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BasR DNA-binding transcriptional dual regulator

Synonyms: BasR-phosphorylated, BasR
Summary:
The transcriptional regulatory protein BasR is part of the two-component BasS/BasR signal transduction system [6] BasS functions as a membrane-associated protein kinase that phosphorylates BasR in response to elevated levels of Fe(III) which can permeabilize the outer membrane and result in cell death [6, 7] Phosphorylation of BasR increases the affinity for its specific DNA binding sites, leading to the transcriptional expression of several genes involved in modification of lipopolysaccharide to prevent excessiveFe(III) binding [4] basR expression is necessary for lipid A modifications when E. coli is grown in low concentrations of Mg2+. These modifications are necessary for the survival of cells exposed to polymyxin B. []. Deletion of basR resulted in susceptibility to cell-killing by elevated levels of Fe(III) [] Deletion of basSR resulted in acid sensitivity during growth at elevated iron concentrations [4] Expression of the arnBCADTEF operon increased during growth with elevated FeSO4 or FeCl3 and was dependent upon the BasSR two-component signal transduction system [4] Deletion of basR prevents the FeSO4-, ZnSO4-, and NH4VO3-mediated induction of eptA, arnB, and yibD and results in sensitivity to the cationic agent polymyxin B [8] A basRG53V (constitutive) mutant is resistant to polymyxin B and colistin, sensitive to the anionic agent deoxycholic acid, and expresses eptA, arnB, and yibD at high levels [8] Activation of the BasSR two-component system by Fe3+ results in the post-translational inhibition of |FRAME: G7146-MONOMER "LpxT"| and a near total loss of 1-diphosphate lipid A from the cell surface [9].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
BasR Non-Functional   Apo nd nd
BasR-phosphorylated Functional   Holo nd nd
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: basR
  Genome position: 4333282-4333950
  Length: 669 bp / 222 aa
Operon name: basRS
TU(s) encoding the TF:
Transcription unit        Promoter
basRS
 


Regulon       
Regulated gene(s) csgD, csgE, csgF, csgG, cspI, dgkA, fimB, hha, putA, qseB, qseC, tomB, yrbL
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Transcription related (4)
activator (2)
repressor (2)
fimbri, pili (2)
membrane (2)
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Regulated operon(s) csgDEFG, cspI, dgkA, fimB, putA, qseBC, tomB-hha, yrbL
First gene in the operon(s) csgD, cspI, dgkA, fimB, putA, qseB, tomB, yrbL
Simple and complex regulons BasR
BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp
BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
BasR,CpxR,PdhR
BasR,DksA,DksA-ppGpp,H-NS,IHF,NagC,NanR,ppGpp
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[BasR,-](2)
[BasR,+](7)


Transcription factor regulation    


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
  BasR-phosphorylated activator csgDp1 Sigma70 -90.5 -238.5 csgD, csgE, csgF, csgG
ctatcatttcTAAACTTAATAAAACCTTAAGgttaacattt
1103425 1103444 [APIORCISFBSCS], [BPP], [GEA] [1]
  BasR-phosphorylated activator csgDp3 Sigma38 -90.5 -238.5 csgD, csgE, csgF, csgG
ctatcatttcTAAACTTAATAAAACCTTAAGgttaacattt
1103425 1103444 [APIORCISFBSCS], [BPP], [GEA] [1]
  BasR-phosphorylated activator cspIp nd -137.5 -282.5 cspI
ttccatgagcCAAAATTCCTGAAATCTTAAGggtaagataa
1638940 1638959 [APIORCISFBSCS], [BPP] [1]
  BasR-phosphorylated activator dgkAp1 nd -30.5 -210.5 dgkA
taccaggatgCTTAATGGTAAATTCAGTAATttgtagtaaa
4256417 4256436 [APIORCISFBSCS], [BPP], [GEA], [SM] [2]
  BasR-phosphorylated activator fimBp2 nd -41.5 -331.5 fimB
ttgaacgaatATTAAATTTTGCTGAATTTTTtatgttgatt
4540616 4540635 [APIORCISFBSCS], [BPP] [1]
  BasR-phosphorylated repressor putAp Sigma70 2.5 -41.5 putA
aacatcatggATATTTCACGATAACGTTAAGttgcaccttt
1078914 1078933 [APIORCISFBSCS], [BPP] [1]
  BasR-phosphorylated activator qseBp2 Sigma70 -13.5 -92.5 qseB, qseC
caagatagtcCTTAACAACTTCTTAAGGGAAaaaaataaaa
3169726 3169745 [BPP], [GEA] [3]
  BasR-phosphorylated activator tomBp1 Sigma70 -394.5 -480.5 tomB, hha
cataacctacGAACATTAAGGAGTAATTGAAccaccaactc
481179 481198 [APIORCISFBSCS], [BPP] [1]
  BasR-phosphorylated repressor yrbLp nd -52.5 -83.5 yrbL
ctttcagaagAACCTTAAGAAAACCTTAAGAggcattgttt
3348359 3348378 [APIORCISFBSCS], [BPP], [GEA] [1]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence (Confirmed, Strong, Weak) References
  BasR-phosphorylated activator eptA Transcription-Unit nd
accttaagaaCTTAAGGTTGGCTTAATTTTgctttgcgag
4335634 4335653 4335643.5 nd [APIORCISFBSCS], [BPP], [GEA] [1]
  BasR-phosphorylated activator arnBCADTEF Transcription-Unit nd
atattagtttCTTAAGGTTAAGTTAATATTctatccttaa
2365813 2365832 2365822.5 nd [APIORCISFBSCS], [BPP], [GEA] [1], [4], [5]
  BasR-phosphorylated activator yibD Transcription-Unit nd
atctcacaggCTTAATAGTTTCTTAATACAaagcctgtaa
3790127 3790146 3790136.5 nd [APIORCISFBSCS], [GEA] nd
Other High-throughput regulatory interactions with weak evidence


