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Escherichia coli K-12 substr. MG1655 Transporter: nitrate:nitrite antiporter NarK



Gene: narK Accession Numbers: EG10642 (EcoCyc), b1223, ECK1217

Synonyms: NarK MFS nitrite transporter

Regulation Summary Diagram: ?

Summary:
NarK is a nitrate/nitrite transporter with a physiological role during the anaerobic growth of E.coli K-12 in the presence of nitrate. NarK catalyses nitrate uptake, nitrite uptake and nitrite export - the exact mechanism of transport has been debated but structural constraints suggest that NarK functions as a nitrate:nitrite exchanger [Zheng13].

Physiological studies of narK deletion mutants [DeMoss91, Noji89] and of strains expressing narK but lacking the second E.coli transporter NarU and the nitrite transport protein NirC [Jia05, Clegg02], suggest that NarK functions as a nitrate/nitrite antiporter. Additionally deletion of both narK and nirC decreased nitrite uptake to a basal level (thought to be due to the passive diffusion of nitrite across the inner membrane) which could be restored by a single chromosomal copy of either narK or nirC [Clegg02]. The suggestion that NarK functions primarily as a nitrite extrusion protein [Rowe94] is now thought to be incorrect [Jia09]. Competition experiments using chemostat cultures show narK+ Delta narU strains out-compete Delta narK narU+ strains during exponential growth, but the opposite is true during stationary phase leading to the suggestion that NarK confers a selective advantage during rapid growth while NarU has selctive advantage under nutrient starvation [Clegg06].

NarK consists of an amino terminal domain and a carboxy terminal domain each containing 6 transmembrane (TM) helices. NarK contains two nitrogen signature (NS) motifs located in TM5 and TM11. The substrate translocation pathway lies at the domain interface and polar residues lining the central pore form a substrate binding pocket. The substrate pathway is positively charged and does not contain protonable residues suggesting that NarK functions as a nitrate:nitrite exchanger [Zheng13].

Expression of narK is regulated by nitrate and oxygen via the regulatory proteins NarL, NarX, NarQ, FNR, IHF, and Fis [Stewart88, Nohno89, Kolesnikow92, Bonnefoy92, Li94, Melville96]. Expression of narK is also stimulated by nitrite [Kolesnikow92]. The nitrate-induced expression of narK is partially dependent upon ModE-molybdate as a transcriptional activator [Self99] as well as the catalyzed product of MoeA [Hasona98], and iron [Kolesnikow92].

NarK is a member of the major facilitator superfamily (MFS) of transporters [Griffith92].

Reviews: [Stewart93, Bonnefoy94, Moir01]

Citations: [Bonnefoy97, Stewart88a, Miller83]

Locations: inner membrane

Map Position: [1,277,180 -> 1,278,571] (27.53 centisomes)
Length: 1392 bp / 463 aa

Molecular Weight of Polypeptide: 49.693 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004111 , CGSC:18112 , EchoBASE:EB0636 , EcoGene:EG10642 , EcoliWiki:b1223 , ModBase:P10903 , OU-Microarray:b1223 , PortEco:narK , PR:PRO_000023355 , Protein Model Portal:P10903 , RefSeq:NP_415741 , RegulonDB:EG10642 , SMR:P10903 , String:511145.b1223 , UniProt:P10903

Relationship Links: InterPro:IN-FAMILY:IPR004737 , InterPro:IN-FAMILY:IPR011701 , InterPro:IN-FAMILY:IPR016196 , PDB:Structure:4JR9 , PDB:Structure:4JRE , Pfam:IN-FAMILY:PF07690 , Prosite:IN-FAMILY:PS50850

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0015706 - nitrate transport Inferred from experiment Inferred by computational analysis [GOA01, Clegg02]
GO:0015707 - nitrite transport Inferred from experiment Inferred by computational analysis [GOA01, Clegg02]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0042128 - nitrate assimilation Inferred by computational analysis [UniProtGOA11]
GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01]
Molecular Function: GO:0005452 - inorganic anion exchanger activity Inferred from experiment [Zheng13, Clegg02]
GO:0015112 - nitrate transmembrane transporter activity Inferred from experiment Inferred by computational analysis [GOA01, Clegg02]
GO:0015513 - nitrite uptake transmembrane transporter activity Inferred from experiment [Clegg02]
GO:0015514 - nitrite efflux transmembrane transporter activity Inferred from experiment [Clegg02]
GO:0015113 - nitrite transmembrane transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Zheng13]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

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

Essentiality data for narK 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]

Credits:
Curated 29-Oct-2007 by Johnson A , JCVI
Last-Curated ? 12-Dec-2012 by Mackie A , Macquarie University


Enzymatic reaction of: transport of nitrite (nitrate:nitrite antiporter NarK)


Enzymatic reaction of: nitrate:nitrite antiporter


Sequence Features

Feature Class Location Common Name Citations Comment
Transmembrane-Region 38 -> 58  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 79 -> 99  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 89  
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: probable.
Transmembrane-Region 104 -> 124  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 132 -> 152  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 164 -> 175 nitrogen signature motif 1
[Zheng13]
 
Transmembrane-Region 178 -> 198  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 212 -> 232  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 257 -> 277  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 284 -> 304  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 305  
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: probable.
Transmembrane-Region 320 -> 340  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 345 -> 365  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 405 -> 425  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 408 -> 420 nitrogen signature motif 2
[Zheng13]
 
Transmembrane-Region 436 -> 456  
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1223 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10642; 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

