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BaeR DNA-binding transcriptional activator

Synonyms: BaeR-Phosphorylated
Summary:
BaeR has been shown to regulate directly genes involved in drug resistance |CITS: [15716448][12107134][12618449][12951338]| and indirectly appears to regulate genes involved in several cellular processes, such as flagellum biosynthesis, chemotaxis, and maltose transport |CITS: [15716448]|.
BaeR belongs to the BaeS/BaeR two-component system |CITS: [8282725][15522865]|. 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 |CITS: [12107134]|.
It has been suggested that BaeS senses envelope disorder |CITS: [17884222][12354228]|. Indole |CITS: [15686558][12354228]| and zinc |CITS: [17884222]| have been used as inducers of this disorder. BaeR is the primary regulator of the ethanol stress response |CITS: [24999585]|. Leblanc et al. identified two flavonoids and also sodium tungstate as novel inducers to BaeSR |CITS: [21515766]|. 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 |CITS: [21515766]|. As a consequence of this sensing, BaeS is autophosphorylated, followed by the transfer of the phosphate group to BaeR |CITS: [8282725]|, which is converted to an active form |CITS: [12107134]| that appears to recognize and bind a DNA sequence with a direct repeat symmetry |CITS: [17884222]|.
BaeR exhibits high degrees of sequence similarity with the transcriptional regulators OmpR and PhoB |CITS: [8282725]| and belongs to the OmpR subfamily whose members contain a DNA-binding motif in the C-terminal domain |CITS: [8282725]|.
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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
baeSR
null
mdtABCD-baeSR
mdtAp


Regulon       
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)
[BaeR,+](3)


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
acattaactcCTTTTTTTCTCCACGATTGGctcgtacctt
2587504 2587523 [BPP], [GEA], [IC] [2]
  BaeR-Phosphorylated activator mdtAp Sigma38 -27.5 -64.5 mdtA, mdtB, mdtC, mdtD, baeS, baeR
cataattcctCCATTTTTCTCCCTTATTGGctggctacac
2153942 2153961 [AIBSCS], [BPP], [GEA] [2], [3], [4], [5]
  BaeR-Phosphorylated activator spyp Sigma70 -157.5 -220.5 spy
ccagtcatccGGTATAGTTCTTCATAATCTctgcaaaatc
1825836 1825855 [BPP], [HIBSCS], [IC] [6]
  BaeR-Phosphorylated activator spyp Sigma70 -86.5 -149.5 spy
atcaaattttCTTTTTTTCTCCATAATTGGcgcaaaagtg
1825765 1825784 [AIBSCS], [BPP], [GEA], [HIBSCS] [5], [6], [7]


Alignment and PSSM for BaeR TFBSs    

Aligned TFBS of BaeR   
  Sequence
  TTTTTCTCCATAATTGGC
  TAGTTCTTCATAATCTCT
  TTTTTCTCCCTTATTGGC
  TTTTTCTCCACGATTGGC

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


Evidence    

 [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



Reference(s)    

 [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



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