Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: acid resistance protein



Gene: ydeP Accession Numbers: G6791 (EcoCyc), b1501, ECK1494

Regulation Summary Diagram: ?

Summary:
Overexpression of the response regulator evgA confers acid resistance to exponentially growing cells and induces the expression of many genes including ydeP. Deletion of ydeP decreases the acid resistance of exponential phase cells overexpressing evgA [Masuda02]. Overexpression of ydeP results in acid resistance and a reduced growth rate in exponential phase cells [Masuda03]

Transcription is activated by EvgA, which binds to inverted repeat sequences located upstream. Mutation of these inverted repeat sequences causes a defect in acid resistance [Masuda03].

ydeP has sequence similarity with fdnG, fdhF and fdoG - encoding subunits from formate dehydrogenases [Masuda02, Johnson14].

Locations: periplasmic space, membrane

Map Position: [1,582,231 <- 1,584,510] (34.1 centisomes)
Length: 2280 bp / 759 aa

Molecular Weight of Polypeptide: 83.495 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005001 , DIP:DIP-28057N , EchoBASE:EB3559 , EcoGene:EG13798 , EcoliWiki:b1501 , ModBase:P77561 , OU-Microarray:b1501 , PortEco:ydeP , Pride:P77561 , Protein Model Portal:P77561 , RefSeq:NP_416018 , RegulonDB:G6791 , SMR:P77561 , String:511145.b1501 , UniProt:P77561

Relationship Links: InterPro:IN-FAMILY:IPR006656 , InterPro:IN-FAMILY:IPR006657 , InterPro:IN-FAMILY:IPR009010 , InterPro:IN-FAMILY:IPR010046 , Pfam:IN-FAMILY:PF00384 , Pfam:IN-FAMILY:PF01568

In Paralogous Gene Group: 222 (14 members) , 285 (5 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0010447 - response to acidic pH Inferred from experiment [Masuda02, Masuda03]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a, Gaudet10]
GO:0030151 - molybdenum ion binding Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0016020 - membrane Inferred by computational analysis [Gaudet10]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations pH
metabolism

Essentiality data for ydeP 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]

Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 49
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 52
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

Johnson14: Johnson MD, Bell J, Clarke K, Chandler R, Pathak P, Xia Y, Marshall RL, Weinstock GM, Loman NJ, Winn PJ, Lund PA (2014). "Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli." Mol Microbiol. PMID: 24995530

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

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."

Other References Related to Gene Regulation

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

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

Oberto10: Oberto J (2010). "FITBAR: a web tool for the robust prediction of prokaryotic regulons." BMC Bioinformatics 11;554. PMID: 21070640


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 26, 2014, BIOCYC13A.