RegulonDB RegulonDB 11.0:Regulon Page

PdhR DNA-binding transcriptional dual regulator

Synonyms: PdhR-pyruvate, PdhR
PdhR, "pyruvate dehydrogenase complex regulator," regulates genes involved in the pyruvate dehydrogenase complex [2, 6, 8, 9] Moreover, PdhR participates in positive regulation of fatty acid degradation genes and negative regulation of cell mobility genes. Gas chromatography analysis indicated an increase in free fatty acids in a mutant lacking PdhR [6] Activity of PdhR is controlled by pyruvate. In the absence of this compound, the PdhR regulator binds to its target promoters [6] This binding is antagonized by pyruvate [1, 2, 6] PdhR activates a set of genes for fatty acid degradation only in the absence of effector pyruvate. Therefore, the activation of the fatty acid degradation genes by PdhR could be lost in the presence of pyruvate. Likewise, RpoF-regulated synthesis of flagellar components is also controlled by the pyruvate-sensing PdhR. In the absence of PdhR, the expression level of the flagellar component increased, indicating a new model in which the level of flagella is controlled by the level of pyruvate [6] PdhR controls the synthesis of two key enzymes (Ndh and CyoA) in the terminal electron transport system [1] the enzymes for producing pyruvate and the enzymes involved in the utilization of pyruvate as a substrate [6] The pdhR deletion mutant enhanced glucose metabolism under oxygen-limited conditions.
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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
TFBs length: 17
TFBs symmetry: inverted-repeat
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

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,HprR,PdhR
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  PdhR repressor cyoAp Sigma70 -177.0 -220.0 cyoA, cyoB, cyoC, cyoD, cyoE
451822 451838 [GEA], [APIORCISFBSCS], [BPP] [1]
  PdhR activator fecAp nd -21.0 -71.0 fecA, fecB, fecC, fecD, fecE
4516740 4516756 [GEA], [AIBSCS] [3]
  PdhR repressor glcDp Sigma70 -56.0 -111.0 glcD, glcE, glcF, glcG, glcB, glcA
3128124 3128140 [GEA], [AIBSCS], [BPP] [4]
  PdhR repressor grcAp1 Sigma70 17.0 -58.0 grcA
2716499 2716515 [GEA], [APIORCISFBSCS] [5]
  PdhR repressor hemLp Sigma28 -165.0 -204.0 hemL
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
89546 89562 [GEA], [AIBSCS], [BPP] [4]
  PdhR repressor ndhp Sigma70 -35.0 -128.0 ndh
1165949 1165965 [GEA], [APIORCISFBSCS], [BPP], [GS] [1], [6]
  PdhR repressor pdhRp Sigma70 19.0 -40.0 pdhR, aceE, aceF, lpd
122044 122060 [GEA], [AIBSCS], [APIORCISFBSCS], [BCE], [BPP], [GS] [2], [4], [6], [7]
  PdhR repressor pdhRp2 Sigma38 19.0 -40.0 pdhR, aceE, aceF, lpd
122044 122060 [GEA], [AIBSCS], [APIORCISFBSCS], [BCE], [BPP], [GS] [2], [4], [6], [7]
  PdhR repressor tomBp Sigma70 -178.0 -264.0 tomB, hha
480964 480980 [AIBSCS] [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
  PdhR activator ppsA Gene nd
1787066 1787082 1787074.0 nd [GEA], [APIORCISFBSCS], [BPP], [GS] [6]
  PdhR activator ppsR Gene nd
1787066 1787082 1787074.0 nd [GEA], [APIORCISFBSCS], [BPP], [GS] [6]
Other High-throughput regulatory interactions with weak evidence

Alignment and PSSM for PdhR TFBSs    

Aligned TFBS of PdhR   

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

;	consensus.strict             	caAttGGtctaACCAattT
;	consensus.strict.rc          	AAATTGGTTAGACCAATTG
;	consensus.IUPAC              	swAyyGGtmwdACMAwtdT
;	consensus.IUPAC.rc           	AHAWTKGTHWKACCRRTWS
;	consensus.regexp             	[cg][at]A[ct][ct]GGt[ac][at][agt]AC[AC]A[at]t[agt]T
;	consensus.regexp.rc          	A[ACT]A[AT]T[GT]GT[ACT][AT][GT]ACC[AG][AG]T[AT][CG]

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


 [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] Anzai T., Imamura S., Ishihama A., Shimada T., 2020, Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility., Microb Genom 6(10)

 [7] 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

 [8] 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

 [9] 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

 [10] Maeda S, Shimizu K, Kihira C, Iwabu Y, Kato R, Sugimoto M, Fukiya S, Wada M, Yokota A, 2017, Pyruvate dehydrogenase complex regulator (PdhR) gene deletion boosts glucose metabolism in Escherichia coli under oxygen-limited culture conditions., J Biosci Bioeng, 123(4):437 10.1016/j.jbiosc.2016.11.004

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

 [12] 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

 [13] 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

 [14] Shimada T, Nakazawa K, Tachikawa T, Saito N, Niwa T, Taguchi H, Tanaka K, 2021, Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli., FEBS Lett, 595(15):2047 10.1002/1873-3468.14151