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Escherichia coli K-12 substr. MG1655 Polypeptide: ferredoxin-type protein



Gene: napF Accession Numbers: EG12068 (EcoCyc), b2208, ECK2200

Synonyms: yojG

Regulation Summary Diagram: ?

Summary:
The napF gene encodes a predicted 3Fe-4S iron sulfur protein that is not essential for the activity of periplasmic nitrate reductase (Nap), but contributes to the maximum rate of nitrate reduction [Grove96, Potter99]. NapF does not appear to be involved in the electron transfer from menaquinol or ubiquinol to periplasmic nitrate reductase [Brondijk02]. Loss of NapF alone causes a growth defect under anaerobic conditions on glycerol/nitrate medium; concurrent loss of NapG and NapH suppresses that defect. However, loss of NapF does not significantly affect nitrate reduction rates; it may therefore play a role in energy conservation rather than a direct role in nitrate reduction [Brondijk02].

NapF is located in the cytoplasm, and it can interact directly with NapA, which is exported to the periplasm via the Tat pathway. This indicates a possible role for NapF during NapA maturation [Nilavongse06].

napF shows differential codon adaptation, resulting in differential translation efficiency signatures, in aerotolerant compared to obligate anaerobic microbes. It was therefore predicted to play a role in the oxidative stress response. A napF deletion mutant was shown to be more sensitive than wild-type specifically to hydrogen peroxide exposure, but not other stresses [Krisko14].

NapF: "nitrate reductase in the periplasm" [Grove96]

Citations: [Wang99c, Stewart02, McNicholas02, Stewart03a, Stewart03, Giel06, Stewart09, Nesbit09, Lin10a, Kurata13]

Gene Citations: [Darwin95]

Locations: periplasmic space, cytosol

Map Position: [2,301,025 <- 2,301,519] (49.59 centisomes)
Length: 495 bp / 164 aa

Molecular Weight of Polypeptide: 18.047 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007293 , CGSC:36544 , EchoBASE:EB1995 , EcoGene:EG12068 , EcoliWiki:b2208 , ModBase:P0AAL0 , OU-Microarray:b2208 , PortEco:napF , Protein Model Portal:P0AAL0 , RefSeq:NP_416712 , RegulonDB:EG12068 , SMR:P0AAL0 , String:511145.b2208 , UniProt:P0AAL0

Relationship Links: InterPro:IN-FAMILY:IPR001450 , InterPro:IN-FAMILY:IPR004496 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , Pfam:IN-FAMILY:PF00037 , Pfam:IN-FAMILY:PF12800 , Pfam:IN-FAMILY:PF12838 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 223 (21 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Krisko14]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Nilavongse06]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Nilavongse06]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for napF 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:
Last-Curated ? 08-May-2014 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 28 -> 57
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 37
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 40
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 43
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 47
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 58 -> 89
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 69
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 72
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 75
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 79
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 132 -> 161
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 3;
Metal-Binding-Site 141
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 144
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 147
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 151
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2208 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12068; 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

Brondijk02: Brondijk TH, Fiegen D, Richardson DJ, Cole JA (2002). "Roles of NapF, NapG and NapH, subunits of the Escherichia coli periplasmic nitrate reductase, in ubiquinol oxidation." Mol Microbiol 44(1);245-55. PMID: 11967083

Darwin95: Darwin AJ, Stewart V (1995). "Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site." J Mol Biol 1995;251(1);15-29. PMID: 7643383

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

Giel06: Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli." Mol Microbiol 60(4);1058-75. PMID: 16677314

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

Grove96: Grove J, Tanapongpipat S, Thomas G, Griffiths L, Crooke H, Cole J (1996). "Escherichia coli K-12 genes essential for the synthesis of c-type cytochromes and a third nitrate reductase located in the periplasm." Mol Microbiol 1996;19(3);467-81. PMID: 8830238

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

Krisko14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Kurata13: Kurata T, Katayama A, Hiramatsu M, Kiguchi Y, Takeuchi M, Watanabe T, Ogasawara H, Ishihama A, Yamamoto K (2013). "Identification of the set of genes, including nonannotated morA, under the direct control of ModE in Escherichia coli." J Bacteriol 195(19);4496-505. PMID: 23913318

Lin10a: Lin AV, Stewart V (2010). "Functional roles for the GerE-family carboxyl-terminal domains of nitrate response regulators NarL and NarP of Escherichia coli K-12." Microbiology 156(Pt 10);2933-43. PMID: 20634237

McNicholas02: McNicholas PM, Gunsalus RP (2002). "The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability." J Bacteriol 184(12);3253-9. PMID: 12029041

Nesbit09: Nesbit AD, Giel JL, Rose JC, Kiley PJ (2009). "Sequence-specific binding to a subset of IscR-regulated promoters does not require IscR Fe-S cluster ligation." J Mol Biol 387(1);28-41. PMID: 19361432

Nilavongse06: Nilavongse A, Brondijk TH, Overton TW, Richardson DJ, Leach ER, Cole JA (2006). "The NapF protein of the Escherichia coli periplasmic nitrate reductase system: demonstration of a cytoplasmic location and interaction with the catalytic subunit, NapA." Microbiology 152(Pt 11);3227-37. PMID: 17074894

Potter99: Potter LC, Cole JA (1999). "Essential roles for the products of the napABCD genes, but not napFGH, in periplasmic nitrate reduction by Escherichia coli K-12." Biochem J 1999;344 Pt 1;69-76. PMID: 10548535

Stewart02: Stewart V, Lu Y, Darwin AJ (2002). "Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12." J Bacteriol 184(5);1314-23. PMID: 11844760

Stewart03: Stewart V, Bledsoe PJ, Williams SB (2003). "Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12." J Bacteriol 185(19);5862-70. PMID: 13129959

Stewart03a: Stewart V, Bledsoe PJ (2003). "Synthetic lac operator substitutions for studying the nitrate- and nitrite-responsive NarX-NarL and NarQ-NarP two-component regulatory systems of Escherichia coli K-12." J Bacteriol 185(7);2104-11. PMID: 12644479

Stewart09: Stewart V, Bledsoe PJ, Chen LL, Cai A (2009). "Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12." J Bacteriol 191(3);996-1005. PMID: 19060147

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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."

Wang99c: Wang H, Tseng CP, Gunsalus RP (1999). "The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite." J Bacteriol 181(17);5303-8. PMID: 10464201

Other References Related to Gene Regulation

Choe93: Choe M, Reznikoff WS (1993). "Identification of the regulatory sequence of anaerobically expressed locus aeg-46.5." J Bacteriol 1993;175(4);1165-72. PMID: 8432709

Darwin98: Darwin AJ, Ziegelhoffer EC, Kiley PJ, Stewart V (1998). "Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro." J Bacteriol 1998;180(16);4192-8. PMID: 9696769

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Pruss01: Pruss BM, Liu X, Hendrickson W, Matsumura P (2001). "FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions." FEMS Microbiol Lett 2001;197(1);91-7. PMID: 11287152


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 Sun Dec 21, 2014, BIOCYC13B.