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PdhR DNA-binding transcriptional dual regulator

Synonyms: PdhR, PdhR-pyruvate
Summary:
PdhR, pyruvate dehydrogenase complex regulator, regulates genes involved in the pyruvate dehydrogenase complex [2, 7, 8]
Activity of PdhR is controlled by pyruvate. In the absence of this compound, the PdhR regulator binds to its target promoters. This repression is antagonized by its coeffector, pyruvate [1, 2] In addition to the role described above, PdhR also controls the synthesis of two key enzymes (Ndh and CyoA) in the terminal electron transport system [1]
The PdhR belongs to the GntR family of transcriptional regulatory proteins, which share sequence similarities in their N-terminal DNA-binding domains [9, 10] PdhR is negatively autoregulated [11]
The pdhR consensus sequences has been determined to be 17bp [2] and more recently as 15 bp [1]
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PdhR Functional   Apo [BPP], [IDA] [1], [2]
PdhR-pyruvate Non-Functional Allosteric Holo [BPP], [IDA] [1], [2]
Evolutionary Family: GntR
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: pdhR
  Genome position: 122092-122856
  Length: 765 bp / 254 aa
Operon name: pdhR-aceEF-lpd
TU(s) encoding the TF:
Transcription unit        Promoter
pdhR-aceEF-lpd
pdhRp


Regulon       
Regulated gene(s) aceE, aceF, cyoA, cyoB, cyoC, cyoD, cyoE, ddlB, fecA, fecB, fecC, fecD, fecE, ftsA, ftsI, ftsL, ftsQ, ftsW, ftsZ, glcA, glcB, glcD, glcE, glcF, glcG, grcA, hemL, hha, lpd, lpxC, mraY, mraZ, murC, murD, murE, murF, murG, ndh, pdhR, rsmH, tomB
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (12)
murein (peptidoglycan) (8)
murein (8)
cell division (7)
aerobic respiration (6)
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Regulated operon(s) cyoABCDE, fecABCDE, glcDEFGBA, grcA, hemL, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, ndh, pdhR-aceEF-lpd, tomB-hha
First gene in the operon(s) cyoA, fecA, glcD, grcA, hemL, mraZ, ndh, pdhR, tomB
Simple and complex regulons ArcA,CRP,Cra,CusR,FNR,Fis,Fur,GadE,PdhR,YedW
ArcA,CRP,FNR,Fis,Fur,PdhR
ArcA,FNR,Fis,Fur,IHF,NsrR,PdhR
ArcA,GlcC,IHF,PdhR
BasR,CpxR,PdhR
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PdhR,-](8)
[PdhR,+](1)


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
  PdhR repressor cyoAp Sigma70 -177.0 -220.0 cyoA, cyoB, cyoC, cyoD, cyoE
ttttatttcaCATTGGTTATACCAATTgcccgcccag
451822 451838 [BPP], [GEA], [HIBSCS] [1]
  PdhR activator fecAp Sigma19 -21.0 -71.0 fecA, fecB, fecC, fecD, fecE
taaggaaaatAATTCTTATTTCGATTGtcctttttac
4516740 4516756 [AIBSCS], [GEA] [3]
  PdhR repressor glcDp Sigma70 -56.0 -111.0 glcD, glcE, glcF, glcG, glcB, glcA
gctggaaaaaAAATGGTCTGACCGGTAgctaaagaga
3128124 3128140 [AIBSCS], [BPP], [GEA] [4]
  PdhR repressor grcAp1 Sigma70 17.0 -58.0 grcA
actcaagcaaCAATGGTTTTACCAATTggccgcgaca
2716499 2716515 [GEA], [HIBSCS] [5]
  PdhR repressor hemLp Sigma28 -165.0 -204.0 hemL
aatgatcactTATTGGTCATACAAATAagatgacggc
175078 175094 [AIBSCS] [1]
  PdhR repressor mraZp Sigma70 -42.0 -80.0 mraZ, rsmH, ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, lpxC
tatgccttgtGACTGGCTTGACAAGCTtttcctcagc
89546 89562 [AIBSCS], [BPP], [GEA] [4]
  PdhR repressor ndhp Sigma70 -35.0 -128.0 ndh
ttaacatcaaTTTTGGTATGACCAATGcaccattcat
1165949 1165965 [BPP], [GEA], [HIBSCS] [1]
  PdhR repressor pdhRp Sigma70 19.0 -40.0 pdhR, aceE, aceF, lpd
acagacatgaAATTGGTAAGACCAATTgacttcggca
122044 122060 [AIBSCS], [BCE], [BPP], [GEA], [HIBSCS] [2], [4], [6]
  PdhR repressor tomBp1 Sigma70 -178.0 -264.0 tomB, hha
gcaatcctggTATTAGTGTCACCAATTtcatctggcg
480964 480980 [AIBSCS] [1]


Alignment and PSSM for PdhR TFBSs    

Aligned TFBS of PdhR   
  Sequence
 

Position weight matrix (PWM).   
A	6	7	0	0	0	0	0	6	5	3	7	0	0	9	5	0
C	0	0	2	1	1	0	0	2	0	1	0	9	7	0	0	0
G	0	1	0	0	6	8	0	1	0	4	1	0	1	0	1	0
T	3	1	7	8	2	1	9	0	4	1	1	0	1	0	3	9

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

 [IDA] Inferred from direct assay

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts



Reference(s)    

 [1] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol. 189(15):5534-41

 [2] Quail MA., Guest JR., 1995, Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli., Mol Microbiol. 15(3):519-29

 [3] Faith JJ., Hayete B., Thaden JT., Mogno I., Wierzbowski J., Cottarel G., Kasif S., Collins JJ., Gardner TS., 2007, Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles., PLoS Biol. 5(1):e8

 [4] Gohler AK., Kokpinar O., Schmidt-Heck W., Geffers R., Guthke R., Rinas U., Schuster S., Jahreis K., Kaleta C., 2011, More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli., BMC Syst Biol. 5(1):197

 [5] Wyborn NR., Messenger SL., Henderson RA., Sawers G., Roberts RE., Attwood MM., Green J., 2002, Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products., Microbiology. 148(Pt 4):1015-26

 [6] Quail MA., Haydon DJ., Guest JR., 1994, The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex., Mol Microbiol. 12(1):95-104

 [7] Haydon DJ., Quail MA., Guest JR., 1993, A mutation causing constitutive synthesis of the pyruvate dehydrogenase complex in Escherichia coli is located within the pdhR gene., FEBS Lett. 336(1):43-7

 [8] Urbanowski ML., Stauffer LT., Stauffer GV., 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli., Mol Microbiol. 37(4):856-68

 [9] Haydon DJ., Guest JR., 1991, A new family of bacterial regulatory proteins., FEMS Microbiol Lett. 63(2-3):291-5

 [10] Dong JM., Taylor JS., Latour DJ., Iuchi S., Lin EC., 1993, Three overlapping lct genes involved in L-lactate utilization by Escherichia coli., J Bacteriol. 175(20):6671-8

 [11] Buck D., Guest JR., 1989, Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon., Biochem J. 260(3):737-47



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