RegulonDB

Gene
Name:	aer
Synonym(s):	ECK3062, G7595, air, b3072, yqjJ
Genome position(nucleotides):	3217556 <-- 3219076
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.77
External database links:

ASAP:	ABE-0010087
ECHOBASE:	EB2789
ECOLIHUB:	aer
OU-MICROARRAY:	b3072
STRING:	511145.b3072
COLOMBOS:	aer

Gene

Name:

aer

Synonym(s):

ECK3062, G7595, air, b3072, yqjJ

Genome position(nucleotides):

3217556 <-- 3219076

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.77

External database links:

ASAP:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

31 -> 113

THANDTFVQVSGYTLQELQGQPHNMVRHPDMPKAAFADMWFTLKKGEPWSGIVKNRRKNGDHYWVRANAVPMVREGKISGYMS

167 -> 186

GVMTLMFILLAAMLWFVAAP

UniProt: Helical.

191 -> 209

ILCALVVLLASACFEWQIV

UniProt: Helical.

263 -> 492

QVSSVRNGSETLAKGTDELNEHTQQTVDNVQQTVATMNQMAASVKQNSATASAADKLSITASNAAVQGGEAMTTVIKTMDDIADSTQRIGTITSLINDIAFQTNILALNAAVEAARAGEQGKGFAVVAGEVRHLASRSANAANDIRKLIDASADKVQSGSQQVHAAGRTMEDIVAQVKNVTQLIAQISHSTLEQADGLSSLTRAVDELNLITQKNAELVEESAQVSAMVK

UniProt: Methyl-accepting transducer.

319 -> 472

LSITASNAAVQGGEAMTTVIKTMDDIADSTQRIGTITSLINDIAFQTNILALNAAVEAARAGEQGKGFAVVAGEVRHLASRSANAANDIRKLIDASADKVQSGSQQVHAAGRTMEDIVAQVKNVTQLIAQISHSTLEQADGLSSLTRAVDELNL

Type

Positions

Sequence

Comment

31 -> 113

THANDTFVQVSGYTLQELQGQPHNMVRHPDMPKAAFADMWFTLKKGEPWSGIVKNRRKNGDHYWVRANAVPMVREGKISGYMS

167 -> 186

GVMTLMFILLAAMLWFVAAP

UniProt: Helical.

191 -> 209

ILCALVVLLASACFEWQIV

UniProt: Helical.

263 -> 492

UniProt: Methyl-accepting transducer.

319 -> 472

LSITASNAAVQGGEAMTTVIKTMDDIADSTQRIGTITSLINDIAFQTNILALNAAVEAARAGEQGKGFAVVAGEVRHLASRSANAANDIRKLIDASADKVQSGSQQVHAAGRTMEDIVAQVKNVTQLIAQISHSTLEQADGLSSLTRAVDELNL

Multifun Terms (GenProtEC)

3 - regulation --> 3.1 - type of regulation --> 3.1.4 - unknown

5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0004888 - transmembrane signaling receptor activity
GO:0042802 - identical protein binding

biological_process

GO:0007165 - signal transduction
GO:0006935 - chemotaxis
GO:0052131 - positive aerotaxis

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, FNR

Transcriptional Regulation

Display Regulation

Activated by:

CRP, FNR

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_3379	3219118		reverse	nd	[RS-EPT-CBR]	[13]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_3379

3219118

reverse

[RS-EPT-CBR]

[13]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] 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
[2] Buron-Barral MC., Gosink KK., Parkinson JS., 2006, Loss- and gain-of-function mutations in the F1-HAMP region of the Escherichia coli aerotaxis transducer Aer., J Bacteriol 188(10):3477-86
[3] Gosink KK., Buron-Barral MC., Parkinson JS., 2006, Signaling interactions between the aerotaxis transducer Aer and heterologous chemoreceptors in Escherichia coli., J Bacteriol 188(10):3487-93
[4] Herrmann S., Ma Q., Johnson MS., Repik AV., Taylor BL., 2004, PAS domain of the Aer redox sensor requires C-terminal residues for native-fold formation and flavin adenine dinucleotide binding., J Bacteriol 186(20):6782-91
[5] Samanta D., Widom J., Borbat PP., Freed JH., Crane BR., 2016, Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor., J Biol Chem 291(50):25809-25814
[6] 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
[7] Taylor BL., 2004, An alternative strategy for adaptation in bacterial behavior., J Bacteriol 186(12):3671-3
[8] Taylor BL., Zhulin IB., 1998, In search of higher energy: metabolism-dependent behaviour in bacteria., Mol Microbiol 28(4):683-90
[9] Taylor BL., Zhulin IB., Johnson MS., 1999, Aerotaxis and other energy-sensing behavior in bacteria., Annu Rev Microbiol 53:103-28
[10] Watts KJ., Johnson MS., Taylor BL., 2006, Minimal requirements for oxygen sensing by the aerotaxis receptor Aer., Mol Microbiol 59(4):1317-26
[11] Watts KJ., Johnson MS., Taylor BL., 2008, Structure-function relationships in the HAMP and proximal signaling domains of the aerotaxis receptor Aer., J Bacteriol 190(6):2118-27
[12] Watts KJ., Ma Q., Johnson MS., Taylor BL., 2004, Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer., J Bacteriol 186(21):7440-9
[13] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] 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

[2] Buron-Barral MC., Gosink KK., Parkinson JS., 2006, Loss- and gain-of-function mutations in the F1-HAMP region of the Escherichia coli aerotaxis transducer Aer., J Bacteriol 188(10):3477-86

[3] Gosink KK., Buron-Barral MC., Parkinson JS., 2006, Signaling interactions between the aerotaxis transducer Aer and heterologous chemoreceptors in Escherichia coli., J Bacteriol 188(10):3487-93

[4] Herrmann S., Ma Q., Johnson MS., Repik AV., Taylor BL., 2004, PAS domain of the Aer redox sensor requires C-terminal residues for native-fold formation and flavin adenine dinucleotide binding., J Bacteriol 186(20):6782-91

[5] Samanta D., Widom J., Borbat PP., Freed JH., Crane BR., 2016, Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor., J Biol Chem 291(50):25809-25814

[6] 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

[7] Taylor BL., 2004, An alternative strategy for adaptation in bacterial behavior., J Bacteriol 186(12):3671-3

[8] Taylor BL., Zhulin IB., 1998, In search of higher energy: metabolism-dependent behaviour in bacteria., Mol Microbiol 28(4):683-90

[9] Taylor BL., Zhulin IB., Johnson MS., 1999, Aerotaxis and other energy-sensing behavior in bacteria., Annu Rev Microbiol 53:103-28

[10] Watts KJ., Johnson MS., Taylor BL., 2006, Minimal requirements for oxygen sensing by the aerotaxis receptor Aer., Mol Microbiol 59(4):1317-26

[11] Watts KJ., Johnson MS., Taylor BL., 2008, Structure-function relationships in the HAMP and proximal signaling domains of the aerotaxis receptor Aer., J Bacteriol 190(6):2118-27

[12] Watts KJ., Ma Q., Johnson MS., Taylor BL., 2004, Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer., J Bacteriol 186(21):7440-9

[13] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.