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Escherichia coli K-12 substr. MG1655 Protein: regulator of acid resistance, influenced by indole



Gene: ariR Accession Numbers: G6606 (EcoCyc), b1166, ECK1153

Synonyms: ymgB

Regulation Summary Diagram: ?

Subunit composition of regulator of acid resistance, influenced by indole = [AriR]2
         regulator of acid resistance, influenced by indole = AriR

Summary:
AriR appears to be a regulator of acid resistance and biofilm formation. AriR binds DNA, and in vivo target sites were identified by nickel-enrichment DNA microarray studies. In vitro, AriR binds DNA non-specifically [Lee07a]. Acting via AriR, 5-fluorouracil inhibits biofilm formation [Attila09].

The crystal structure of a C-terminal proteolytic fragment of AriR has been solved at 1.8 Å resolution; despite very low sequence identity, the protein is structurally homologous to the regulatory protein Hha [Lee07a].

Expression of ariR is regulated under conditions of biofilm formation. Deletion of tqsA (encoding the AI-2 transporter) [Herzberg06] and the presence of AI-2 [Ren04c] or the stationary phase biofilm signal indole [Lee07c] repress ariR expression. ariR is repressed in young and mature biofilms, but is induced in the intermediate, developed biofilms [Domka07], by rapid acid treatment [Kannan08] and under low temperature growth conditions [WhiteZiegler08]. Expression of ariR is regulated by the repressor BluR [Tschowri09] and the alternative sigma factor RpoS [Weber05, Tschowri09]. When placed on a low copy number plasmid, ariR increases production of capsule material and reduces expression of curli; AriR appears to modulate the activity of the Rcs two-component signaling pathway [Tschowri09].

Deletion of ariR increases biofilm formation and motility and reduces acid resistance. The defect in acid resistance is not complemented by overexpression of ariR [Lee07a].

AriR: "regulator of acid resistance influenced by indole" [Lee07a]

Locations: cytosol

Map Position: [1,215,592 -> 1,215,858] (26.2 centisomes)
Length: 267 bp / 88 aa

Molecular Weight of Polypeptide: 9.694 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003911 , EchoBASE:EB4038 , EcoGene:EG14290 , EcoliWiki:b1166 , OU-Microarray:b1166 , PortEco:ariR , PR:PRO_000022137 , Protein Model Portal:P75993 , RefSeq:NP_415684 , RegulonDB:G6606 , SMR:P75993 , String:511145.b1166 , UniProt:P75993

Relationship Links: InterPro:IN-FAMILY:IPR024753 , PDB:Structure:2OXL , Pfam:IN-FAMILY:PF10798 , ProDom:IN-FAMILY:PD865043

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0042542 - response to hydrogen peroxide Inferred from experiment [Lee07a]
GO:0042710 - biofilm formation Inferred from experiment Inferred by computational analysis [GOA01a, Lee07a]
GO:0071229 - cellular response to acid chemical Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lee07a]
GO:0042803 - protein homodimerization activity Inferred from experiment [Lee07a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations other (mechanical, nutritional, oxidative stress)
cell processes adaptations pH
regulation type of regulation unknown

Essentiality data for ariR 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 25-Sep-2007 by Keseler I , SRI International
Last-Curated ? 17-Jul-2012 by Keseler I , SRI International


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

Attila09: Attila C, Ueda A, Wood TK (2009). "5-Fluorouracil reduces biofilm formation in Escherichia coli K-12 through global regulator AriR as an antivirulence compound." Appl Microbiol Biotechnol 82(3);525-33. PMID: 19172264

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

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

Domka07: Domka J, Lee J, Bansal T, Wood TK (2007). "Temporal gene-expression in Escherichia coli K-12 biofilms." Environ Microbiol 9(2);332-46. PMID: 17222132

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."

Herzberg06: Herzberg M, Kaye IK, Peti W, Wood TK (2006). "YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport." J Bacteriol 188(2);587-98. PMID: 16385049

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

Kannan08: Kannan G, Wilks JC, Fitzgerald DM, Jones BD, Bondurant SS, Slonczewski JL (2008). "Rapid acid treatment of Escherichia coli: transcriptomic response and recovery." BMC Microbiol 8;37. PMID: 18302792

Lee07a: Lee J, Page R, Garcia-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W (2007). "Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance." J Mol Biol 373(1);11-26. PMID: 17765265

Lee07c: Lee J, Jayaraman A, Wood TK (2007). "Indole is an inter-species biofilm signal mediated by SdiA." BMC Microbiol 7;42. PMID: 17511876

Ren04c: Ren D, Bedzyk LA, Ye RW, Thomas SM, Wood TK (2004). "Differential gene expression shows natural brominated furanones interfere with the autoinducer-2 bacterial signaling system of Escherichia coli." Biotechnol Bioeng 88(5);630-42. PMID: 15470704

Tschowri09: Tschowri N, Busse S, Hengge R (2009). "The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli." Genes Dev 23(4);522-34. PMID: 19240136

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

Weber05: Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005). "Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity." J Bacteriol 187(5);1591-603. PMID: 15716429

WhiteZiegler08: White-Ziegler CA, Um S, Perez NM, Berns AL, Malhowski AJ, Young S (2008). "Low temperature (23 degrees C) increases expression of biofilm-, cold-shock- and RpoS-dependent genes in Escherichia coli K-12." Microbiology 154(Pt 1);148-66. PMID: 18174134

Other References Related to Gene Regulation

GamaCastro08: Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue);D120-4. PMID: 18158297

Majdalani07: Majdalani N, Gottesman S (2007). "Genetic dissection of signaling through the Rcs phosphorelay." Methods Enzymol 423;349-62. PMID: 17609140

Tschowri12: Tschowri N, Lindenberg S, Hengge R (2012). "Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli." Mol Microbiol 85(5);893-906. PMID: 22783906


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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 Sat Dec 20, 2014, biocyc11.