RegulonDB

RegulonDB RegulonDB 10.8:Regulon Page

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, 4, 9] 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 [3, 4] 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 [3] The pdhR deletion mutant enhanced glucose metabolism under oxygen-limited conditions. This mutant strain showed an increased activity of the pyruvate dehydrogenase complex and NADH dehydrogenase [] The PdhR belongs to the GntR family of transcriptional regulatory proteins, which share sequence similarities in their N-terminal DNA-binding domains [1, 10] PdhR is negatively autoregulated [11] The pdhR consensus sequences has been determined to be 17bp [4] and more recently as 15 bp [3] Read more >

Transcription factor

TF conformation(s):

Name	Conformation Type	TF-Effector Interaction Type	Apo/Holo Conformation	Evidence (Confirmed, Strong, Weak)	References
PdhR	Functional		Apo	[APP], [APPH], [BPP], [GEA], [HIFS], [IDA]	[1], [2], [3], [4], [5]
PdhR-pyruvate	Non-Functional	Allosteric	Holo	[BPP], [IDA]	[3], [4]

Evolutionary Family:

GntR

Sensing class:

Using internal synthesized signals

Connectivity class:

Local Regulator

Gene name:

Genome position:

122092-122856

Length:

765 bp / 254 aa

Operon name:

TU(s) encoding the TF:

Transcription unit	Promoter
pdhR-aceEF-lpdA	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) cyoA, cyoB, cyoC, cyoD, cyoE, fecC, fecD, ftsA, ftsW, glcA, mraY, murG murein (peptidoglycan) (8) ddlB, ftsI, mraY, murC, murD, murE, murF, murG murein (8) ddlB, ftsI, mraY, murC, murD, murE, murF, murG cell division (7) ftsA, ftsI, ftsL, ftsQ, ftsW, ftsZ, murF aerobic respiration (6) cyoA, cyoB, cyoC, cyoD, cyoE, ndh carbon compounds (5) aceE, aceF, glcA, glcB, lpd electron acceptors (4) cyoA, cyoB, cyoC, cyoD Fe aquisition (4) fecA, fecB, fecC, fecE pyruvate dehydrogenase (3) aceE, aceF, lpd glyoxylate degradation (3) aceE, aceF, glcB Oxidoreduction-driven Active Transporters (3) cyoA, cyoB, cyoC glycolate metabolism (3) glcD, glcE, glcF ABC superfamily, membrane component (2) fecC, fecD Transcription related (2) hha, pdhR Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (1) fecA ABC superfamily, periplasmic binding component (1) fecB ABC superfamily ATP binding cytoplasmic component (1) fecE drug resistance/sensitivity (1) ftsI Porters (Uni-, Sym- and Antiporters) (1) glcA anaerobic respiration (1) grcA pH (1) grcA other (mechanical, nutritional, oxidative stress) (1) grcA heme, porphyrine (1) hemL complex regulation (1) hha global (1) hha cell killing (1) hha amino acids (1) lpd formyl-THF biosynthesis (1) lpd lipid A (1) lpxC surface antigens (ECA, O antigen of LPS) (1) lpxC murein turnover, recycling (1) murF electron donors (1) ndh glycolysis (1) pdhR activator (1) pdhR repressor (1) pdhR operon (1) pdhR RNA modification (1) rsmH cell processes (1) tomB Read more >
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 ArcA,CRP,FNR,Fis,Fur,PdhR ArcA,FNR,Fis,Fur,IHF,NsrR,PdhR ArcA,GlcC,IHF,PdhR BasR,CpxR,PdhR BtsR,CRP,Cra,FNR,PdhR CRP,Fur,HypT,PdhR MraZ,PdhR PdhR,PhoP Read more >
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase) [PdhR,+](1) fecAp [PdhR,-](8) cyoAp, glcDp, grcAp1, hemLp, mraZp, ndhp, pdhRp, tomBp1

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	ttttatttcaCATTGGTTATACCAATTgcccgcccag nd	451822	451838	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[3]
	PdhR	activator	fecAp	nd	-21.0	-71.0	fecA, fecB, fecC, fecD, fecE	taaggaaaatAATTCTTATTTCGATTGtcctttttac nd	4516740	4516756	[AIBSCS], [CV(GEA)], [GEA]	[6]
	PdhR	repressor	glcDp	Sigma70	-56.0	-111.0	glcD, glcE, glcF, glcG, glcB, glcA	gctggaaaaaAAATGGTCTGACCGGTAgctaaagaga nd	3128124	3128140	[AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[7]
	PdhR	repressor	grcAp1	Sigma70	17.0	-58.0	grcA	actcaagcaaCAATGGTTTTACCAATTggccgcgaca nd	2716499	2716515	[APIORCISFBSCS], [CV(GEA)], [GEA]	[8]
	PdhR	repressor	hemLp	Sigma28	-165.0	-204.0	hemL	aatgatcactTATTGGTCATACAAATAagatgacggc nd	175078	175094	[AIBSCS]	[3]
	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 nd	89546	89562	[AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[7]
	PdhR	repressor	ndhp	Sigma70	-35.0	-128.0	ndh	ttaacatcaaTTTTGGTATGACCAATGcaccattcat nd	1165949	1165965	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[3]
	PdhR	repressor	pdhRp	Sigma70, Sigma38	19.0	-40.0	pdhR, aceE, aceF, lpd	acagacatgaAATTGGTAAGACCAATTgacttcggca nd	122044	122060	[AIBSCS], [APIORCISFBSCS], [BCE], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[4], [5], [7]
	PdhR	repressor	tomBp1	Sigma70	-178.0	-264.0	tomB, hha	gcaatcctggTATTAGTGTCACCAATTtcatctggcg nd	480964	480980	[AIBSCS]	[3]

Alignment and PSSM for PdhR TFBSs

Aligned TFBS of PdhR

	Sequence
	CAATTGGTCTTACCAATTT
	CAATTGGTATAACCAATGT
	CAATTGGTAAAACCATTGT
	CTACCGGTCAGACCATTTT
	GCATTGGTCATACCAAAAT
	TTATTGGTCATACAAATAA
	GTATTAGTGTCACCAATTT
	CAATCGAAATAAGAATTAT
	TGACTGGCTTGACAAGCTT

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

;	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

Evidence
[APP] Assay of partially-purified protein
[APPH] Assay of protein purified to homogeneity
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIFS] Human inference of function from sequence
[IDA] Inferred from direct assay
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(GEA)] cross validation(GEA)
[AIBSCS] Automated inference based on similarity to consensus sequences
[BCE] Binding of cellular extracts

Reference(s)
[1] Haydon DJ., Guest JR., 1991, A new family of bacterial regulatory proteins., FEMS Microbiol Lett 63(2-3):291-5
[2] 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
[3] 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
[4] 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
[5] 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
[6] 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
[7] 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
[8] 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
[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] 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

RegulonDB

Contact us Funding Terms & conditions How to cite