RegulonDB RegulonDB 10.9: Operon Form
   

frdABCD operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: frdABCD
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: frdABCD
Synonym(s): OP00030, frd
Gene(s): frdD, frdC, frdB, frdA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The frdABCD transcription unit is expressed under anaerobiosis.
frdABCD was significantly upregulated in response to quinonas anthraquinone-2-sulfonate (AQSim) reduction and azo dye acid red 18 (AR 18) decolorization under anaerobic conditions 23820558.
Based on microarray and RT-qPCR analyses, it was determined that the fecA and frdB genes are downregulated upon exposure to glutathione (GSH) Goswami M,2018
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for frdA and for frdD . This structure could regulate the expression of the genes, as observed for hemL gene expression 31964733.

Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Grundstrom T., et al., 1980
[2] Jones HM., et al., 1985
[3] Tseng CP., et al., 1996
[4] Tseng CP., et al., 1994
Promoter
Name: frdAp
+1: 4382412
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 94
Sequence: taaaaaaatcgatctcgtcaaatttcagacttatccatcagactatactgttgtacctatAaaggagcagtggaatagcgt
                       -35                  -10             +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [5] Huerta AM., et al., 2003
[2] Jones HM., et al., 1985
Terminator(s)
Type: rho-independent
Sequence: tccatacaaaACGGCCCGCCATAGGCGGGCCGgatttacatt
Reference(s): [1] Grundstrom T., et al., 1980
[6] Jaurin B., et al., 1981
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote DcuR-P1 activator frdAp 4382508 4382524 -104.0 acgatctgatGGTTTAGTAATTAAATTAatcatcttca nd [BPP], [GEA] [7], [8], [9], [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator frdAp 4382451 4382464 -45.5 cactaaaaaaATCGATCTCGTCAAAtttcagactt nd [BCE], [GEA] [7], [11], [12], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated repressor frdAp 4382396 4382402 14.0 taaaggagcaGTGGAATAgcgttcgcag nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp 4382404 4382410 6.0 tgtacctataAAGGAGCAgtggaatagc nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp 4382413 4382419 -4.0 ctatactgttGTACCTATaaaggagcag nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp 4382421 4382427 -12.0 ccatcagactATACTGTTgtacctataa nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp 4382435 4382441 -26.0 aatttcagacTTATCCATcagactatac nd [APIORCISFBSCS], [BPP] [14]
Note(s): 1DcuR regulates the expression of the frd promoter in response to external C4-dicarboxylates.1DcuR regulates the expression of the frd promoter in response to external C4-dicarboxylates.


Transcription unit          
Name: frdABCD
Synonym(s): OP00030, frd
Gene(s): frdD, frdC, frdB, frdA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The frdABCD transcription unit is expressed under anaerobiosis.
frdABCD was significantly upregulated in response to quinonas anthraquinone-2-sulfonate (AQSim) reduction and azo dye acid red 18 (AR 18) decolorization under anaerobic conditions 23820558.
Based on microarray and RT-qPCR analyses, it was determined that the fecA and frdB genes are downregulated upon exposure to glutathione (GSH) Goswami M,2018
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for frdA and for frdD . This structure could regulate the expression of the genes, as observed for hemL gene expression 31964733.

Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Grundstrom T., et al., 1980
[2] Jones HM., et al., 1985
[3] Tseng CP., et al., 1996
[4] Tseng CP., et al., 1994
Promoter
Name: frdAp2
+1: 4382412
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 94
Sequence: taaaaaaatcgatctcgtcaaatttcagacttatccatcagactatactgttgtacctatAaaggagcagtggaatagcgt
                       -35                  -10             +1                   
Evidence: [TIM]
Reference(s): [2] Jones HM., et al., 1985
Terminator(s)
Type: rho-independent
Sequence: tccatacaaaACGGCCCGCCATAGGCGGGCCGgatttacatt
Reference(s): [1] Grundstrom T., et al., 1980
[6] Jaurin B., et al., 1981
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote DcuR-P1 activator frdAp2 4382508 4382524 -104.0 acgatctgatGGTTTAGTAATTAAATTAatcatcttca nd [BPP], [GEA] [7], [8], [9], [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator frdAp2 4382451 4382464 -45.5 cactaaaaaaATCGATCTCGTCAAAtttcagactt nd [BCE], [GEA] [7], [11], [12], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated repressor frdAp2 4382396 4382402 14.0 taaaggagcaGTGGAATAgcgttcgcag nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp2 4382404 4382410 6.0 tgtacctataAAGGAGCAgtggaatagc nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp2 4382413 4382419 -4.0 ctatactgttGTACCTATaaaggagcag nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp2 4382421 4382427 -12.0 ccatcagactATACTGTTgtacctataa nd [APIORCISFBSCS], [BPP] [14]
proximal NarL-Phosphorylated repressor frdAp2 4382435 4382441 -26.0 aatttcagacTTATCCATcagactatac nd [APIORCISFBSCS], [BPP] [14]
Note(s): 1DcuR regulates the expression of the frd promoter in response to external C4-dicarboxylates.1DcuR regulates the expression of the frd promoter in response to external C4-dicarboxylates.




Reference(s)    

 [1] Grundstrom T., Jaurin B., Edlund T., Normark S., 1980, Physical mapping and expression of hybrid plasmids carrying chromosomal beta-lactamase genes of Escherichia coli K-12., J Bacteriol 143(3):1127-34

 [2] Jones HM., Gunsalus RP., 1985, Transcription of the Escherichia coli fumarate reductase genes (frdABCD) and their coordinate regulation by oxygen, nitrate, and fumarate., J Bacteriol 164(3):1100-9

 [3] Tseng CP., Albrecht J., Gunsalus RP., 1996, Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli., J Bacteriol 178(4):1094-8

 [4] Tseng CP., Hansen AK., Cotter P., Gunsalus RP., 1994, Effect of cell growth rate on expression of the anaerobic respiratory pathway operons frdABCD, dmsABC, and narGHJI of Escherichia coli., J Bacteriol 176(21):6599-605

 [5] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [6] Jaurin B., Grundstrom T., Edlund T., Normark S., 1981, The E. coli beta-lactamase attenuator mediates growth rate-dependent regulation., Nature 290(5803):221-5

 [7] Abo-Amer AE., Munn J., Jackson K., Aktas M., Golby P., Kelly DJ., Andrews SC., 2004, DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli., J Bacteriol 186(6):1879-89

 [8] Golby P., Davies S., Kelly DJ., Guest JR., Andrews SC., 1999, Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli., J Bacteriol 181(4):1238-48

 [9] Janausch IG., Garcia-Moreno I., Lehnen D., Zeuner Y., Unden G., 2004, Phosphorylation and DNA binding of the regulator DcuR of the fumarate-responsive two-component system DcuSR of Escherichia coli., Microbiology 150(Pt 4):877-83

 [10] Zientz E., Bongaerts J., Unden G., 1998, Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR genes) two-component regulatory system., J Bacteriol 180(20):5421-5

 [11] Jones HM., Gunsalus RP., 1987, Regulation of Escherichia coli fumarate reductase (frdABCD) operon expression by respiratory electron acceptors and the fnr gene product., J Bacteriol 169(7):3340-9

 [12] 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

 [13] Tyson KL., Bell AI., Cole JA., Busby SJ., 1993, Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL., Mol Microbiol 7(1):151-7

 [14] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65


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