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Escherichia coli K-12 substr. MG1655 Protein: ArgP DNA-binding transcriptional activator



Gene: argP Accession Numbers: EG10490 (EcoCyc), b2916, ECK2912

Synonyms: iciA

Regulation Summary Diagram: ?

Component of:
ArgP-arginine DNA binding transcriptional dual regulator (extended summary available)
ArgP-lysine

Subunit composition of ArgP DNA-binding transcriptional activator = [ArgP]2
         ArgP transcriptional activator = ArgP

Summary:
ArgP, "arginine protein," controls the transcription of genes involved in the arginine transport system and genes involved in DNA replication. DNA replication is also regulated directly by ArgP when it binds to three 13-mers located in the origin of replication (OriC), blocking the DNA opening by DnaA and inhibiting this cellular process [Thony91, Hwang90, Hwang92a]. DNA binding by ArgP is prevented when the serine protease Do (DegP) hydrolyzes this transcriptional regulator [Yoo93].

ArgP was first identified as an inhibitor of oriC-initiated DNA replication in vitro. It has also subsequently been described as a nucleoid-associated protein that shows apparently sequence-nonspecific DNA-binding activity [Azam99].

ArgP is a noncanonical regulator, as it binds to a number of additional sites in the genome without an apparent direct regulatory effect, exhibiting low-affinity binding to these sites [Marbaniang11, Hwang92a, Ruiz11].

To activate transcription, ArgP recognizes AT-rich DNA-binding sites, but no consensus sequence has been identified. When this protein activates genes involved in replication, it appears to bind to their regulatory regions without a coeffector [Lee97a, Han98]. However, the activity of ArgP depends on arginine and lysine to regulate genes involved in arginine metabolism. These amino acids, which bind to ArgP, do not seem to help the protein to form dimers or to bind to DNA, but they contribute to recruitment of the RNA polymerase and in forming the open complex. However, only the ArgP-arginine complex can produce transcripts, whereas ArgP-lysine appears to inhibit transcription [Laishram07, Nandineni04].

ArgP is a dimer with an estimated concentration of 100 to 400 molecules per cell (that is, around 200 to 800 nM monomers) [Ali99, Hwang92a].

ArgP, which belongs to the LysR family, has a helix-turn-helix motif located close to the N terminus. Members of the LysR family that show considerable homology to ArgP are AmpR from Citrobacter freundii, MetR from Salmonella enterica serotype Typhimurium, and NhaR from Pseudomonas putida [Thony91].

The expression of argP is induced by PhoB under phosphate starvation [Han99]. Contrary to the suggestion made by [Celis99], [Nandineni04] has suggested that argP is not autoregulated.

ArgP is also called IciA ( for "inhibitor of chromosome initiation") [Thony91].

Citations: [Lee96]

Locations: cytosol

Map Position: [3,057,775 -> 3,058,668] (65.9 centisomes)
Length: 894 bp / 297 aa

Molecular Weight of Polypeptide: 33.472 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009574 , CGSC:28646 , DIP:DIP-48015N , EchoBASE:EB0485 , EcoGene:EG10490 , EcoliWiki:b2916 , Mint:MINT-1262794 , ModBase:P0A8S1 , OU-Microarray:b2916 , PortEco:argP , PR:PRO_000022990 , Pride:P0A8S1 , Protein Model Portal:P0A8S1 , RefSeq:NP_417391 , RegulonDB:EG10490 , SMR:P0A8S1 , String:511145.b2916 , UniProt:P0A8S1

Relationship Links: InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR005119 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR017685 , InterPro:IN-FAMILY:IPR023490 , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03466 , Prints:IN-FAMILY:PR00039 , Prosite:IN-FAMILY:PS50931

In Paralogous Gene Group: 6 (42 members)

In Reactions of unknown directionality:

Not in pathways:
ArgP + L-arginine = ArgP transcriptional activator
ArgP + L-lysine = ArgP-lysine

