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Escherichia coli K-12 substr. MG1655 Polypeptide: FabR DNA-binding transcriptional repressor



Gene: fabR Accession Numbers: EG11394 (EcoCyc), b3963, ECK3955

Synonyms: yijC

Regulation Summary Diagram: ?

Summary:
FabR, "Fatty acid biosynthesis Regulator," represses expression of the fabA and fabB genes, which are essential for the synthesis of monounsaturated fatty acids [Marrakchi02, Zhang02]. FabR directly influences membrane lipid homeostasis [Marrakchi02, Zhang02, Cronan75]. It is a unique example of a transcription factor exclusively regulating expression of type II fatty acid synthase enzymes [Zhang02].

The FabR consensus sequence has been identified as a palindromic sequence with a length of 18 bp [Zhang02, McCue01]. DNA binding and repression require the binding of unsaturated acyl-ACP (acyl-acyl carrier protein) or acyl-CoA. Saturated acyl-ACP or acyl-CoA competes with the unsaturated fatty acids for binding to FabR but does not trigger DNA binding [Zhu09]. Thus, FabR senses the ratio, rather than the absolute amount, of unsaturated and saturated fatty acids and adjusts expression of fabA and fabB to balance the composition of saturated and unsaturated acyl-ACP [Zhu09].

The binding site for FabR overlaps with the binding site for FadR, the transcriptional activator for fabA and fabB in the promoter regions of both fabA and fabB. Both regulators can bind simultaneously to the promoter of fabB in the presence of unsaturated acyl-ACP [Zhu09].

FabR belongs to the TetR family [Ramos05, McCue01, Bateman00] and has a helix-turn-helix motif at the N terminus typical of repressors [PerezRueda00]. Homologs of FabR are found exclusively in γ-protobacteria [McCue01].

Reviews: [Zhang09a, Fujita07]

Locations: cytosol

Map Position: [4,159,090 -> 4,159,794] (89.64 centisomes)
Length: 705 bp / 234 aa

Molecular Weight of Polypeptide: 26.553 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012979 , EchoBASE:EB1367 , EcoGene:EG11394 , EcoliWiki:b3963 , ModBase:P0ACU5 , OU-Microarray:b3963 , PortEco:fabR , PR:PRO_000022566 , Pride:P0ACU5 , Protein Model Portal:P0ACU5 , RefSeq:NP_418398 , RegulonDB:EG11394 , SMR:P0ACU5 , String:511145.b3963 , UniProt:P0ACU5

Relationship Links: InterPro:IN-FAMILY:IPR001647 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR015893 , InterPro:IN-FAMILY:IPR023764 , Pfam:IN-FAMILY:PF00440 , Prosite:IN-FAMILY:PS01081 , Prosite:IN-FAMILY:PS50977

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Zhang02, McCue01]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006631 - fatty acid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006633 - fatty acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0045717 - negative regulation of fatty acid biosynthetic process Inferred by computational analysis [GOA06]
Molecular Function: GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred from experiment Inferred by computational analysis [GOA06, McCue01, Zhang02]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level repressor

DNA binding site length: 18 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: aGCGTACAcGTGTacGCT

Regulated Transcription Units (2 total): ?

Notes:

Essentiality data for fabR 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 ? 02-Apr-2008 by Santos-Zavaleta A , UNAM


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 28
[Gustafsson92, UniProt10]
Alternate sequence: E → T; UniProt: (in Ref. 1; CAA46823);
Sequence-Conflict 42
[Gustafsson92, UniProt10]
Alternate sequence: L → V; UniProt: (in Ref. 1; CAA46823);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3963 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11394; 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

Bateman00: Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL (2000). "The Pfam protein families database." Nucleic Acids Res 28(1);263-6. PMID: 10592242

Cronan75: Cronan JE, Gelmann EP (1975). "Physical properties of membrane lipids: biological relevance and regulation." Bacteriol Rev 39(3);232-56. PMID: 1100043

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

Fujita07: Fujita Y, Matsuoka H, Hirooka K (2007). "Regulation of fatty acid metabolism in bacteria." Mol Microbiol 66(4);829-39. PMID: 17919287

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."

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

Gustafsson92: Gustafsson C, Warne SR (1992). "Physical map of the oxyR-trmA region (minute 89.3) of the Escherichia coli chromosome." J Bacteriol 174(23);7878-9. PMID: 1447162

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

Marrakchi02: Marrakchi H, Zhang YM, Rock CO (2002). "Mechanistic diversity and regulation of Type II fatty acid synthesis." Biochem Soc Trans 30(Pt 6);1050-5. PMID: 12440970

McCue01: McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE (2001). "Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes." Nucleic Acids Res 2001;29(3);774-82. PMID: 11160901

PerezRueda00: Perez-Rueda E, Collado-Vides J (2000). "The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12." Nucleic Acids Res 28(8);1838-47. PMID: 10734204

Ramos05: Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R (2005). "The TetR family of transcriptional repressors." Microbiol Mol Biol Rev 69(2);326-56. PMID: 15944459

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Zhang02: Zhang YM, Marrakchi H, Rock CO (2002). "The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli." J Biol Chem 2002;277(18);15558-65. PMID: 11859088

Zhang09a: Zhang YM, Rock CO (2009). "Transcriptional regulation in bacterial membrane lipid synthesis." J Lipid Res 50 Suppl;S115-9. PMID: 18941141

Zhu09: Zhu K, Zhang YM, Rock CO (2009). "Transcriptional regulation of membrane lipid homeostasis in Escherichia coli." J Biol Chem 284(50);34880-8. PMID: 19854834


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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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