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Escherichia coli K-12 substr. MG1655 Polypeptide: inner membrane protein with a role in acid resistance



Gene: yhiM Accession Numbers: EG12228 (EcoCyc), b3491, ECK3476

Regulation Summary Diagram: ?

Summary:
YhiM is an inner membrane protein with ten predicted membrane spanning domains; its C terminus is located in the cytoplasm [Daley05].

Expression of yhiM is negatively regulated by trimethylamine N-oxide (TMAO) via the TorR transcriptional regulator [Bordi03]. Expression of yhiM is induced under acid stress [Tucker02]. Transposon insertion mutants of E.coli yhiM are unable to grow at pH 2.5 [Nguyen12]. YhiM is necessary for RpoS, glutamine and lysine-dependent acid resistance but is not required for arginine-dependent acid resistance [Nguyen12].

Locations: inner membrane

Map Position: [3,632,864 -> 3,633,916] (78.3 centisomes)
Length: 1053 bp / 350 aa

Molecular Weight of Polypeptide: 37.657 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011400 , EchoBASE:EB2140 , EcoGene:EG12228 , EcoliWiki:b3491 , PortEco:yhiM , Protein Model Portal:P37630 , RefSeq:NP_417948 , RegulonDB:EG12228 , String:511145.b3491 , UniProt:P37630

Relationship Links: InterPro:IN-FAMILY:IPR021240 , Pfam:IN-FAMILY:PF10951

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0071229 - cellular response to acid chemical Inferred from experiment [Nguyen12, Tucker02]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment Inferred by computational analysis [Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes adaptations pH

Essentiality data for yhiM 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]

Credits:
Created 23-Dec-2005 by Keseler I , SRI International
Curated 17-May-2007 by Keseler I , SRI International
Last-Curated ? 04-Mar-2012 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 3 -> 23
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 42 -> 62
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 75 -> 95
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 105 -> 125
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 158 -> 178
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 191 -> 211
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 226 -> 246
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 258 -> 278
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 291 -> 311
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 325 -> 345
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b3491 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12228; confirmed by SwissProt match.


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

Bordi03: Bordi C, Theraulaz L, Mejean V, Jourlin-Castelli C (2003). "Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli." Mol Microbiol 48(1);211-23. PMID: 12657056

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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

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

Nguyen12: Nguyen TM, Sparks-Thissen RL (2012). "The inner membrane protein, YhiM, is necessary for Escherichia coli (E. coli) survival in acidic conditions." Arch Microbiol. PMID: 22327802

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Tucker02: Tucker DL, Tucker N, Conway T (2002). "Gene expression profiling of the pH response in Escherichia coli." J Bacteriol 184(23);6551-8. PMID: 12426343

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Other References Related to Gene Regulation

GamaCastro08: Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue);D120-4. PMID: 18158297

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

Tucker03: Tucker DL, Tucker N, Ma Z, Foster JW, Miranda RL, Cohen PS, Conway T (2003). "Genes of the GadX-GadW regulon in Escherichia coli." J Bacteriol 185(10);3190-201. PMID: 12730179


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 Tue Nov 25, 2014, BIOCYC13A.