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Escherichia coli K-12 substr. MG1655 Polypeptide: 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit

Gene: yiaM Accession Numbers: EG12281 (EcoCyc), b3577, ECK3566

Regulation Summary Diagram

Regulation summary diagram for yiaM

Component of: 2,3-diketo-L-gulonate:Na+ symporter (extended summary available)

Based on sequence similarity, YiaM is a membrane-spanning component of the YiaMNO Binding Protein-dependent Secondary (TRAP) Transporter [Kelly01]

Gene Citations: [Ibanez00, Yew02, Ibanez00a]

Locations: inner membrane

Map Position: [3,742,351 -> 3,742,824] (80.66 centisomes, 290°)
Length: 474 bp / 157 aa

Molecular Weight of Polypeptide: 17.516 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011690, EchoBASE:EB2189, EcoliWiki:b3577, PortEco:yiaM, Protein Model Portal:P37674, RefSeq:NP_418034, RegulonDB:EG12281, String:511145.b3577, UniProt:P37674

Relationship Links: InterPro:IN-FAMILY:IPR007387, Pfam:IN-FAMILY:PF04290, Prosite:IN-FAMILY:PS51257

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for yiaM

GO Terms:
Biological Process:
Inferred from experimentGO:0034219 - carbohydrate transmembrane transport [Thomas06]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0015144 - carbohydrate transmembrane transporter activity [Thomas06]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05, Plantinga04]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a]

MultiFun Terms: cell structuremembrane
transportElectrochemical potential driven transportersPorters (Uni-, Sym- and Antiporters)

Essentiality data for yiaM knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of: 2,3-diketo-L-gulonate:Na+ symporter

Synonyms: YiaMNO binding protein-dependent secondary (TRAP) transporter

Subunit composition of 2,3-diketo-L-gulonate:Na+ symporter = [YiaO][YiaN][YiaM]
         2,3-diketo-L-gulonate:Na+ symporter - periplasmic binding protein = YiaO (summary available)
         2,3-diketo-L-gulonate:Na+ symporter - membrane subunit = YiaN (summary available)
         2,3-diketo-L-gulonate:Na+ symporter - membrane subunit = YiaM (summary available)

Based on sequence similarity, the yiaMNO genes encode the only tri-partite ATP-independent periplasmic (TRAP) transporter in Escherichia coli. The TRAP transporters share characteristics of both the ATP-binding cassette (ABC) and secondary families of transporters [Kelly01]. Like the ABC transporters TRAP transporters use an extracytoplasmic solute-binding protein, but, rather than ATP hydrolysis, the driving force is provided by either proton-(pmf) and/or sodium ion motive force (smf) [Kelly01]. Based on sequence similarity, YiaO is the periplasmic solute-binding protein and YiaM and YiaN are the large and small membrane-spanning proteins, respectively [Plantinga04].

The YiaMNO TRAP transporter is responsible for the uptake of 2,3-diketo-L-gulonate which is known to form spontaneously in aqueous solutions from oxidation of ascorbic acid and dehydroascorbic acid [Deutsch98, Deutsch97, Deutsch98a, Deutsch97a]. Binding experiments with purified YiaO revealed that YiaO binds 2,3-diketo-L-gulonate with high affinity but does not bind L- or D-xylulose [Thomas06]. These newer experiments refute the results of prior experiments which suggested L-xylulose might be the natural substrate of the transporter [Plantinga04].

Deletion of yiaMNO resulted in a delay of entry into stationary phase of cells grown in LB with glucose, or minimal medium with glucose or other compounds. These cultures obtained a higher stationary phase OD660 and higher c.f.u. numbers. Deletion of yiaMNO also resulted in an increased lag time in cultures with high NaCl concentrations, and a reduction in biofilm formation in minimal medium with glucose [Plantinga05].

Expression of the yiaKLMNO-lyxK-sgbHUE operon increased moderately in response to L-ascorbate [Ibanez00].

Enzymatic reaction of: 2,3-diketo-L-gulonate:Na+ symporter

Inferred from experiment

Synonyms: transport of 2,3-diketo-L-gulonate

Transport reaction diagram for 2,3-diketo-L-gulonate:Na+ symporter

Sequence Features

Protein sequence of 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 7 -> 29
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Pfam PF04290 18 -> 145
Inferred by computational analysis[Finn14]
DctQ : Tripartite ATP-independent periplasmic transporters, DctQ component
Transmembrane-Region 44 -> 66
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 79 -> 98
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 113 -> 135
Inferred by computational analysis[UniProt15]
UniProt: Helical.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


8/27/2004 (paley) Merged genes G0-8481/yiaM into EG12281/b3577
10/20/97 Gene b3577 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12281; confirmed by SwissProt match.
Martha Arnaud on Mon Jan 6, 2003:
Added from Blattner ORF tables by M. Arnaud 1/6/03.


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

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

Deutsch97: Deutsch JC (1997). "Ascorbic acid and dehydroascorbic acid interconversion without net oxidation or reduction." Anal Biochem 247(1);58-62. PMID: 9126371

Deutsch97a: Deutsch JC (1997). "Gas chromatographic/mass spectrometric measurement of ascorbic acid and analysis of ascorbic acid degradation in solution." Methods Enzymol 279;13-24. PMID: 9211252

Deutsch98: Deutsch JC (1998). "Ascorbic acid oxidation by hydrogen peroxide." Anal Biochem 255(1);1-7. PMID: 9448835

Deutsch98a: Deutsch JC (1998). "Spontaneous hydrolysis and dehydration of dehydroascorbic acid in aqueous solution." Anal Biochem 260(2);223-9. PMID: 9657882

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

Ibanez00: Ibanez E, Campos E, Baldoma L, Aguilar J, Badia J (2000). "Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors." J Bacteriol 182(16);4617-24. PMID: 10913096

Ibanez00a: Ibanez E, Gimenez R, Pedraza T, Baldoma L, Aguilar J, Badia J (2000). "Role of the yiaR and yiaS genes of Escherichia coli in metabolism of endogenously formed L-xylulose." J Bacteriol 2000;182(16);4625-7. PMID: 10913097

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

Kelly01: Kelly DJ, Thomas GH (2001). "The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea." FEMS Microbiol Rev 25(4);405-24. PMID: 11524131

Plantinga04: Plantinga TH, Van Der Does C, Badia J, Aguilar J, Konings WN, Driessen AJ (2004). "Functional characterization of the Escherichia coli K-12 yiaMNO transport protein genes." Mol Membr Biol 21(1);51-7. PMID: 14668138

Plantinga05: Plantinga TH, van der Does C, Tomkiewicz D, van Keulen G, Konings WN, Driessen AJ (2005). "Deletion of the yiaMNO transporter genes affects the growth characteristics of Escherichia coli K-12." Microbiology 151(Pt 5);1683-9. PMID: 15870475

Thomas06: Thomas GH, Southworth T, Leon-Kempis MR, Leech A, Kelly DJ (2006). "Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters." Microbiology 152(Pt 1);187-98. PMID: 16385129

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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

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

Yew02: Yew WS, Gerlt JA (2002). "Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons." J Bacteriol 2002;184(1);302-6. PMID: 11741871

Other References Related to Gene Regulation

Campos08: Campos E, de la Riva L, Garces F, Gimenez R, Aguilar J, Baldoma L, Badia J (2008). "The yiaKLX1X2PQRS and ulaABCDEFG gene systems are required for the aerobic utilization of L-ascorbate in Klebsiella pneumoniae strain 13882 with L-ascorbate-6-phosphate as the inducer." J Bacteriol 190(20);6615-24. PMID: 18708499

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

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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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