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Escherichia coli K-12 substr. MG1655 Protein: ArgR transcriptional dual regulator



Gene: argR Accession Numbers: EG10070 (EcoCyc), b3237, ECK3226

Synonyms: Rarg, xerA

Regulation Summary Diagram: ?

Component of:
ArgR-arg
ArgR-L-arginine DNA-binding transcriptional dual regulator (extended summary available)

Subunit composition of ArgR transcriptional dual regulator = [ArgR]6

Summary:
ArgR complexed with L-arginine represses the transcription of several genes involved in biosynthesis and transport of arginine, transport of histidine, and its own synthesis [Caldara06, Lim87, Charlier92] and activates genes for arginine catabolism [Kiupakis02]. ArgR is also essential for a site-specific recombination reaction that resolves plasmid ColE1 multimers to monomers and is necessary for plasmid stability [Stirling88]. The role of ArgR in this latter reaction may be structural [Stirling88].

The hexamer is the active form of ArgR, and L-arginine binds to ArgR and stabilizes the hexamer [Van96a]and increases its DNA affinity by allosteric activation [Van96a, Jin05].

ArgR belongs to the ArgR/AhrC family, whose members are widely distributed in bacteria [Makarova01]. The DNA sequence which the proteins of the family recognize and to which they bind are also well-conserved among genomes [Makarova01]. This DNA sequence consists of a palindromic sequence of 18 bp, called the ARG box [Makarova01, Charlier92]. An ArgR hexamer binds to a pair of these boxes that are generally separated by 3 bp [Charlier92, Tian92]. The repressor can bind to a single box but with a greatly reduced affinity [Charlier92, Tian92]. The ARG box generally overlaps the promoter sequence and the transcriptional start site [Charlier92]; therefore, it was suggested that it represses the transcription by steric exclusion of RNA polymerase binding [Caldara07].

ArgR has two domains: the N-terminal domain, which contains a winged helix-turn-helix DNA-binding motif [Sunnerhagen97], and the C-terminal domain, which contains a motif that binds L-arginine and a motif for oligomerization [Van96a]. Based on cross-linking analysis of wild-type and mutant ArgR proteins, it has been shown that the C-terminus is more important in cer/Xer site-specific recombination than in DNA binding [Senechal10].

Citations: [Tian94]

Gene Citations: [Cunin83]

Locations: cytosol

Map Position: [3,382,725 -> 3,383,195] (72.91 centisomes)
Length: 471 bp / 156 aa

Molecular Weight of Polypeptide: 16.994 kD (from nucleotide sequence)

pI: 4.83

Unification Links: ASAP:ABE-0010620 , CGSC:1011 , DIP:DIP-47999N , EchoBASE:EB0068 , EcoGene:EG10070 , EcoliWiki:b3237 , Mint:MINT-1252219 , ModBase:P0A6D0 , OU-Microarray:b3237 , PortEco:argR , PR:PRO_000022134 , Protein Model Portal:P0A6D0 , RefSeq:NP_417704 , RegulonDB:EG10070 , SMR:P0A6D0 , String:511145.b3237 , UniProt:P0A6D0

Relationship Links: InterPro:IN-FAMILY:IPR001669 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR020899 , InterPro:IN-FAMILY:IPR020900 , InterPro:IN-FAMILY:IPR024946 , PDB:Structure:1AOY , PDB:Structure:1XXA , PDB:Structure:1XXB , PDB:Structure:1XXC , Pfam:IN-FAMILY:PF01316 , Pfam:IN-FAMILY:PF02863 , Prints:IN-FAMILY:PR01467 , ProDom:IN-FAMILY:PD007402

In Reactions of unknown directionality:

Not in pathways:
ArgR + L-arginine = ArgR-arg

In Reactions of unknown directionality:

Not in pathways:
ArgR + L-arginine = ArgR-arg

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0042150 - plasmid recombination Inferred from experiment [Stirling88]
GO:2000143 - negative regulation of DNA-templated transcription, initiation Inferred from experiment [Caldara07]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a]
GO:0006525 - arginine metabolic process Inferred by computational analysis [GOA06, GOA01a]
GO:0006526 - arginine biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0051259 - protein oligomerization Inferred by computational analysis [GOA01a]
Molecular Function: GO:0044212 - transcription regulatory region DNA binding Inferred from experiment [Caldara07]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA06, GOA01a]
GO:0034618 - arginine binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids arginine
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 18 base-pairs

Essentiality data for argR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of: ArgR-arg

Subunit composition of ArgR-arg = [ArgR][L-arginine]

Sequence Length: 156 AAs

In Reactions of unknown directionality:

Not in pathways:
ArgR + L-arginine = ArgR-arg

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids arginine
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor


Subunit of: ArgR-L-arginine DNA-binding transcriptional dual regulator

Synonyms: ArgR-arg

Subunit composition of ArgR-L-arginine DNA-binding transcriptional dual regulator = [(ArgR)6][L-arginine]
         ArgR transcriptional dual regulator = (ArgR)6 (extended summary available)

Summary:
ArgR complexed with L-arginine represses the transcription of several genes involved in biosynthesis and transport of arginine, transport of histidine, and its own synthesis [Caldara06, Lim87, Charlier92] and activates genes for arginine catabolism [Kiupakis02]. ArgR is also essential for a site-specific recombination reaction that resolves plasmid ColE1 multimers to monomers and is necessary for plasmid stability [Stirling88]. The role of ArgR in this latter reaction may be structural [Stirling88].

The hexamer is the active form of ArgR, and L-arginine binds to ArgR and stabilizes the hexamer [Van96a]and increases its DNA affinity by allosteric activation [Van96a, Jin05].