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0032297 - negative regulation of DNA-dependent DNA replication initiation Inferred from experiment [Hwang92]
GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [Thony91, Celis99]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [Thony91, Celis99]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01]
GO:0008156 - negative regulation of DNA replication Inferred by computational analysis [GOA06]
Molecular Function: GO:0003681 - bent DNA binding Inferred from experiment [Azam99]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred from experiment Inferred by computational analysis [GOA01, Thony91, Celis99]
GO:0043565 - sequence-specific DNA binding Inferred from experiment [Celis99]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA06]
Cellular Component: GO:0005737 - cytoplasm Inferred by curator
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA replication
information transfer protein related nucleoproteins, basic proteins
information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TTTnTGnnATAtnnCAnAAA

Regulated Transcription Units (9 total): ?

Notes:

Essentiality data for argP 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 06-Mar-2008 by Gama-Castro S , UNAM


Subunit of: ArgP-arginine DNA binding transcriptional dual regulator

Subunit composition of ArgP-arginine DNA binding transcriptional dual regulator = [(ArgP)2][L-arginine]
         ArgP DNA-binding transcriptional activator = (ArgP)2 (extended summary available)
                 ArgP transcriptional activator = ArgP

Summary:
ArgP, "arginine protein," controls the transcription of genes involved in the arginine transport system and genes involved in DNA replication. DNA replication is also regulated directly by ArgP when it binds to three 13-mers located in the origin of replication (OriC), blocking the DNA opening by DnaA and inhibiting this cellular process [Thony91, Hwang90, Hwang92a]. DNA binding by ArgP is prevented when the serine protease Do (DegP) hydrolyzes this transcriptional regulator [Yoo93].

ArgP was first identified as an inhibitor of oriC-initiated DNA replication in vitro. It has also subsequently been described as a nucleoid-associated protein that shows apparently sequence-nonspecific DNA-binding activity [Azam99].

ArgP is a noncanonical regulator, as it binds to a number of additional sites in the genome without an apparent direct regulatory effect, exhibiting low-affinity binding to these sites [Marbaniang11, Hwang92a, Ruiz11].

To activate transcription, ArgP recognizes AT-rich DNA-binding sites, but no consensus sequence has been identified. When this protein activates genes involved in replication, it appears to bind to their regulatory regions without a coeffector [Lee97a, Han98]. However, the activity of ArgP depends on arginine and lysine to regulate genes involved in arginine metabolism. These amino acids, which bind to ArgP, do not seem to help the protein to form dimers or to bind to DNA, but they contribute to recruitment of the RNA polymerase and in forming the open complex. However, only the ArgP-arginine complex can produce transcripts, whereas ArgP-lysine appears to inhibit transcription [Laishram07, Nandineni04].

ArgP is a dimer with an estimated concentration of 100 to 400 molecules per cell (that is, around 200 to 800 nM monomers) [Ali99, Hwang92a].

ArgP, which belongs to the LysR family, has a helix-turn-helix motif located close to the N terminus. Members of the LysR family that show considerable homology to ArgP are AmpR from Citrobacter freundii, MetR from Salmonella enterica serovar Typhimurium, and NhaR from Pseudomonas putida [Thony91].

The expression of argP is induced by PhoB under phosphate starvation [Han99]. Contrary to the suggestion made by [Celis99], [Nandineni04] has suggested that argP is not autoregulated.

ArgP is also called IciA ( for "inhibitor of chromosome initiation") [Thony91].

Sequence Length: 297 AAs

In Reactions of unknown directionality:

Not in pathways:
ArgP + L-arginine = ArgP transcriptional activator

MultiFun Terms: information transfer DNA related DNA replication
information transfer protein related nucleoproteins, basic proteins
information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

Credits:
Last-Curated ? 13-Mar-2008 by Gama-Castro S , UNAM

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TTTnTGnnATAtnnCAnAAA

Regulated Transcription Units (2 total): ?

