RegulonDB RegulonDB 10.8: Operon Form
   

pdhR-aceEF-lpd operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: pdhR-aceEF-lpd
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: pdhR-aceEF-lpdA
Gene(s): pdhR, aceE, aceF, lpd   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of this operon is enhanced during and after the switch from aerobic to anaerobic growth conditions 21980479
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cunningham L., et al., 1998
Promoter
Name: pdhRp
+1: 122034
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 58
Sequence: ttcatgatttcaatcaaaacctgtatggacataaggtgaatactttgttactttagcgtcAcagacatgaaattggtaaga
                          -35                    -10        +1                   
Note(s): The genes are expressed from two major promoters: Ppdh, which generates a 7.4-kb pdhR-lpdA readthrough transcript, and Plpd, which generates an independent 1.7-kb lpda transcript.
Like pdhRp, ndhp and cyoAp are repressed by PdhR and derepressed by the addition of pyruvate Ogasawara H,2007
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HIPP]
[HTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Cunningham L., et al., 1998
[2] Olvera L., et al., 2009
[3] Quail MA., et al., 1995
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca
Reference(s): [5] Spencer ME., et al., 1985
TF binding sites (TFBSs)
[BtsR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote BtsR-Phosphorylated repressor pdhRp 121826 121837 -203.0 tgaattaaaaATCACAAAATTGgtaagtgaat nd , [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/GS)], [CV(GEA/ROMA)], [GEA], [GS] [7]
remote BtsR-Phosphorylated repressor pdhRp 121841 121852 -188.0 aaaattggtaAGTGAATCGGTTcaattcggat nd , [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/GS)], [CV(GEA/ROMA)], [GEA], [GS] [7]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP activator pdhRp 121646 121667 -377.5 tacatcaaagAAGTTTGAATTGTTACAAAAAGacttccgtca nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [6]
remote CRP-cAMP activator pdhRp 121913 121934 -110.5 taaagtctacATTTGTGCATAGTTACAACTTTgaaacgttat nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [6]
proximal CRP-cAMP activator pdhRp 121941 121962 -82.5 ctttgaaacgTTATATATGTCAAGTTGTTAAAatgtgcacag nd [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [6], [10]
proximal CRP-cAMP activator pdhRp 121953 121974 -70.5 atatatgtcaAGTTGTTAAAATGTGCACAGTTtcatgatttc nd [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [6], [10]
proximal CRP-cAMP activator pdhRp 121961 121982 -62.5 caagttgttaAAATGTGCACAGTTTCATGATTtcaatcaaaa nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [6]
proximal CRP-cAMP activator pdhRp 121973 121994 -50.5 atgtgcacagTTTCATGATTTCAATCAAAACCtgtatggaca nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [6]
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor pdhRp 121840 121857 -185.5 caaaattggtAAGTGAATCGGTTCAATTcggattttta nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [8], [9]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator pdhRp 121977 121990 -50.5 gcacagtttcATGATTTCAATCAAaacctgtatg nd [AIBSCS], [BCE], [CV(GEA/ROMA)], [GEA] [10], [11], [12]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 repressor pdhRp 121977 121990 -50.5 gcacagtttcATGATTTCAATCAAaacctgtatg nd [AIBSCS], [BCE], [CV(GEA/ROMA)], [GEA] [10], [11], [12]
[PdhR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PdhR repressor pdhRp 122044 122060 19.0 acagacatgaAATTGGTAAGACCAATTgacttcggca nd [AIBSCS], [APIORCISFBSCS], [BCE], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [3], [10], [13]
Note(s): 1FNR affects pdhRp promoter under anaerobic conditions.1FNR affects the pdhRp promoter under anaerobic conditions.10FNR affects pdhRp promoter under anaerobic conditions.
11FNR affects the pdhRp promoter under anaerobic conditions.


Transcription unit          
Name: aceEF
Gene(s): aceE, aceF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [5] Spencer ME., et al., 1985
Promoter
Name: aceEp
+1: 122969
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 48
Sequence: aaagcgcggcaactaaacgtagaacctgtcttattgagctttccggcgagagttcaatggGacaggttccagaaaactcaa
                          -35              -10              +1                   
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Olvera L., et al., 2009
[4] Salgado H, et al., 2012
[5] Spencer ME., et al., 1985
Terminator(s)
Type: rho-independent
Sequence: tgatgtaagtAAAAGAGCCGGCCCAACGGCCGGCTTTTTTctggtaatct
Note(s): This potential stem-loop structure is a pdhR-aceEF terminator or an mRNA processing site.
Reference(s): [14] Cunningham L., et al., 1998
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated1 repressor aceEp nd nd nd nd nd [GEA] [16]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 repressor aceEp nd nd nd nd nd [GEA] [10], [16]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NsrR repressor aceEp 122883 122894 -81.0 aattatccagAAGATGTTGTAAatcaagcgca nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [15]
Note(s): 1It appears that the negative effects of ArcA and Fnr on aceE are not additive Shalel-Levanon S,20051FNR represses the aceEp promoter under anaerobic conditions.2It appears that the negative effects of ArcA and Fnr on aceE are not additive Shalel-Levanon S,2005
3FNR represses the aceEp promoter under anaerobic conditions.


