Escherichia coli K-12 substr. MG1655 Transporter: formate channel FocA

Gene: focA Accession Numbers: EG11258 (EcoCyc), b0904, ECK0895

Synonyms: ycaE

Regulation Summary Diagram: ?

Regulation summary diagram for focA

Subunit composition of formate channel FocA = [FocA]5

FocA is a pH dependent, bidirectional formate transporter with an important role in regulating intracellular formate levels during anaerobic respiration and mixed acid fermentation in E.coli K-12. Formate, produced by the action of pyruvate:formate lyase is exported from the cytoplasm where, in the presence of terminal electron acceptors, it is a substrate of the periplasmic formate dehydrogenases. In the absence of terminal electron acceptors it is reimported to the cytoplasm for use by the formate:hydrogen lyase complex (reviewed in [Sawers05])

Analysis of formate levels in fermenting E.coli cultures indicate that initially, formate is exported out of the cell in order to prevent acidification of the cytoplasm. focA knock-out mutants grown in this manner are associated with increased intracellular levels of formate and decreased excretion of formate. However, if the pH of the culture medium drops below about 6.8, formate is re-imported and FocA has also been implicated in this process [Suppmann94]. FocA is required for the import of the toxic formate analogue, hypophosphite [Suppmann94].

The FocA compex is a symmetric pentamer forming a single central pore believed to be occupied by lipid molecules, plus 5 axial pores (one per protomer) that may be the site of transport [Wang09, Falke09]. Each protomer contains six transmembrane helices [Suppmann94, Wang09]. Both the amino and carboxy termini of FocA protomers are located on the cytoplasmic side of the inner membrane [Wang09].

The energetics of formate transport are unclear although structural evidence suggests that FocA functions as a channel rather than a transporter [Wang09]. The FocA complex must undergo some sort of pH dependent functional switch [Suppmann94]. Molecular dynamics simulations suggest that the axial channel size is affected by the pH environment [Feng12a].

The focA gene is encoded in an anaerobically-induced operon with pflA and pflB, encoding pyruvate-formate lyase [Sawers89, Suppmann94]. E. coli is also likely to have a second formate transporter [Suppmann94].

FocA belongs to the formate-nitrite transporter (FNT) family [Saier99]

Locations: inner membrane

Map Position: [952,832 <- 953,689] (20.54 centisomes, 74°)
Length: 858 bp / 285 aa

Molecular Weight of Polypeptide: 30.991 kD (from nucleotide sequence), 23.0 kD (experimental) [Falke09 ]

Unification Links: ASAP:ABE-0003073 , CGSC:31732 , DIP:DIP-9670N , EchoBASE:EB1238 , EcoGene:EG11258 , EcoliWiki:b0904 , Mint:MINT-1274847 , OU-Microarray:b0904 , PortEco:focA , Pride:P0AC23 , Protein Model Portal:P0AC23 , RefSeq:NP_415424 , RegulonDB:EG11258 , SMR:P0AC23 , String:511145.b0904 , UniProt:P0AC23

Relationship Links: InterPro:IN-FAMILY:IPR000292 , InterPro:IN-FAMILY:IPR023271 , InterPro:IN-FAMILY:IPR023999 , InterPro:IN-FAMILY:IPR024002 , Pfam:IN-FAMILY:PF01226 , Prosite:IN-FAMILY:PS01005 , Prosite:IN-FAMILY:PS01006

In Paralogous Gene Group: 520 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for focA

GO Terms:

Biological Process: GO:0015724 - formate transport Inferred from experiment Inferred by computational analysis [GOA01a, Suppmann94]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0015499 - formate transmembrane transporter activity Inferred from experiment Inferred by computational analysis [GOA01a, Suppmann94]
GO:0005215 - transporter activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Falke09, Wang09]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structure membrane
metabolism carbon utilization carbon compounds
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for focA 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]
Yes [Feist07, Comment 4]

Last-Curated ? 23-Aug-2012 by Mackie A , Macquarie University

Enzymatic reaction of: formate transporter (formate channel FocA)

Transport reaction diagram for formate transporter

Sequence Features

Protein sequence of FocA with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 37 -> 53
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 69 -> 85
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 117 -> 133
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 165 -> 183
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 192 -> 207
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 260 -> 279
UniProt: Helical;; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Socorro Gama-Castro on Fri Oct 29, 2004:
The start site of this gene was originally assigned solely on the basis of sequence considerations [Blattner97 ] . However, it was changed because Sawers and Bock [Sawers89 ] attested that the real start site is actually located 183 bp downstream. The demonstration is based on identification of both a plausible ribosome binding site and three promoters at an appropriate distance from the new start site. The promoters were identified using primer extension analysis.
10/20/97 Gene b0904 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11258; confirmed by SwissProt match.