Alignment and PSSM for BasR TFBSs    

Aligned TFBS of BasR   
  Sequence
  TTAACCTTAAGGTTTTATTAAGT
  TGCCTCTTAAGGTTTTCTTAAGG
  TTACCCTTAAGATTTCAGGAATT
  TTTCCCTTAAGAAGTTGTTAAGG
  CGAACATTAAGGAGTAATTGAAC
  TGCAACTTAACGTTATCGTGAAA
  CGAATATTAAATTTTGCTGAATT
  GGATGCTTAATGGTAAATTCAGT

Position weight matrix (PWM). BasR matrix-quality result   
A	0	0	5	4	1	2	0	0	8	8	1	2	2	0	2	2	4	0	0	5	8	2	1
C	2	0	2	3	4	6	0	0	0	0	1	0	0	0	0	1	3	0	0	1	0	0	1
G	1	5	0	0	1	0	0	0	0	0	5	5	1	2	0	1	1	2	2	2	0	4	2
T	5	3	1	1	2	0	8	8	0	0	1	1	5	6	6	4	0	6	6	0	0	2	4

Consensus   
;	consensus.strict             	tGaccCTTAAGGttttcttaAgt
;	consensus.strict.rc          	ACTTAAGAAAACCTTAAGGGTCA
;	consensus.IUPAC              	yKmmcCTTAAGGtkttmkkrAgk
;	consensus.IUPAC.rc           	MCTYMMKAAMACCTTAAGGKKMR
;	consensus.regexp             	[ct][GT][ac][ac]cCTTAAGGt[gt]tt[ac][gt][gt][ag]Ag[gt]
;	consensus.regexp.rc          	[AC]CT[CT][AC][AC][GT]AA[AC]ACCTTAAGG[GT][GT][AC][AG]

PWM logo   


 


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




Reference(s)    

 [1] Ogasawara H., Shinohara S., Yamamoto K., Ishihama A., 2012, Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli., Microbiology 158(Pt 6):1482-92

 [2] Wahl A., My L., Dumoulin R., Sturgis JN., Bouveret E., 2011, Antagonistic regulation of dgkA and plsB genes of phospholipid synthesis by multiple stress responses in Escherichia coli., Mol Microbiol 80(5):1260-75

 [3] Guckes KR., Kostakioti M., Breland EJ., Gu AP., Shaffer CL., Martinez CR., Hultgren SJ., Hadjifrangiskou M., 2013, Strong cross-system interactions drive the activation of the QseB response regulator in the absence of its cognate sensor., Proc Natl Acad Sci U S A 110(41):16592-7

 [4] Hagiwara D., Yamashino T., Mizuno T., 2004, A Genome-wide view of the Escherichia coli BasS-BasR two-component system implicated in iron-responses., Biosci Biotechnol Biochem 68(8):1758-67

 [5] Lee LJ., Barrett JA., Poole RK., 2005, Genome-wide transcriptional response of chemostat-cultured Escherichia coli to zinc., J Bacteriol 187(3):1124-34

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

 [7] 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

 [8] Froelich JM., Tran K., Wall D., 2006, A pmrA constitutive mutant sensitizes Escherichia coli to deoxycholic acid., J Bacteriol 188(3):1180-3

 [9] Herrera CM., Hankins JV., Trent MS., 2010, Activation of PmrA inhibits LpxT-dependent phosphorylation of lipid A promoting resistance to antimicrobial peptides., Mol Microbiol 76(6):1444-60



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