||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.
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
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
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
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
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/
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