460, PubMed: 15797195

  4. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R. Transcriptional regulation by the numbers: models. Curr Opin Genet Dev 15, 116-24 (2005). WholeCell: PUB_0459, PubMed: 15797194

  5. 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:

  6. ... 14 more

  7. Choi SY, Reyes D, Leelakriangsak M, Zuber P. The global regulator Spx functions in the control of organosulfur metabolism in Bacillus subtilis. J Bacteriol 188, 5741-51 (2006). WholeCell: PUB_0436, PubMed: 16885442

  8. Erwin KN, Nakano S, Zuber P. Sulfate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J Bacteriol 187, 4042-9 (2005). WholeCell: PUB_0435, PubMed: 15937167

  9. Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36, D120-4 (2008). WholeCell: PUB_0568, PubMed: 18158297, URL:

  10. Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268-71 (2009). WholeCell: PUB_0418, PubMed: 19965477

  11. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  12. Musatovova O, Dhandayuthapani S, Baseman JB. Transcriptional heat shock response in the smallest known self-replicating cell, Mycoplasma genitalium. J Bacteriol 188, 2845-55 (2006). WholeCell: PUB_0186, PubMed: 16585746

  13. Nakano MM, Lin A, Zuber CS, Newberry KJ, Brennan RG, Zuber P. Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit. PLoS One 5, e8664 (2010). WholeCell: PUB_0420, PubMed: 20084284

  14. Nakano S, Küster-Schöck E, Grossman AD, Zuber P. Spx-dependent global transcriptional control is induced by thiol-specific oxidative stress in Bacillus subtilis. Proc Natl Acad Sci U S A 100, 13603-8 (2003). WholeCell: PUB_0434, PubMed: 14597697

  15. Newberry KJ, Nakano S, Zuber P, Brennan RG. Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase. Proc Natl Acad Sci U S A 102, 15839-44 (2005). WholeCell: PUB_0112, PubMed: 16249335

  16. Pamp SJ, Frees D, Engelmann S, Hecker M, Ingmer H. Spx is a global effector impacting stress tolerance and biofilm formation in Staphylococcus aureus. J Bacteriol 188, 4861-70 (2006). WholeCell: PUB_0437, PubMed: 16788195

  17. 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

  18. 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:

  19. Weiner J 3rd, Herrmann R, Browning GF. Transcription in Mycoplasma pneumoniae. Nucleic Acids Res 28, 4488-96 (2000). WholeCell: PUB_0411, PubMed: 11071937, URL:

  20. 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

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:59