ArgR belongs to the ArgR/AhrC family, whose members are widely distributed in bacteria [Makarova01]. The DNA sequence which the proteins of the family recognize and to which they bind are also well-conserved among genomes [Makarova01]. This DNA sequence consists of a palindromic sequence of 18 bp, called the ARG box [Makarova01, Charlier92]. An ArgR hexamer binds to a pair of these boxes that are generally separated by 3 bp [Charlier92, Tian92]. The repressor can bind to a single box but with a greatly reduced affinity [Charlier92, Tian92]. The ARG box generally overlaps the promoter sequence and the transcriptional start site [Charlier92]; therefore, it was suggested that it represses the transcription by steric exclusion of RNA polymerase binding [Caldara07].

ArgR has two domains: the N-terminal domain, which contains a winged helix-turn-helix DNA-binding motif [Sunnerhagen97], and the C-terminal domain, which contains a motif that binds L-arginine and a motif for oligomerization [Van96a]. Based on cross-linking analysis of wild-type and mutant ArgR proteins, it has been shown that the C-terminus is more important in cer/Xer site-specific recombination than in DNA binding [Senechal10].

Citations: [Szwajkajzer01]

Sequence Length: 156 AAs

In Reactions of unknown directionality:

Not in pathways:
ArgR + L-arginine = ArgR-arg

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids arginine
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 18 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (16 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 21
[UniProt10]
Alternate sequence: E → K; UniProt: Increased affinity for ARG box in the presence of arginine;
Mutagenesis-Variant 44
[UniProt10]
Alternate sequence: S → F; UniProt: Defective binding to ARG box;
Mutagenesis-Variant 47
[UniProt10]
Alternate sequence: S → L; UniProt: Defective binding to ARG box;
Mutagenesis-Variant 76
[UniProt10]
Alternate sequence: P → L; UniProt: Increased affinity for ARG box in the absence of arginine;
Mutagenesis-Variant 105
[UniProt10]
Alternate sequence: A → V; UniProt: Defective binding to arginine and to ARG box;
Mutagenesis-Variant 123
[UniProt10]
Alternate sequence: G → D; UniProt: Defective binding to arginine and to ARG box. Forms dimers not hexamers;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3237 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10070; 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

Caldara06: Caldara M, Charlier D, Cunin R (2006). "The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation." Microbiology 152(Pt 11);3343-54. PMID: 17074904

Caldara07: Caldara M, Minh PN, Bostoen S, Massant J, Charlier D (2007). "ArgR-dependent Repression of Arginine and Histidine Transport Genes in Escherichia coli K-12." J Mol Biol 373(2);251-67. PMID: 17850814

Charlier92: Charlier D, Roovers M, Van Vliet F, Boyen A, Cunin R, Nakamura Y, Glansdorff N, Pierard A (1992). "Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression." J Mol Biol 1992;226(2);367-86. PMID: 1640456

Cunin83: Cunin R, Eckhardt T, Piette J, Boyen A, Pierard A, Glansdorff N (1983). "Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12." Nucleic Acids Res 1983;11(15);5007-19. PMID: 6348703

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

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."

Jin05: Jin L, Xue WF, Fukayama JW, Yetter J, Pickering M, Carey J (2005). "Asymmetric allosteric activation of the symmetric ArgR hexamer." J Mol Biol 346(1);43-56. PMID: 15663926

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

Kiupakis02: Kiupakis AK, Reitzer L (2002). "ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli." J Bacteriol 184(11);2940-50. PMID: 12003934

Lim87: Lim DB, Oppenheim JD, Eckhardt T, Maas WK (1987). "Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor." Proc Natl Acad Sci U S A 1987;84(19);6697-701. PMID: 3116542

Makarova01: Makarova KS, Mironov AA, Gelfand MS (2001). "Conservation of the binding site for the arginine repressor in all bacterial lineages." Genome Biol 2(4);RESEARCH0013. PMID: 11305941

Senechal10: Senechal H, Delesques J, Szatmari G (2010). "Escherichia coli ArgR mutants defective in cer/Xer recombination, but not in DNA binding." FEMS Microbiol Lett 305(2);162-9. PMID: 20659168

Stirling88: Stirling CJ, Szatmari G, Stewart G, Smith MC, Sherratt DJ (1988). "The arginine repressor is essential for plasmid-stabilizing site-specific recombination at the ColE1 cer locus." EMBO J 1988;7(13);4389-95. PMID: 3149585

Sunnerhagen97: Sunnerhagen M, Nilges M, Otting G, Carey J (1997). "Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA." Nat Struct Biol 4(10);819-26. PMID: 9334747

Szwajkajzer01: Szwajkajzer D, Dai L, Fukayama JW, Abramczyk B, Fairman R, Carey J (2001). "Quantitative analysis of DNA binding by the Escherichia coli arginine repressor." J Mol Biol 312(5);949-62. PMID: 11580241

Tian92: Tian G, Lim D, Carey J, Maas WK (1992). "Binding of the arginine repressor of Escherichia coli K12 to its operator sites." J Mol Biol 226(2);387-97. PMID: 1640457

Tian94: Tian G, Maas WK (1994). "Mutational analysis of the arginine repressor of Escherichia coli." Mol Microbiol 1994;13(4);599-608. PMID: 7997172

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 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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Van96a: Van Duyne GD, Ghosh G, Maas WK, Sigler PB (1996). "Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli." J Mol Biol 1996;256(2);377-91. PMID: 8594204

Other References Related to Gene Regulation

Levitt92: Levitt M (1992). "Accurate modeling of protein conformation by automatic segment matching." J Mol Biol 226(2);507-33. PMID: 1640463


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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 Dec 19, 2014, biocyc13.