RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

baeR gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	baeR
Synonym(s):	ECK2075, EG11618, b2079
Genome position(nucleotides):	2164276 --> 2164998 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.08
Note(s):	An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-Moré et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σ^E pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses 19763168 Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-Moré et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress 19763168 baeR mutant strains are capable of increasing the number of replication origins, the amount of DnaA protein per cell, and the growth rate 26681035
External database links:

ASAP:	ABE-0006884
CGSC:	30764
ECHOBASE:	EB1575
OU-MICROARRAY:	b2079
PortEco:	baeR
STRING:	511145.b2079
COLOMBOS:	baeR

Product

Name:

DNA-binding transcriptional activator BaeR

Synonym(s):

BaeR, BaeR response regulator

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

OmpR

Cellular location:

cytosol

Molecular weight:

27.656

Isoelectric point:

5.448

Motif(s):

Type	Positions	Sequence
	131 -> 234	QRELQQQDAESPLIIDEGRFQASWRGKMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGYRWEA
	12 -> 125	RILIVEDEPKLGQLLIDYLRAASYAPTLISHGDQVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTIL
	13 -> 121	ILIVEDEPKLGQLLIDYLRAASYAPTLISHGDQVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARV
	157 -> 231	KMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGYR

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.4 - complex regulation --> 3.1.2.4.3 - two component regulatory systems (external signal)
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol GO:0032993 - protein-DNA complex
	molecular_function	GO:0003677 - DNA binding GO:0003700 - DNA-binding transcription factor activity GO:0000156 - phosphorelay response regulator activity GO:0042802 - identical protein binding GO:0000976 - transcription regulatory region sequence-specific DNA binding GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding GO:0001216 - DNA-binding transcription activator activity
	biological_process	GO:0006355 - regulation of transcription, DNA-templated GO:0000160 - phosphorelay signal transduction system GO:2000144 - positive regulation of DNA-templated transcription, initiation GO:2001023 - regulation of response to drug

Evidence:

[APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis

Reference(s):

[1] Baranova N., et al., 2002
[2] Pao GM., et al., 1995
[3] Parkinson JS. 1993
[4] Parkinson JS., et al., 1992
[5] Stock JB., et al., 1990

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PANTHER:

PDB:

PFAM:

PFAM:

PRIDE:

PRODB:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMART:

SMR:

SWISSMODEL:

UNIPROT:

Operon

Name:

mdtABCD-baeSR

Operon arrangement:

Transcription unit	Promoter
mdtABCD-baeSR	mdtAp
baeSR

Transcriptional Regulation

Display Regulation

Activated by:

BaeR, CpxR

Growth Conditions:

[1]	C: Escherichia coli\| plasmid pBAD/Myc-HisA mutant\| LB medium\| 37.0 C\| mid exponential phase E: Escherichia coli\| plasmid pBADBaeR (arabinose-induced baeR) mutant\| LB medium\| 37.0 C\| mid exponential phase

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_2404	2164246		forward	nd	[RS-EPT-CBR]	[6]

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

Reference(s)
[1] Baranova N., Nikaido H., 2002, The baeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate., J Bacteriol 184(15):4168-76
[2] Pao GM., Saier MH., 1995, Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution., J Mol Evol 40(2):136-54
[3] Parkinson JS., 1993, Signal transduction schemes of bacteria., Cell 73(5):857-71
[4] Parkinson JS., Kofoid EC., 1992, Communication modules in bacterial signaling proteins., Annu Rev Genet 26:71-112
[5] Stock JB., Stock AM., Mottonen JM., 1990, Signal transduction in bacteria., Nature 344(6265):395-400
[6] 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.

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