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

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

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

Falke09: Falke D, Schulz K, Doberenz C, Beyer L, Lilie H, Thiemer B, Sawers RG (2009). "Unexpected oligomeric structure of the FocA formate channel of Escherichia coli : a paradigm for the formate-nitrite transporter family of integral membrane proteins." FEMS Microbiol Lett. PMID: 20041954

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

Feng12a: Feng Z, Hou T, Li Y (2012). "Concerted movement in pH-dependent gating of FocA from molecular dynamics simulations." J Chem Inf Model 52(8);2119-31. PMID: 22747061

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."

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

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

Saier99: Saier MH, Eng BH, Fard S, Garg J, Haggerty DA, Hutchinson WJ, Jack DL, Lai EC, Liu HJ, Nusinew DP, Omar AM, Pao SS, Paulsen IT, Quan JA, Sliwinski M, Tseng TT, Wachi S, Young GB (1999). "Phylogenetic characterization of novel transport protein families revealed by genome analyses." Biochim Biophys Acta 1999;1422(1);1-56. PMID: 10082980

Sawers05: Sawers RG (2005). "Formate and its role in hydrogen production in Escherichia coli." Biochem Soc Trans 33(Pt 1);42-6. PMID: 15667260

Sawers89: Sawers G, Bock A (1989). "Novel transcriptional control of the pyruvate formate-lyase gene: upstream regulatory sequences and multiple promoters regulate anaerobic expression." J Bacteriol 1989;171(5);2485-98. PMID: 2651404

Suppmann94: Suppmann B, Sawers G (1994). "Isolation and characterization of hypophosphite--resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter." Mol Microbiol 1994;11(5);965-82. PMID: 8022272

UniProt10a: 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 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."

Wang09: Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N, Shi Y (2009). "Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel." Nature 462(7272);467-72. PMID: 19940917

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Drapal95: Drapal N, Sawers G (1995). "Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region." Mol Microbiol 1995;16(3);597-607. PMID: 7565118

Kaiser95: Kaiser M, Sawers G (1995). "Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP." J Bacteriol 1995;177(13);3647-55. PMID: 7601827

Kaiser95a: Kaiser M, Sawers G (1995). "Fnr activates transcription from the P6 promoter of the pfl operon in vitro." Mol Microbiol 1995;18(2);331-42. PMID: 8709852

Kaiser97: Kaiser M, Sawers G (1997). "Overlapping promoters modulate Fnr- and ArcA-dependent anaerobic transcriptional activation of the focApfl operon in Escherichia coli." Microbiology 1997;143 ( Pt 3);775-83. PMID: 9084161

Sawers92: Sawers G, Suppmann B (1992). "Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins." J Bacteriol 1992;174(11);3474-8. PMID: 1592804

Sawers93: Sawers G (1993). "Specific transcriptional requirements for positive regulation of the anaerobically inducible pfl operon by ArcA and FNR." Mol Microbiol 1993;10(4);737-47. PMID: 7934836

Sawers97: Sawers G, Kaiser M, Sirko A, Freundlich M (1997). "Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition." Mol Microbiol 1997;23(4);835-45. PMID: 9157253

ShalelLevanon05a: Shalel-Levanon S, San KY, Bennett GN (2005). "Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions." Biotechnol Bioeng 92(2):147-59. PMID: 15988767

Sirko93: Sirko A, Zehelein E, Freundlich M, Sawers G (1993). "Integration host factor is required for anaerobic pyruvate induction of pfl operon expression in Escherichia coli." J Bacteriol 1993;175(18);5769-77. PMID: 8376324

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470

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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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