Escherichia coli K-12 substr. MG1655 Polypeptide: BaeR-Phosphorylated DNA-binding transcriptional activator

Gene: baeR Accession Numbers: EG11618 (EcoCyc), b2079, ECK2075

Synonyms: BaeR-Pasp61, BaeR response regulator - phosphorylated

Regulation Summary Diagram: ?

Regulation summary diagram for baeR

Alternative forms of BaeR-Phosphorylated DNA-binding transcriptional activator: BaeR transcriptional regulator

BaeR has been shown to regulate directly genes involved in drug resistance [Nishino05, Baranova02, Hirakawa03a, Hirakawa03] and indirectly appears to regulate genes involved in several cellular processes, such as flagellum biosynthesis, chemotaxis, and maltose transport [Nishino05].

BaeR belongs to the BaeS/BaeR two-component system [Nagasawa93, Yamamoto05]. Both genes, baeR, encoding the response regulator, and baeS, encoding the sensor kinase, are located at the end of the operon (mdtABCD-baeSR) regulated by BaeR [Baranova02].

It has been suggested that BaeS senses envelope disorder [Yamamoto08a, Raffa02]. Indole [Hirakawa05, Raffa02] and zinc [Yamamoto08a] have been used as inducers of this disorder. BaeR is the primary regulator of the ethanol stress response [Srivastava14]. Leblanc et al. identified two flavonoids and also sodium tungstate as novel inducers to BaeSR [Leblanc11]. These new inducers are natural substrates of the MdtABC efflux pump, and they lead to much stronger induction of the BaeST response in an mdtA efflux pump mutant, while indole does not [Leblanc11]. As a consequence of this sensing, BaeS is autophosphorylated, followed by the transfer of the phosphate group to BaeR [Nagasawa93], which is converted to an active form [Baranova02] that appears to recognize and bind a DNA sequence with a direct repeat symmetry [Yamamoto08a].

BaeR exhibits high degrees of sequence similarity with the transcriptional regulators OmpR and PhoB [Nagasawa93] and belongs to the OmpR subfamily whose members contain a DNA-binding motif in the C-terminal domain [Nagasawa93].The BaeSR, PhoBR, and CreBC two-component systems have been shown to interact in the regulation of gene expression [Nishino05]. BaeR suppresses envZ and phoR/creC mutations [Nagasawa93].

The crystal structure of the unphosphorylated dimeric form of BaeR has been determined [Choudhury13].

BaeR: "bacterial adaptive response, response-regulator " [Nagasawa93].
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 σE 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 [BuryMone09].

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 [BuryMone09].

Gene Citations: [Nagakubo02]

Locations: cytosol

Map Position: [2,162,300 -> 2,163,022] (46.6 centisomes, 168°)
Length: 723 bp / 240 aa

Molecular Weight: 27.656 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006884 , CGSC:30764 , EchoBASE:EB1575 , EcoGene:EG11618 , ModBase:P30846 , OU-Microarray:b2079 , PortEco:baeR , RefSeq:NP_416583 , RegulonDB:EG11618

Relationship Links: Pfam:IN-FAMILY:PF00072 , UniProt:PART-OF:P69228

In Paralogous Gene Group: 121 (40 members)

Reactions known to produce the compound:

BaeSR Two-Component Signal Transduction System :
BaeR + BaeS sensory histidine kinase - phosphorylated → BaeR-Pasp61 + BaeS

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for baeR

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment [Baranova02]
Cellular Component: GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: CCAtTTtTctccAtAAtTGG

Regulated Transcription Units (4 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Last-Curated ? 30-Apr-2009 by Gama-Castro S , UNAM

Sequence Features

Protein sequence of BaeR-Phosphorylated DNA-binding transcriptional activator with features indicated

Feature Class Location Citations Comment State
Conserved-Region 12 -> 125
UniProt: Response regulatory;
4-aspartylphosphate-Modification 61
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2079 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11618; confirmed by SwissProt match.


Baranova02: 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. PMID: 12107134

BuryMone09: Bury-Mone S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P (2009). "Global analysis of extracytoplasmic stress signaling in Escherichia coli." PLoS Genet 5(9);e1000651. PMID: 19763168

Choudhury13: Choudhury HG, Beis K (2013). "The dimeric form of the unphosphorylated response regulator BaeR." Protein Sci 22(9);1287-93. PMID: 23868292

Hirakawa03: Hirakawa H, Nishino K, Yamada J, Hirata T, Yamaguchi A (2003). "Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli." J Antimicrob Chemother 52(4);576-82. PMID: 12951338

Hirakawa03a: Hirakawa H, Nishino K, Hirata T, Yamaguchi A (2003). "Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli." J Bacteriol 185(6);1851-6. PMID: 12618449

Hirakawa05: Hirakawa H, Inazumi Y, Masaki T, Hirata T, Yamaguchi A (2005). "Indole induces the expression of multidrug exporter genes in Escherichia coli." Mol Microbiol 55(4);1113-26. PMID: 15686558

Leblanc11: Leblanc SK, Oates CW, Raivio TL (2011). "Characterization of the induction and cellular role of the BaeSR two-component envelope stress response of Escherichia coli." J Bacteriol 193(13);3367-75. PMID: 21515766

Nagakubo02: Nagakubo S, Nishino K, Hirata T, Yamaguchi A (2002). "The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC." J Bacteriol 184(15);4161-7. PMID: 12107133

Nagasawa93: Nagasawa S, Ishige K, Mizuno T (1993). "Novel members of the two-component signal transduction genes in Escherichia coli." J Biochem (Tokyo) 1993;114(3);350-7. PMID: 8282725

Nishino05: Nishino K, Honda T, Yamaguchi A (2005). "Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system." J Bacteriol 187(5);1763-72. PMID: 15716448

Raffa02: Raffa RG, Raivio TL (2002). "A third envelope stress signal transduction pathway in Escherichia coli." Mol Microbiol 45(6);1599-611. PMID: 12354228

Srivastava14: Srivastava SK, Lambadi PR, Ghosh T, Pathania R, Navani NK (2014). "Genetic regulation of spy gene expression in Escherichia coli in the presence of protein unfolding agent ethanol." Gene 548(1);142-8. PMID: 24999585

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

Yamamoto05: Yamamoto K, Hirao K, Oshima T, Aiba H, Utsumi R, Ishihama A (2005). "Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli." J Biol Chem 280(2);1448-56. PMID: 15522865

Yamamoto08a: Yamamoto K, Ogasawara H, Ishihama A (2008). "Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli." J Biotechnol 133(2):196-200. PMID: 17884222

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

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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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