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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 [8]. 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 [8, 9, 10]. 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 [6]. 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 [11]. BasR is not an essential protein [12].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
BasR Non-Functional   Apo nd nd nd
BasR-phosphorylated Functional   Holo nd nd nd
Evolutionary Family: OmpR
TFBs length: 20
TFBs symmetry: inverted-repeat
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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  BasR-phosphorylated activator csgDp1 Sigma70 -90.5 -238.5 csgD, csgE, csgF, csgG
tatcatttctAAACTTAATAAAACCTTAAGgttaacattt
 1103425 1103444 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  BasR-phosphorylated activator csgDp3 Sigma38 -90.5 -238.5 csgD, csgE, csgF, csgG
tatcatttctAAACTTAATAAAACCTTAAGgttaacattt
 1103425 1103444 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  BasR-phosphorylated activator cspIp1 nd -137.5 -282.5 cspI
tccatgagccAAAATTCCTGAAATCTTAAGggtaagataa
 1638940 1638959 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  BasR-phosphorylated activator dgkAp1 nd -30.5 -210.5 dgkA
taccaggatgCTTAATGGTAAATTCAGTAAtttgtagtaa
 4256417 4256436 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2]
  BasR-phosphorylated activator fimBp2 nd -41.5 -331.5 fimB
ttgaacgaatATTAAATTTTGCTGAATTTTttatgttgat
 4540616 4540635 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  BasR-phosphorylated repressor putAp Sigma70 2.5 -41.5 putA
acatcatggaTATTTCACGATAACGTTAAGttgcaccttt
 1078914 1078933 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  BasR-phosphorylated activator qseBp2 Sigma70 -13.5 -92.5 qseB, qseC
caagatagtcCTTAACAACTTCTTAAGGGAaaaaaataaa
 3169726 3169745 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  BasR-phosphorylated activator tomBp Sigma70 -394.5 -480.5 tomB, hha
ataacctacgAACATTAAGGAGTAATTGAAccaccaactc
 481179 481198 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  BasR-phosphorylated repressor yrbLp nd -52.5 -83.5 yrbL
ctttcagaagAACCTTAAGAAAACCTTAAGaggcattgtt
 3348359 3348378 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [4]



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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  BasR-phosphorylated activator eptA Transcription-Unit nd
ctcgcaaagcAAAATTAAGCCAACCTTAAGttcttaaggt
4335634 4335653 4335643.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1]
  BasR-phosphorylated activator arnBCADTEF Transcription-Unit nd
atattagtttCTTAAGGTTAAGTTAATATTctatccttaa
2365813 2365832 2365822.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [5], [6], [7]
  BasR-phosphorylated activator yibD Transcription-Unit nd
ttacaggcttTGTATTAAGAAACTATTAAGcctgtgagat
3790127 3790146 3790136.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5]
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


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


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] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

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

 [6] 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

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

 [8] 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

 [9] 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

 [10] Chamnongpol S, Dodson W, Cromie MJ, Harris ZL, Groisman EA, 2002, Fe(III)-mediated cellular toxicity., Mol Microbiol, 45(3):711 10.1046/j.1365-2958.2002.03041.x

 [11] Rubin EJ, Herrera CM, Crofts AA, Trent MS, 2015, PmrD is required for modifications to escherichia coli endotoxin that promote antimicrobial resistance., Antimicrob Agents Chemother, 59(4):2051 10.1128/AAC.05052-14

 [12] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661

 [13] 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

 [14] Ho YH, Sung TC, Chen CS, 2012, Lactoferricin B inhibits the phosphorylation of the two-component system response regulators BasR and CreB., Mol Cell Proteomics, 11(4):M111.014720 10.1074/mcp.M111.014720


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