RegulonDB RegulonDB 11.1: Operon Form
   

dcuB-fumB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: fumB
Synonym(s): OP00218
Gene(s): fumB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Conceivably, genF (dcuB) and fumB are both expressed from an FNR-regulated promoter situated upstream of genF. Fumarate and TMAO increase fumB expression under anaerobiosis, while nitrate and changes of the DNA superhelicity decrease its expression.
fumB is sensitive under microaerobic conditions, and it is activated under highly oxidative conditions Chen YP,2012.
Based on in vitro and in vivo analyses, it was determined that fumBp is not under CRP control Chen YP,2012.
The transcription of the gene fumB is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Bell PJ., et al., 1989
[2] Golby P., et al., 1998
[3] Gruer MJ., et al., 1994
[4] Park SJ., et al., 1995
[5] Woods SA., et al., 1988
Promoter
Name: fumBp
+1: 4347348
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 22
Sequence: tataaatgcactttgcgtgccgcccgtgactacgcggcacgccattttcgaataacaaatAcagagttacaggctggaagc
                               -35                        -1+1                   
Evidence: [COMP]
[COMP-AINF]
Reference(s): [1] Bell PJ., et al., 1989
[6] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: aaaagaggtgGCCAGGGGGATCACCTGGCAgcatgctgcc
Reference(s): [1] Bell PJ., et al., 1989
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-phosphorylated activator fumBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator fumBp 4347399 4347412 -57.5 gatgtacgggTTCTTATAAATGCActttgcgtgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1], [8]
proximal FNR activator fumBp 4347403 4347416 -61.5 ccgcgatgtaCGGGTTCTTATAAAtgcactttgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1], [8]
remote FNR activator fumBp 4347456 4347469 -114.5 tctgccggggTTGATTGGTGTGAGcgtatcgtgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1], [7], [8]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis repressor fumBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[Fur,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ activator fumBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]


Transcription unit          
Name: dcuB-fumB
Gene(s): fumB, dcuB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [2] Golby P., et al., 1998
Promoter
Name: dcuBp1
+1: 4348764
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 20
Sequence: gaaaacagttcatacaaaacagaacgtgactgtgatctattcagcaaaaatttaaataggAttatcgcgagggttcacaca
                                                   -10      +1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Golby P., et al., 1998
Terminator(s)
Type: rho-independent
Sequence: aaaagaggtgGCCAGGGGGATCACCTGGCAgcatgctgcc
Reference(s): [1] Bell PJ., et al., 1989
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator dcuBp1 4348860 4348881 -106.5 agccaatattCACTGTGAGGTATTTGCTAAAGccggtaacga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator dcuBp1 4348803 4348816 -45.5 ctgaaaacagTTCATACAAAACAGaacgtgactg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NarL-phosphorylated repressor dcuBp1 4348719 4348725 43.0 actatccaacTTATCATaatactgata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
proximal NarL-phosphorylated repressor dcuBp1 4348738 4348744 24.0 gggttcacacATGTTATttactatcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
proximal NarL-phosphorylated repressor dcuBp1 4348743 4348749 19.0 cgcgagggttCACACATgttatttact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
proximal NarL-phosphorylated repressor dcuBp1 4348760 4348766 2.0 aatttaaataGGATTATcgcgagggtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
proximal NarL-phosphorylated repressor dcuBp1 4348806 4348812 -45.0 aaacagttcaTACAAAAcagaacgtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
remote NarL-phosphorylated repressor dcuBp1 4348870 4348876 -109.0 atattcactgTGAGGTAtttgctaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]


Transcription unit          
Name: dcuB-fumB
Gene(s): fumB, dcuB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Cross-regulation of dcuB occurs also on the level of transcriptional regulation of the target operons, as expression of dcuB, encoding the fumarate:succinate antiporter, is activated by both TtdR and DcuR, in response to L-tartrate and fumarate respectively Kim OB,2009. Scheu PD,2012
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [9] Abo-Amer AE., et al., 2004
[2] Golby P., et al., 1998
Promoter
Name: dcuBp2
+1: 4349091
Distance from start of the gene: 347
Sequence: caaaacgctaacaaaagttaattaactattatgtcacccgcattatgtgtatttttacccAcaaatgggtagatcagatta
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [9] Abo-Amer AE., et al., 2004
[10] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aaaagaggtgGCCAGGGGGATCACCTGGCAgcatgctgcc
Reference(s): [1] Bell PJ., et al., 1989
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)
LeftPos RightPos Central Rel-Pos Sequence
proximal DcuR-phosphorylated activator dcuBp2 4349124 4349140 -41.0 aaaacgctaaCAAAAGTTAATTAACTAttatgtcacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9], [11], [12]
proximal DcuR-phosphorylated activator dcuBp2 4349146 4349162 -63.0 ggtgaacggtGTTTTTAATTTCAAAACgctaacaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9], [11], [12]


Evidence    

 [COMP] Inferred by computational analysis

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Bell PJ., Andrews SC., Sivak MN., Guest JR., 1989, Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12., J Bacteriol 171(6):3494-503

 [2] Golby P., Kelly DJ., Guest JR., Andrews SC., 1998, Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli., J Bacteriol 180(24):6586-96

 [3] Gruer MJ., Guest JR., 1994, Two genetically-distinct and differentially-regulated aconitases (AcnA and AcnB) in Escherichia coli., Microbiology 140 ( Pt 10):2531-41

 [4] Park SJ., Gunsalus RP., 1995, Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: role of the arcA, fnr, and soxR gene products., J Bacteriol 177(21):6255-62

 [5] Woods SA., Schwartzbach SD., Guest JR., 1988, Two biochemically distinct classes of fumarase in Escherichia coli., Biochim Biophys Acta 954(1):14-26

 [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] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4

 [8] Tseng CP., 1997, Regulation of fumarase (fumB) gene expression in Escherichia coli in response to oxygen, iron and heme availability: role of the arcA, fur, and hemA gene products., FEMS Microbiol Lett 157(1):67-72

 [9] 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

 [10] 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.

 [11] 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

 [12] Scheu PD., Witan J., Rauschmeier M., Graf S., Liao YF., Ebert-Jung A., Basche T., Erker W., Unden G., 2012, CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo., J Bacteriol 194(3):636-45

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