Escherichia coli K-12 substr. MG1655 Polypeptide: aerotaxis sensor receptor, flavoprotein

Gene: aer Accession Numbers: G7595 (EcoCyc), b3072, ECK3062

Synonyms: yqjJ, air

Regulation Summary Diagram: ?

Regulation summary diagram for aer

The flavoprotein Aer is one of two sensory proteins which mediate the aerotactic response in E. coli. Aer senses the oxygen and energy state of the cell rather than the external environment [Bibikov97, Rebbapragada97]. Aer mediates tactic responses towards rapidly oxidizable substrates such as ribose, galactose, maltose, malate, proline, alanine, glucose, mannitol, mannose, sorbitol, and fructose. Aer mutants show a decreased ability to grow on sugar acids and a decreased ability to colonise the mouse intestine (where sugar acids are the predominant C source) [Horne09]. The FAD cofactor is essential for the tactic response [GreerPhillips03].

Aer belongs to the superfamily of PAS domain proteins, which are involved in sensing oxygen, redox potential and light. Site-directed mutagenesis of amino acid residues within the PAS domain of Aer has identified critical functional residues [Repik00]. The amino-terminal domain containing the PAS motif binds FAD noncovalently and is sufficient for aerosensing [Bibikov00].

The C-terminal domain of Aer is similar to the signaling domains of the methyl-accepting chemotaxis proteins (MCPs). However, the aerotactic response was shown to be methylation-independent [Niwano82], and the Aer protein is not methylated [Bibikov04].

aer expression is regulated by FlhD/FlhC, and the Aer protein in turn regulates expression of a number of genes involved in anaerobic respiration and the Entner-Doudoroff pathway [Pruss03].

Citations: [Taylor98a, Taylor99a, Taylor04, Stock97]

Locations: inner membrane

Map Position: [3,215,578 <- 3,217,098] (69.31 centisomes, 250°)
Length: 1521 bp / 506 aa

Molecular Weight of Polypeptide: 55.066 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010087 , DIP:DIP-9061N , EchoBASE:EB2789 , EcoGene:EG12955 , EcoliWiki:b3072 , ModBase:P50466 , OU-Microarray:b3072 , PortEco:aer , PR:PRO_000022063 , Pride:P50466 , Protein Model Portal:P50466 , RefSeq:NP_417543 , RegulonDB:G7595 , SMR:P50466 , String:511145.b3072 , Swiss-Model:P50466 , UniProt:P50466

Relationship Links: InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR001610 , InterPro:IN-FAMILY:IPR003660 , InterPro:IN-FAMILY:IPR004089 , InterPro:IN-FAMILY:IPR004090 , InterPro:IN-FAMILY:IPR013655 , Pfam:IN-FAMILY:PF00015 , Pfam:IN-FAMILY:PF00672 , Pfam:IN-FAMILY:PF08447 , Prints:IN-FAMILY:PR00260 , Prosite:IN-FAMILY:PS50111 , Smart:IN-FAMILY:SM00086 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00283

Genetic Regulation Schematic: ?

Genetic regulation schematic for aer

GO Terms:

Biological Process: GO:0007165 - signal transduction Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Repik00]
GO:0052131 - positive aerotaxis Inferred from experiment [Bibikov97]
GO:0006935 - chemotaxis Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0004871 - signal transducer activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Repik00]
GO:0042802 - identical protein binding Inferred from experiment [Watts11, Campbell11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell processes motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
cell structure membrane
regulation type of regulation unknown

Essentiality data for aer 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]

Sequence Features

Protein sequence of aerotaxis sensor receptor, flavoprotein with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 167 -> 186
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 191 -> 209
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 263 -> 492
UniProt: Methyl-accepting transducer;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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

Bibikov00: Bibikov SI, Barnes LA, Gitin Y, Parkinson JS (2000). "Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of Escherichia coli." Proc Natl Acad Sci U S A 97(11);5830-5. PMID: 10811894

Bibikov04: Bibikov SI, Miller AC, Gosink KK, Parkinson JS (2004). "Methylation-independent aerotaxis mediated by the Escherichia coli Aer protein." J Bacteriol 186(12);3730-7. PMID: 15175286

Bibikov97: Bibikov SI, Biran R, Rudd KE, Parkinson JS (1997). "A signal transducer for aerotaxis in Escherichia coli." J Bacteriol 179(12);4075-9. PMID: 9190831

Campbell11a: Campbell AJ, Watts KJ, Johnson MS, Taylor BL (2011). "Role of the F1 region in the Escherichia coli aerotaxis receptor Aer." J Bacteriol 193(2);358-66. PMID: 21097634

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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."

