|Gene:||ydeO||Accession Numbers: G6789 (EcoCyc), b1499, ECK1493|
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 [Gallegos97, Ibarra08]. 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 [Gallegos97, Martin01].
YdeO activates genes involved in the cellular response to acid resistance [Masuda02, Masuda03, Ma04]. 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 [Masuda02, Masuda03, Ma04]. Several of the genes directly regulated by YdeO are also directly regulated by GadX [Masuda03].
The YdeO regulon has been determined [Durban13]. 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 [Durban13].
YdeO plays an important role in survival under both acidic and anaerobic conditions [Durban13].
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 [Durban13].
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 [Durban13].
ydeO is transcribed in an operon together with the gene safA [Masuda03]. 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 [Eguchi07].
YdeO expression is induced by UV irradiation via the EvgS/EvgA system and thus controls the expression of 21 genes [Yamanaka12].
|Map Position: [1,580,950 <- 1,581,711] (34.07 centisomes, 123°)||Length: 762 bp / 253 aa|
Molecular Weight of Polypeptide: 28.725 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0004992 , EchoBASE:EB3558 , EcoGene:EG13797 , EcoliWiki:b1499 , ModBase:P76135 , OU-Microarray:b1499 , PortEco:ydeO , Protein Model Portal:P76135 , RefSeq:NP_416016 , RegulonDB:G6789 , SMR:P76135 , String:511145.b1499 , UniProt:P76135
Relationship Links: InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR018060 , InterPro:IN-FAMILY:IPR018062 , InterPro:IN-FAMILY:IPR020449 , Pfam:IN-FAMILY:PF12833 , Prints:IN-FAMILY:PR00032 , Prosite:IN-FAMILY:PS00041 , Prosite:IN-FAMILY:PS01124 , Smart:IN-FAMILY:SM00342
In Paralogous Gene Group: 22 (29 members)
|Biological Process:||GO:0006351 - transcription, DNA-templated
[UniProtGOA11a, Masuda03, Masuda02, Ma04]
GO:0045893 - positive regulation of transcription, DNA-templated [Yamanaka14]
GO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a, GOA01a]
|Molecular Function:||GO:0003700 - sequence-specific DNA binding transcription factor activity
GO:0003677 - DNA binding [UniProtGOA11a, GOA01a]
GO:0043565 - sequence-specific DNA binding [GOA01a]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09]|
|MultiFun Terms:||information transfer → RNA related → Transcription related|
|regulation → type of regulation → transcriptional level → activator|
Symmetry: Inverted Repeat
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB enriched||Yes||37||Aerobic||6.95||Yes [Gerdes03, Comment 1]|
|LB Lennox||Yes||37||Aerobic||7||Yes [Baba06, Comment 2]|
|M9 medium with 1% glycerol||Yes||37||Aerobic||7.2||0.35||Yes [Joyce06, Comment 3]|
|MOPS medium with 0.4% glucose||Yes||37||Aerobic||7.2||0.22||Yes [Baba06, Comment 2]|
|DNA-Binding-Region||153 -> 172|
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
Burton10: 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. PMID: 20603130
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Durban13: Durban J, Perez A, Sanz L, Gomez A, Bonilla F, Rodriguez S, Chacon D, Sasa M, Angulo Y, Gutierrez JM, Calvete JJ (2013). "Integrated "omics" profiling indicates that miRNAs are modulators of the ontogenetic venom composition shift in the Central American rattlesnake, Crotalus simus simus." BMC Genomics 14;234. PMID: 23575160
Eguchi07: 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. PMID: 17998538
Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938
Ibarra08: Ibarra JA, Perez-Rueda E, Segovia L, Puente JL (2008). "The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors." Genetica 133(1);65-76. PMID: 17712603
Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394
Ma04: 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. PMID: 15489450
Yamanaka12: Yamanaka Y, Ishihama A, Yamamoto K (2012). "Induction of YdeO, a regulator for acid resistance genes, by ultraviolet irradiation in Escherichia coli." Biosci Biotechnol Biochem 76(6);1236-8. PMID: 22790954
Itou09: Itou J, Eguchi Y, Utsumi R (2009). "Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12." Biosci Biotechnol Biochem 73(4);870-8. PMID: 19352034
Johnson11: Johnson MD, Burton NA, Gutierrez B, Painter K, Lund PA (2011). "RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters." J Bacteriol 193(14);3653-6. PMID: 21571995
Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065
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