Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Protein: iron-sulfur cluster scaffold protein



Gene: nfuA Accession Numbers: G7748 (EcoCyc), b3414, ECK3401

Synonyms: yhgI, gntY

Regulation Summary Diagram: ?

Subunit composition of iron-sulfur cluster scaffold protein = [NfuA]2
         iron-sulfur cluster scaffold protein = NfuA

Summary:
NfuA is an iron-sulfur protein which is able to transfer its [4Fe-4S] iron-sulfur cluster to apo-aconitase in vitro, thus identifying it as an iron-sulfur cluster scaffold protein [Angelini08].

The N-terminal domain of NfuA is similar to A-type iron-sulfur proteins, although it does not contain this domain's conserved Cys residues required for iron-sulfur cluster binding. The C-terminal domain of the protein is similar to the Nfu domain of Azotobacter vinelandii NifU. Both domains as well as the conserved cysteine residues C149 and C152 are important for NfuA function [Angelini08].

Both NfuA and GrxD interact with MiaB. NfuA, but not GrxD, can transfer a 4Fe-4S cluster to apo-MiaB in vitro, and both proteins affect MiaB activity in vivo [Boutigny13].

An nfuA null mutant has a normal growth phenotype in complex media, but is eliminated from the culture after 3 days in co-culture with the wild-type strain. An nfuA null mutant can not utilize DNA as the sole source of carbon and energy [Palchevskiy06]. An nfuA null mutant has a severe growth defect under oxidative stress (addition of paraquat) and iron starvation (addition of 2,2'-dipyridyl) conditions [Angelini08].

Expression of nfuA is repressed by IscR, a transcription factor that regulates expression of genes involved in iron-sulfur cluster biogenesis. Expression of nfuA is lower under anaerobic conditions than under aerobic conditions [Giel06]. Increased nfuA expression by paraquat and 2,2'-dipyridyl is mediated by IscR [Angelini08]. nfuA expression is upregulated in response to cobalt [Fantino10].

The nfuA gene product is required for utilization of DNA as the sole source of carbon and energy; nfuA is homologous to genes involved in natural competence and genetic transformation in other bacteria [Finkel01, Palchevskiy06]. Based on complementation experiments, NfuA/GntY together with GntX were thought to be involved in high-affinity gluconate transport [Porco98]; however, a role for NfuA alone was not tested. An nfuA null mutant does not have a defect in gluconate metabolism [Angelini08].

NfuA: "Nfu-like protein" [Angelini08]

Reviews: [Barras11, Roche13]

Gene Citations: [Nonaka06]

Locations: cytosol

Map Position: [3,543,646 -> 3,544,221] (76.38 centisomes)
Length: 576 bp / 191 aa

Molecular Weight of Polypeptide: 20.998 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011144 , DIP:DIP-48001N , EchoBASE:EB2771 , EcoGene:EG12935 , EcoliWiki:b3414 , ModBase:P63020 , OU-Microarray:b3414 , PortEco:nfuA , PR:PRO_000023378 , Pride:P63020 , Protein Model Portal:P63020 , RefSeq:NP_417873 , RegulonDB:G7748 , SMR:P63020 , String:511145.b3414 , UniProt:P63020

Relationship Links: InterPro:IN-FAMILY:IPR000361 , InterPro:IN-FAMILY:IPR001075 , InterPro:IN-FAMILY:IPR017726 , Panther:IN-FAMILY:PTHR10072:SF35 , Pfam:IN-FAMILY:PF01106 , Pfam:IN-FAMILY:PF01521 , ProDom:IN-FAMILY:PD002830

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Angelini08]
GO:0010106 - cellular response to iron ion starvation Inferred from experiment [Angelini08]
GO:0015976 - carbon utilization Inferred from experiment [Palchevskiy06]
GO:0016226 - iron-sulfur cluster assembly Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Angelini08]
GO:0097428 - protein maturation by iron-sulfur cluster transfer Inferred from experiment [Boutigny13, Angelini08]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
GO:0051604 - protein maturation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Boutigny13]
GO:0042803 - protein homodimerization activity Inferred from experiment [Angelini08]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Angelini08]
GO:0005506 - iron ion binding 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]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transfer protein related chaperoning, repair (refolding)
metabolism central intermediary metabolism incorporation of metal ions

Essentiality data for nfuA 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 31-Mar-2008 by Keseler I , SRI International
Last-Curated ? 19-Apr-2013 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 39
[Angelini08, UniProt11]
Alternate sequence: C → S; UniProt: No effect on activity in vivo. Still able to bind a Fe/S cluster in vitro.
Mutagenesis-Variant 44
[Angelini08, UniProt11]
Alternate sequence: C → S; UniProt: No effect on activity in vivo.
Mutagenesis-Variant 149
[Angelini08, UniProt11]
Alternate sequence: C → S; UniProt: Loss of activity in vivo. Still able to bind a Fe/S cluster in vitro.
Metal-Binding-Site 149
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Mutagenesis-Variant 152
[Angelini08, UniProt11]
Alternate sequence: C → S; UniProt: Loss of activity in vivo. Still able to bind a Fe/S cluster in vitro.
Metal-Binding-Site 152
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Angelini08: Angelini S, Gerez C, Ollagnier-de Choudens S, Sanakis Y, Fontecave M, Barras F, Py B (2008). "NfuA, a new factor required for maturing Fe/S proteins in Escherichia coli under oxidative stress and iron starvation conditions." J Biol Chem 283(20);14084-91. PMID: 18339628

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

Barras11: Barras F, Fontecave M (2011). "Cobalt stress in Escherichia coli and Salmonella enterica: molecular bases for toxicity and resistance." Metallomics 3(11);1130-4. PMID: 21952637

Boutigny13: Boutigny S, Saini A, Baidoo EE, Yeung N, Keasling JD, Butland G (2013). "Physical and Functional Interactions of a Monothiol Glutaredoxin and an Iron Sulfur Cluster Carrier Protein with the Sulfur-donating Radical S-Adenosyl-L-methionine Enzyme MiaB." J Biol Chem 288(20);14200-11. PMID: 23543739

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

Fantino10: Fantino JR, Py B, Fontecave M, Barras F (2010). "A genetic analysis of the response of Escherichia coli to cobalt stress." Environ Microbiol 12(10);2846-57. PMID: 20545747

Finkel01: Finkel SE, Kolter R (2001). "DNA as a nutrient: novel role for bacterial competence gene homologs." J Bacteriol 183(21);6288-93. PMID: 11591672

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Palchevskiy06: Palchevskiy V, Finkel SE (2006). "Escherichia coli Competence Gene Homologs Are Essential for Competitive Fitness and the Use of DNA as a Nutrient." J Bacteriol 188(11);3902-10. PMID: 16707682

Porco98: Porco A, Alonso G, Isturiz T (1998). "The gluconate high affinity transport of GntI in Escherichia coli involves a multicomponent complex system." J Basic Microbiol 38(5-6);395-404. PMID: 9871335

Roche13: Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F (2013). "Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity." Biochim Biophys Acta 1827(3);455-69. PMID: 23298813

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

Other References Related to Gene Regulation

Peekhaus98a: Peekhaus N, Conway T (1998). "Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex." J Bacteriol 1998;180(7);1777-85. PMID: 9537375

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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 Fri Nov 28, 2014, BIOCYC14A.