GreerPhillips03: Greer-Phillips SE, Alexandre G, Taylor BL, Zhulin IB (2003). "Aer and Tsr guide Escherichia coli in spatial gradients of oxidizable substrates." Microbiology 149(Pt 9);2661-7. PMID: 12949190

Horne09: Horne SM, Mattson KR, Pruss BM (2009). "An Escherichia coli aer mutant exhibits a reduced ability to colonize the streptomycin-treated mouse large intestine." Antonie Van Leeuwenhoek 95(2);149-58. PMID: 19130287

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

Niwano82: Niwano M, Taylor BL (1982). "Novel sensory adaptation mechanism in bacterial chemotaxis to oxygen and phosphotransferase substrates." Proc Natl Acad Sci U S A 79(1);11-5. PMID: 6275380

Pruss03: Pruss BM, Campbell JW, Van Dyk TK, Zhu C, Kogan Y, Matsumura P (2003). "FlhD/FlhC is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein Aer." J Bacteriol 185(2);534-43. PMID: 12511500

Rebbapragada97: Rebbapragada A, Johnson MS, Harding GP, Zuccarelli AJ, Fletcher HM, Zhulin IB, Taylor BL (1997). "The Aer protein and the serine chemoreceptor Tsr independently sense intracellular energy levels and transduce oxygen, redox, and energy signals for Escherichia coli behavior." Proc Natl Acad Sci U S A 94(20);10541-6. PMID: 9380671

Repik00: Repik A, Rebbapragada A, Johnson MS, Haznedar JO, Zhulin IB, Taylor BL (2000). "PAS domain residues involved in signal transduction by the Aer redox sensor of Escherichia coli." Mol Microbiol 36(4);806-16. PMID: 10844669

Stock97: Stock AM (1997). "Energy sensors for aerotaxis in Escherichia coli: something old, something new." Proc Natl Acad Sci U S A 94(20);10487-9. PMID: 9380664

Taylor04: Taylor BL (2004). "An alternative strategy for adaptation in bacterial behavior." J Bacteriol 186(12);3671-3. PMID: 15175278

Taylor98a: Taylor BL, Zhulin IB (1998). "In search of higher energy: metabolism-dependent behaviour in bacteria." Mol Microbiol 28(4);683-90. PMID: 9643537

Taylor99a: Taylor BL, Zhulin IB, Johnson MS (1999). "Aerotaxis and other energy-sensing behavior in bacteria." Annu Rev Microbiol 53;103-28. PMID: 10547687

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

Watts11: Watts KJ, Johnson MS, Taylor BL (2011). "Different conformations of the kinase-on and kinase-off signaling states in the Aer HAMP domain." J Bacteriol 193(16);4095-103. PMID: 21665965

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Chilcott00: Chilcott GS, Hughes KT (2000). "Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli." Microbiol Mol Biol Rev 64(4);694-708. PMID: 11104815

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Hollands07: Hollands K, Busby SJ, Lloyd GS (2007). "New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome." FEMS Microbiol Lett 274(1);89-94. PMID: 17608696

Hollands09: Hollands K, Lee DJ, Lloyd GS, Busby SJ (2009). "Activation of sigma-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization." Mol Microbiol. PMID: 19843224

Oberto10: Oberto J (2010). "FITBAR: a web tool for the robust prediction of prokaryotic regulons." BMC Bioinformatics 11;554. PMID: 21070640

Park01: Park K, Choi S, Ko M, Park C (2001). "Novel sigmaF-dependent genes of Escherichia coli found using a specified promoter consensus." FEMS Microbiol Lett 2001;202(2);243-50. PMID: 11520622

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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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