Escherichia coli K-12 substr. MG1655 Polypeptide: YdeO DNA-binding transcriptional dual regulator

Gene: ydeO Accession Numbers: G6789 (EcoCyc), b1499, ECK1493

Regulation Summary Diagram: ?

Regulation summary diagram for ydeO

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].

Locations: cytosol

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)

Genetic Regulation Schematic: ?

Genetic regulation schematic for ydeO

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Masuda03, Masuda02, Ma04]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred by computational analysis Inferred from experiment [Yamanaka14]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred from experiment Inferred by computational analysis [GOA01a, Yamanaka14]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level activator

Symmetry: Inverted Repeat

Regulated Transcription Units (9 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for ydeO knockouts: ?

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]

Reviewed 28-May-2015 by Santos-Zavaleta A , UNAM

Sequence Features

Protein sequence of YdeO DNA-binding transcriptional dual regulator with features indicated

Feature Class Location Citations Comment
DNA-Binding-Region 153 -> 172
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


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

Gallegos97: Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL (1997). "Arac/XylS family of transcriptional regulators." Microbiol Mol Biol Rev 61(4);393-410. PMID: 9409145

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Martin01: Martin RG, Rosner JL (2001). "The AraC transcriptional activators." Curr Opin Microbiol 4(2);132-7. PMID: 11282467

Masuda02: Masuda N, Church GM (2002). "Escherichia coli gene expression responsive to levels of the response regulator EvgA." J Bacteriol 184(22);6225-34. PMID: 12399493

Masuda03: Masuda N, Church GM (2003). "Regulatory network of acid resistance genes in Escherichia coli." Mol Microbiol 48(3);699-712. PMID: 12694615

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Yamanaka14: Yamanaka Y, Oshima T, Ishihama A, Yamamoto K (2014). "Characterization of the YdeO regulon in Escherichia coli." PLoS One 9(11);e111962. PMID: 25375160

Other References Related to Gene Regulation

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

Krin10: Krin E, Danchin A, Soutourina O (2010). "Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli." BMC Microbiol 10;273. PMID: 21034467

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

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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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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