RegulonDB RegulonDB 9.3:Regulon Page

BaeR DNA-binding transcriptional activator

Synonyms: BaeR-Phosphorylated
BaeR has been shown to regulate directly genes involved in drug resistance [3, 5, 8, 9] and indirectly appears to regulate genes involved in several cellular processes, such as flagellum biosynthesis, chemotaxis, and maltose transport [5].
BaeR belongs to the BaeS/BaeR two-component system [1, 10]. 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 [3].
It has been suggested that BaeS senses envelope disorder [6, 7]. Indole [2, 7] and zinc [6] have been used as inducers of this disorder.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
BaeR-Phosphorylated Functional Covalent Holo [BPP], [IPI] [1]
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: baeR
  Genome position: 2164276-2164998
  Length: 723 bp / 240 aa
Operon name: mdtABCD-baeSR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) acrD, baeR, baeS, mdtA, mdtB, mdtC, mdtD, spy
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (6)
Porters (Uni-, Sym- and Antiporters) (4)
two component regulatory systems (external signal) (2)
drug resistance/sensitivity (1)
Transcription related (1)
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Regulated operon(s) acrD, mdtABCD-baeSR, spy
First gene in the operon(s) acrD, mdtA, spy
Simple and complex regulons BaeR,CpxR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  BaeR-Phosphorylated activator acrDp2 Sigma54 -36.5 -81.5 acrD
2587504 2587523 [BPP], [GEA], [IC] [2]
  BaeR-Phosphorylated activator mdtAp Sigma38 -27.5 -64.5 mdtA, mdtB, mdtC, mdtD, baeS, baeR
2153942 2153961 [AIBSCS], [BPP], [GEA] [2], [3], [4], [5]
  BaeR-Phosphorylated activator spyp Sigma70 -157.5 -220.5 spy
1825836 1825855 [BPP], [HIBSCS], [IC] [6]
  BaeR-Phosphorylated activator spyp Sigma70 -86.5 -149.5 spy
1825765 1825784 [AIBSCS], [BPP], [GEA], [HIBSCS] [5], [6], [7]

Alignment and PSSM for BaeR TFBSs    

Aligned TFBS of BaeR   

Position weight matrix (PWM).   
A	0	1	0	0	0	0	0	0	0	3	0	2	4	0	0	0	0	0
C	0	0	0	0	0	4	0	3	4	1	1	0	0	0	1	0	1	3
G	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	3	3	0
T	4	3	3	4	4	0	4	1	0	0	3	1	0	4	3	1	0	1

PWM logo   


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [GEA] Gene expression analysis

 [IC] Inferred by curator

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences


 [1] 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

 [2] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] Raffa RG., Raivio TL., 2002, A third envelope stress signal transduction pathway in Escherichia coli., Mol Microbiol. 45(6):1599-611

 [8] 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

 [9] 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

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

 [11] 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

 [12] 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

 [13] Choudhury HG., Beis K., 2013, The dimeric form of the unphosphorylated response regulator BaeR., Protein Sci. 22(9):1287-93