YdeO belongs to the AraC/XylS family of transcriptional regulators and shows more similarity to YhiW, AppY, AdiY, and GadX than the other AraC/XylS regulators [5, 6]. The members of this family exhibit two domains, an amino-terminal domain involved in coinducer recognition and dimerization and a carboxy-terminal domain that contains a potential helix-turn-helix DNA-binding motif [5, 7].
YdeO activates genes involved in the cellular response to acid resistance [2, 8, 9]. This protein, together with the proteins HNS, EvgA, and GadE, pertains to a specific regulatory circuit that is functional in exponential-phase cells growing in minimal medium [2, 8, 9]. Several of the genes directly regulated by YdeO are also directly regulated by GadX .
The YdeO regulon has been determined .
Based on ChIP-chip, RT-qPCR, EMSA, DNase I footprinting, and reporter assay, 7 new operons were identified as members of the YdeO regulon, including four stress response transcription factors, DctR, NhaR, GadE, and Gad, and several genes involved in respiration .Read more >
YdeO plays an important role in survival under both acidic and anaerobic conditions .
Based on transcriptome analysis, the YdeO -> GadE transcriptional cascade was determined. A total of 106 genes were affected by YdeO, among which 53 genes were upregulated, and 23 of these were induced by GadE; a model has been proposed .
The YdeO-box is an inverted repeat of hexanucleotides, with the sequence 5'-ATTTCA-3', and the length of the spacer between this inverted repeat sequence ranges from 9 to 21 nucleotides .
ydeO is transcribed in an operon together with the gene safA . This gene codes for a protein that directly interacts with PhoQ to activate the PhoQ/PhoP system, which regulates genes, including Mg2+ transporters and lipopolysaccharide modification genes .
YdeO expression is induced by UV irradiation via the EvgS/EvgA system and thus controls the expression of 21 genes .
|Connectivity class:||Local Regulator|
|Length:||762 bp / 253 aa|
|TU(s) encoding the TF:||
|Regulated gene(s)||appA, appB, appC, appX, dctR, gadE, gadF, gadW, hyaA, hyaB, hyaC, hyaD, hyaE, hyaF, mdtE, mdtF, safA, slp, uspD, ydeO, yiiS|
|Multifun term(s) of regulated gene(s)||
MultiFun Term (List of genes associated to the multifun term)
aerobic respiration (6)
hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
anaerobic respiration (6)
hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
appB, appC, hyaC, mdtF, safA
Transcription related (3)
gadE, gadW, ydeO
electron donors (3)
hyaA, hyaB, hyaC
electron acceptors (2)
chaperoning, repair (refolding) (2)
metabolism of other compounds (1)
phosphorous metabolism (1)
posttranslational modification (1)
Porters (Uni-, Sym- and Antiporters) (1)
protein related (1)
inhibition / activation of enzymes (1)
|Regulated operon(s)||appCBXA, gadAXW, gadEF-mdtEF, hyaABCDEF, safA-ydeO, slp-dctR, yiiS-uspD|
|First gene in the operon(s)||appC, gadE, gadE, gadW, hyaA, safA, slp, yiiS|
|Simple and complex regulons||
|Simple and complex regulatory phrases||
Regulatory phrase (List of promoters regulated by the phrase)
|Functional conformation||Function||Promoter||Sigma factor||Central Rel-Pos||Distance to first Gene||Genes||Sequence||LeftPos||RightPos||Evidence (Confirmed, Strong, Weak)||References|
|YdeO||activator||appCp||Sigma70||-27.5||-57.5||appC, appB, appX, appA||
|1037672||1037693||[BPP], [GEA], [IHBCE]|||
|YdeO||activator||gadEp||Sigma38||nd||nd||gadE, gadF, mdtE, mdtF||nd||nd||[BPP], [GEA]|||
|3657746||3657771||[BPP], [GEA], [IHBCE]||, |
|3664654||3664674||[BPP], [GEA], [IHBCE]|||
|YdeO||activator||hyaAp||Sigma70||-61.0||-216.0||hyaA, hyaB, hyaC, hyaD, hyaE, hyaF||
|1031912||1031934||[BPP], [GEA], [IHBCE]|||
|3653884||3653908||[BPP], [GEA], [IHBCE]|||
|4112798||4112830||[BPP], [GEA], [IHBCE]|||
|Evolutionary conservation of regulatory elements|
 Ma Z., Masuda N., Foster JW., 2004, Characterization of EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli., J Bacteriol. 186(21):7378-89
 Burton NA., Johnson MD., Antczak P., Robinson A., Lund PA., 2010, Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics., J Mol Biol. 401(5):726-42
 Eguchi Y., Itou J., Yamane M., Demizu R., Yamato F., Okada A., Mori H., Kato A., Utsumi R., 2007, B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli., Proc Natl Acad Sci U S A. 104(47):18712-7