Bonnefoy92: Bonnefoy V, DeMoss JA (1992). "Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli." Mol Microbiol 1992;6(23);3595-602. PMID: 1474901

Bonnefoy94: Bonnefoy V, Demoss JA (1994). "Nitrate reductases in Escherichia coli." Antonie Van Leeuwenhoek 1994;66(1-3);47-56. PMID: 7747940

Bonnefoy97: Bonnefoy V, Ratouchniak J, Blasco F, Chippaux M (1997). "Organization of the nar genes at the chlZ locus." FEMS Microbiol Lett 1997;147(1);147-9. PMID: 9037773

Clegg02: Clegg S, Yu F, Griffiths L, Cole JA (2002). "The roles of the polytopic membrane proteins NarK, NarU and NirC in Escherichia coli K-12: two nitrate and three nitrite transporters." Mol Microbiol 44(1);143-55. PMID: 11967075

Clegg06: Clegg SJ, Jia W, Cole JA (2006). "Role of the Escherichia coli nitrate transport protein, NarU, in survival during severe nutrient starvation and slow growth." Microbiology 152(Pt 7);2091-100. PMID: 16804183

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

DeMoss91: DeMoss JA, Hsu PY (1991). "NarK enhances nitrate uptake and nitrite excretion in Escherichia coli." J Bacteriol 1991;173(11);3303-10. PMID: 2045360

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Griffith92: Griffith JK, Baker ME, Rouch DA, Page MG, Skurray RA, Paulsen IT, Chater KF, Baldwin SA, Henderson PJ (1992). "Membrane transport proteins: implications of sequence comparisons." Curr Opin Cell Biol 1992;4(4);684-95. PMID: 1419050

Hasona98: Hasona A, Self WT, Ray RM, Shanmugam KT (1998). "Molybdate-dependent transcription of hyc and nar operons of Escherichia coli requires MoeA protein and ModE-molybdate." FEMS Microbiol Lett 169(1);111-6. PMID: 9851041

Jia05: Jia W, Cole JA (2005). "Nitrate and nitrite transport in Escherichia coli." Biochem Soc Trans 33(Pt 1);159-61. PMID: 15667293

Jia09: Jia W, Tovell N, Clegg S, Trimmer M, Cole J (2009). "A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake." Biochem J 417(1);297-304. PMID: 18691156

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

Kolesnikow92: Kolesnikow T, Schroder I, Gunsalus RP (1992). "Regulation of narK gene expression in Escherichia coli in response to anaerobiosis, nitrate, iron, and molybdenum." J Bacteriol 1992;174(22);7104-11. PMID: 1429433

Li94: Li J, Kustu S, Stewart V (1994). "In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12." J Mol Biol 1994;241(2);150-65. PMID: 8057356

Melville96: Melville SB, Gunsalus RP (1996). "Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes." Proc Natl Acad Sci U S A 93(3);1226-31. PMID: 8577745

Miller83: Miller JB, Amy NK (1983). "Molybdenum cofactor in chlorate-resistant and nitrate reductase-deficient insertion mutants of Escherichia coli." J Bacteriol 155(2);793-801. PMID: 6307982

Moir01: Moir JW, Wood NJ (2001). "Nitrate and nitrite transport in bacteria." Cell Mol Life Sci 58(2);215-24. PMID: 11289303

Nohno89: Nohno T, Noji S, Taniguchi S, Saito T (1989). "The narX and narL genes encoding the nitrate-sensing regulators of Escherichia coli are homologous to a family of prokaryotic two-component regulatory genes." Nucleic Acids Res 1989;17(8);2947-57. PMID: 2657652

Noji89: Noji S, Nohno T, Saito T, Taniguchi S (1989). "The narK gene product participates in nitrate transport induced in Escherichia coli nitrate-respiring cells." FEBS Lett 1989;252(1-2);139-43. PMID: 2668029

Rowe94: Rowe JJ, Ubbink-Kok T, Molenaar D, Konings WN, Driessen AJ (1994). "NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli." Mol Microbiol 1994;12(4);579-86. PMID: 7934881

Self99: Self WT, Grunden AM, Hasona A, Shanmugam KT (1999). "Transcriptional regulation of molybdoenzyme synthesis in Escherichia coli in response to molybdenum: ModE-molybdate, a repressor of the modABCD (molybdate transport) operon is a secondary transcriptional activator for the hyc and nar operons." Microbiology 1999;145 ( Pt 1);41-55. PMID: 10206709

Stewart88: Stewart V, Parales J (1988). "Identification and expression of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12." J Bacteriol 1988;170(4);1589-97. PMID: 2832370

Stewart88a: Stewart V, Berg BL (1988). "Influence of nar (nitrate reductase) genes on nitrate inhibition of formate-hydrogen lyase and fumarate reductase gene expression in Escherichia coli K-12." J Bacteriol 170(10);4437-44. PMID: 3049531

Stewart93: Stewart V (1993). "Nitrate regulation of anaerobic respiratory gene expression in Escherichia coli." Mol Microbiol 1993;9(3);425-34. PMID: 8412692

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

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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."

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

Zheng13: Zheng H, Wisedchaisri G, Gonen T (2013). "Crystal structure of a nitrate/nitrite exchanger." Nature 497(7451);647-51. PMID: 23665960

Other References Related to Gene Regulation

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Walker92: Walker MS, DeMoss JA (1992). "Role of alternative promoter elements in transcription from the nar promoter of Escherichia coli." J Bacteriol 1992;174(4);1119-23. PMID: 1735706


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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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