Notes:


Subunit of: ArgP-lysine

Subunit composition of ArgP-lysine = [(ArgP)2][L-lysine]
         ArgP DNA-binding transcriptional activator = (ArgP)2 (extended summary available)
                 ArgP transcriptional activator = ArgP

Sequence Length: 297 AAs

In Reactions of unknown directionality:

Not in pathways:
ArgP + L-lysine = ArgP-lysine

MultiFun Terms: information transfer DNA related DNA replication
information transfer protein related nucleoproteins, basic proteins
information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 4 -> 60
[UniProt12b]
UniProt: HTH lysR-type.
DNA-Binding-Region 21 -> 40
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2916 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10490; confirmed by SwissProt match.


References

Ali99: Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999). "Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid." J Bacteriol 181(20);6361-70. PMID: 10515926

Azam99: Azam TA, Ishihama A (1999). "Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity." J Biol Chem 274(46);33105-13. PMID: 10551881

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

Celis99: Celis RT (1999). "Repression and activation of arginine transport genes in Escherichia coli K 12 by the ArgP protein." J Mol Biol 294(5);1087-95. PMID: 10600368

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

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."

Han98: Han JS, Kwon HS, Yim JB, Hwang DS (1998). "Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli." Mol Gen Genet 259(6);610-4. PMID: 9819053

Han99: Han JS, Park JY, Lee YS, Thony B, Hwang DS (1999). "PhoB-dependent transcriptional activation of the iciA gene during starvation for phosphate in Escherichia coli." Mol Gen Genet 1999;262(3);448-52. PMID: 10589831

Hwang90: Hwang DS, Kornberg A (1990). "A novel protein binds a key origin sequence to block replication of an E. coli minichromosome." Cell 63(2);325-31. PMID: 2208289

Hwang92: Hwang DS, Kornberg A (1992). "Opposed actions of regulatory proteins, DnaA and IciA, in opening the replication origin of Escherichia coli." J Biol Chem 267(32);23087-91. PMID: 1429656

Hwang92a: Hwang DS, Thony B, Kornberg A (1992). "IciA protein, a specific inhibitor of initiation of Escherichia coli chromosomal replication." J Biol Chem 267(4);2209-13. PMID: 1733927

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

Laishram07: Laishram RS, Gowrishankar J (2007). "Environmental regulation operating at the promoter clearance step of bacterial transcription." Genes Dev 21(10);1258-72. PMID: 17504942

Lee96: Lee YS, Kim H, Hwang DS (1996). "Transcriptional activation of the dnaA gene encoding the initiator for oriC replication by IciA protein, an inhibitor of in vitro oriC replication in Escherichia coli." Mol Microbiol 1996;19(2);389-96. PMID: 8825783

Lee97a: Lee Y, Lee H, Yim J, Hwang D (1997). "The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P." Nucleic Acids Res 1997;25(17);3486-9. PMID: 9254708

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697

Nandineni04: Nandineni MR, Gowrishankar J (2004). "Evidence for an arginine exporter encoded by yggA (argO) that is regulated by the LysR-type transcriptional regulator ArgP in Escherichia coli." J Bacteriol 186(11);3539-46. PMID: 15150242

Ruiz11: Ruiz J, Haneburger I, Jung K (2011). "Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli." J Bacteriol 193(10);2536-48. PMID: 21441513

Thony91: Thony B, Hwang DS, Fradkin L, Kornberg A (1991). "iciA, an Escherichia coli gene encoding a specific inhibitor of chromosomal initiation of replication in vitro." Proc Natl Acad Sci U S A 88(10);4066-70. PMID: 2034653

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Yoo93: Yoo SJ, Seol JH, Woo SK, Suh SW, Hwang DS, Ha DB, Chung CH (1993). "Hydrolysis of the IciA protein, an inhibitor of DNA replication initiation, by protease Do in Escherichia coli." FEBS Lett 327(1);17-20. PMID: 8335089

Other References Related to Gene Regulation

Goss08: Goss TJ (2008). "The ArgP protein stimulates the Klebsiella pneumoniae gdhA promoter in a lysine-sensitive manner." J Bacteriol 190(12);4351-9. PMID: 18424527


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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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