RegulonDB

RegulonDB RegulonDB 11.1: 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 Zhang HK, Lu H, Wang J, Liu GF, Zhou JT, Xu MY,2013. 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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] 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:	[COMP-AINF] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[5] Espinosa-Urgel M., et al., 1996 [6] 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 [7] Jaurin B., et al., 1981

TF binding sites (TFBSs)

[DcuR,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	DcuR-phosphorylated	activator	frdAp	4382508	4382524	-104.0	cgatctgatgGTTTAGTAATTAAATTAatcatcttca	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8], [9], [10], [11]

[FNR,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	FNR	activator	frdAp	4382451	4382464	-45.5	actaaaaaaaTCGATCTCGTCAAAtttcagactt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	W	[8], [12], [13], [14]

[NarL,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	NarL-phosphorylated	repressor	frdAp	4382396	4382402	14.0	aaaggagcagTGGAATAgcgttcgcag	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp	4382404	4382410	6.0	gtacctataaAGGAGCAgtggaatagc	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp	4382413	4382419	-4.0	tatactgttgTACCTATaaaggagcag	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp	4382421	4382427	-12.0	catcagactaTACTGTTgtacctataa	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp	4382435	4382441	-26.0	atttcagactTATCCATcagactatac	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]

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 Zhang HK, Lu H, Wang J, Liu GF, Zhou JT, Xu MY,2013. 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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] 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:	[COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[5] Espinosa-Urgel M., et al., 1996 [2] Jones HM., et al., 1985
Terminator(s)
Type:	rho-independent
Sequence:	tccatacaaaACGGCCCGCCATAGGCGGGCCGgatttacatt
Reference(s):	[1] Grundstrom T., et al., 1980 [7] Jaurin B., et al., 1981

TF binding sites (TFBSs)

[DcuR,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	DcuR-phosphorylated	activator	frdAp2	4382508	4382524	-104.0	cgatctgatgGTTTAGTAATTAAATTAatcatcttca	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8], [9], [10], [11]

[FNR,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	FNR	activator	frdAp2	4382451	4382464	-45.5	actaaaaaaaTCGATCTCGTCAAAtttcagactt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	W	[8], [12], [13], [14]

[NarL,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	NarL-phosphorylated	repressor	frdAp2	4382396	4382402	14.0	aaaggagcagTGGAATAgcgttcgcag	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp2	4382404	4382410	6.0	gtacctataaAGGAGCAgtggaatagc	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp2	4382413	4382419	-4.0	tatactgttgTACCTATaaaggagcag	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp2	4382421	4382427	-12.0	catcagactaTACTGTTgtacctataa	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]
proximal	NarL-phosphorylated	repressor	frdAp2	4382435	4382441	-26.0	atttcagactTATCCATcagactatac	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[15]

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-HINF] Inferred by a human based on computational evidence
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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] Espinosa-Urgel M., Chamizo C., Tormo A., 1996, A consensus structure for sigma S-dependent promoters., Mol Microbiol 21(3):657-9
[6] 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
[7] 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
[8] 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
[9] 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
[10] 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
[11] 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
[12] 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
[13] 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
[14] 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
[15] 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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