Transcription unit          
Name: lpdA
Gene(s): lpd   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the lpdA gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased Kumar R,2011
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cunningham L., et al., 1998
Promoter
Name: lpdAp
+1: 127717
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 195
Sequence: tagacaaatcggttgccgtttgttgtttaaaaattgttaacaattttgtaaaataccgacGgatagaacgacccggtggtg
                           -35                   -10        +1                   
Note(s): The genes are expressed from two major promoters: Ppdh, which generates a 7.4-kb pdhR-lpdA readthrough transcript, and Plpd, which generates an independent 1.7-kb lpdA transcript.
The lpdA gene is preceded by an IRU (ERIC) sequence. Expression of lpdA was not affected in an fnr mutant, but a multicopy fnr+ construct repressed expression. This could be an indirect effect mediated by ArcA activation.
Evidence: [HIPP]
[TIM]
Reference(s): [14] Cunningham L., et al., 1998
[1] Cunningham L., et al., 1998
[10] Quail MA., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca
Reference(s): [5] Spencer ME., et al., 1985
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-Phosphorylated repressor lpdAp 127683 127697 -27.0 cgtttgttgtTTAAAAATTGTTAACaattttgtaa nd [AIBSCS] [17]
proximal ArcA-Phosphorylated2 repressor lpdAp 127692 127706 -18.0 tttaaaaattGTTAACAATTTTGTAaaataccgac nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1], [10], [14], [17], [18]
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor lpdAp 127688 127709 -18.5 gttgtttaaaAATTGTTAACAATTTTGTAAAAtaccgacgga nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [1], [6]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator lpdAp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [12], [19]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 repressor lpdAp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [12], [19]
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis1 activator lpdAp 127681 127695 -29.0 gccgtttgttGTTTAAAAATTGTTAacaattttgt nd [BCE], [BPP] [1], [14]
[Fur,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ activator lpdAp nd nd nd nd nd [GEA] [19]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ repressor lpdAp nd nd nd nd nd [GEA] [19]
Note(s): 2The anaerobic repression is mediated by ArcA, as witnessed by the fivefold anaerobic derepression (and up to twofold aerobic derepression) in an arcA mutant. 1Salmon K,2003identified a FNR-binding site in the lpdA regulatory region, but the sequence was not reported in the paper.1Salmon K,2003identified a FNR-binding site in the lpdA regulatory region, but the sequence was not reported in the paper.1Fis is a potential activator of lpdA gene expression. There is a potential Fis-binding site, GTTTAAAAATTGTTa, centered at -29 in the lpd promoter region (coordinates 5770-5784). However, Fis binding at this position would be expected to repress, rather than activate, transcription Cunningham L,1998.1Fis is a potential activator of lpdA gene expression. There is a potential Fis-binding site, GTTTAAAAATTGTTa, centered at -29 in the lpd promoter region (coordinates 5770-5784). However, Fis binding at this position would be expected to repress, rather than activate, transcription Cunningham L,1998.
4The anaerobic repression is mediated by ArcA, as witnessed by the fivefold anaerobic derepression (and up to twofold aerobic derepression) in an arcA mutant.
6Salmon K,2003identified a FNR-binding site in the lpdA regulatory region, but the sequence was not reported in the paper.
8Salmon K,2003identified a FNR-binding site in the lpdA regulatory region, but the sequence was not reported in the paper.


Evidence    

 [CV(RS-EPT-CBR/TA)] cross validation(RS-EPT-CBR/TA)

 [CV(TA/TIM)] cross validation(TA/TIM)

 [HIPP] Human inference of promoter position

 [HTIM] High-throughput transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CV(CHIP-SV/GEA/GS)] cross validation(CHIP-SV/GEA/GS)

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(GEA/GS)] cross validation(GEA/GS)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis

 [GS] genomic SELEX

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Cunningham L., Guest JR., 1998, Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli., Microbiology 144 ( Pt 8):2113-23

 [2] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [3] 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

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Spencer ME., Guest JR., 1985, Transcription analysis of the sucAB, aceEF and lpd genes of Escherichia coli., Mol Gen Genet 200(1):145-54

 [6] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [7] Ogasawara H., Ishizuka T., Yamaji K., Kato Y., Shimada T., Ishihama A., 2019, Regulatory Role of Pyruvate-Sensing BtsSR in Biofilm Formation by Escherichia coli K-12., FEMS Microbiol Lett

 [8] Sarkar D., Siddiquee KA., Arauzo-Bravo MJ., Oba T., Shimizu K., 2008, Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli., Arch Microbiol 190(5):559-71

 [9] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

 [10] 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

 [11] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [12] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [13] 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

 [14] Cunningham L., Georgellis D., Green J., Guest JR., 1998, Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter., FEMS Microbiol Lett 169(2):403-8

 [15] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [16] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions., Biotechnol Bioeng 92(2):147-59

 [17] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [18] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [19] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

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