RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: fumC
Gene(s): fumC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Promoter
Name: fumCp1
+1: 1686654
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 66
Sequence: gggcggtttttttacatggcacgaaagaccaaacatttgttatcaaatggtaaataataaGtgagctaaaagttgcttaac
                                -35                    -10  +1                   
Evidence: [AS-TAS]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Taliaferro LP., et al., 2012
TF binding sites (TFBSs)
[Rob,+] 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 Rob activator fumCp1 1686680 1686699 -35.5 gtttttttacATGGCACGAAAGACCAAACAtttgttatca nd [EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2]


Transcription unit          
Name: fumC
Synonym(s): OP00146
Gene(s): fumC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expresion of the fumC gene is quickly induced under oxidative stress Lu C,2003 and is enhanced during and after the switch from aerobic to anaerobic growth conditions Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J,2011
Under nitrogen-rich growth conditions, the expression of the fumC gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011
Reference(s): [3] Gruer MJ., et al., 1994
[4] Park SJ., et al., 1995
[5] Woods SA., et al., 1988
Promoter
Name: fumCp2
+1: 1686709
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 121
Sequence: cagatacaactcacacaatgcacccgctgtgtgaaataaacagagccgcccttcggggcgGtttttttacatggcacgaaa
                                    -35                  -10+1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [6] Cunningham L., et al., 1997
[7] Huerta AM., et al., 2003
[4] Park SJ., et al., 1995
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 repressor fumCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W nd
[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
proximal CRP-cyclic-AMP activator fumCp2 1686752 1686774 -53.5 aatgacttctTCCAGCAGATACAACTCACACAAtgcacccgct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
[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 unknown fumCp2 1687183 1687205 -484.5 cgattatcgtCGGTCGTGATATTGCTCACGCCAaactgaaaga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [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
nd FNR repressor fumCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [15]
[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+ repressor fumCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [15]
[MarA,+] 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 MarA activator fumCp2 1686746 1686765 -46.5 ttccagcagaTACAACTCACACAATGCACCcgctgtgtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9], [10]
[SoxR,+] 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 SoxR activator fumCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]
[SoxS,+] 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 SoxS activator fumCp2 1686681 1686700 19.5 ggtttttttaCATGGCACGAAAGACCAAACatttgttatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [10], [11], [12], [13]


Transcription unit          
Name: fumAC
Gene(s): fumC, fumA   Genome Browser M3D Gene expression COLOMBOS
Note(s): DcuR appears to affect the expression of fumA in response to fumarate; however, no site to bind DcuR was located around the fumAp promoter Surmann K,2020.
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [4] Park SJ., et al., 1995
Promoter
Name: fumAp
+1: 1688440
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 63
Sequence: caaaaagtcgtactagtctcagtttttgttaaaaaagtgtgtaggatattgttactcgctTttaacagggcaacggaacac
                               -35                  -10     +1                   
Note(s): Based on gene expression, consensus sequence, EMSA, and footprinting analyses, another site for CRP was determined at -484.5 upstream from the fumCp promoter Chen YP,2012. However, when CRP was used to complement mutant crp strains, these were not regulated in wild-type or complemented strains, indicating that this site is not involved in CRP regulation Chen YP,2012.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [7] Huerta AM., et al., 2003
[16] Miles JS., et al., 1984
[17] Miles JS., et al., 1984
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 repressor fumAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
[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 fumAp 1688367 1688389 63.5 ccaggcagtaAGTGAGAGAACAATGTCAAACAAaccctttcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [18]
proximal CRP-cyclic-AMP activator fumAp 1688476 1688499 -47.0 ctggagccgcAAAAAGTCGTACTAGTCTCAGTTTttgttaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [17], [18]
remote CRP-cyclic-AMP activator fumAp 1688539 1688560 -109.5 atccctgtttTAATGTGGAAATTAATCCCACTattaaagcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [16], [18]
remote CRP-cyclic-AMP activator fumAp 1688547 1688568 -117.5 catgatcaatCCCTGTTTTAATGTGGAAATTAatcccactat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [16], [18]
remote CRP-cyclic-AMP activator fumAp 1688832 1688853 -402.5 aatggagagtGGCTGTGCTGCGCATAATACTTtgaacaggaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [18], [19]
[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
nd FNR repressor fumAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]


Transcription unit          
Name: fumA
Synonym(s): OP00145
Gene(s): fumA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The fumA gene is sensitive to oxygen induction, and it is activated under anaerobic conditions Chen YP,2012.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [3] Gruer MJ., et al., 1994
[16] Miles JS., et al., 1984
[17] Miles JS., et al., 1984
[4] Park SJ., et al., 1995
[5] Woods SA., et al., 1988
Promoter
Name: fumAp
+1: 1688440
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 63
Sequence: caaaaagtcgtactagtctcagtttttgttaaaaaagtgtgtaggatattgttactcgctTttaacagggcaacggaacac
                               -35                  -10     +1                   
Note(s): Based on gene expression, consensus sequence, EMSA, and footprinting analyses, another site for CRP was determined at -484.5 upstream from the fumCp promoter Chen YP,2012. However, when CRP was used to complement mutant crp strains, these were not regulated in wild-type or complemented strains, indicating that this site is not involved in CRP regulation Chen YP,2012.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [7] Huerta AM., et al., 2003
[16] Miles JS., et al., 1984
[17] Miles JS., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: gccatgtaaaAAAACCGCCCCGAAGGGCGGCtctgtttatt
Reference(s): [16] Miles JS., et al., 1984
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 repressor fumAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
[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 fumAp 1688367 1688389 63.5 ccaggcagtaAGTGAGAGAACAATGTCAAACAAaccctttcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [18]
proximal CRP-cyclic-AMP activator fumAp 1688476 1688499 -47.0 ctggagccgcAAAAAGTCGTACTAGTCTCAGTTTttgttaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [17], [18]
remote CRP-cyclic-AMP activator fumAp 1688539 1688560 -109.5 atccctgtttTAATGTGGAAATTAATCCCACTattaaagcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [16], [18]
remote CRP-cyclic-AMP activator fumAp 1688547 1688568 -117.5 catgatcaatCCCTGTTTTAATGTGGAAATTAatcccactat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [16], [18]
remote CRP-cyclic-AMP activator fumAp 1688832 1688853 -402.5 aatggagagtGGCTGTGCTGCGCATAATACTTtgaacaggaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [18], [19]
[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
nd FNR repressor fumAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA RyhB fumA repressor 1688373 1688388 GACAUUGUUCUCUCAC MRNA-DEGRADATION [EXP-IEP], [EXP-IPI] [20], [21], [22]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.5 1686701 1686726 aaataaacagAGCCGCCCTTCGGGGCGGTTTTTTTacatggcacg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [AS-TAS] Traceable author statement

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP] Inferred from expression pattern

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

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

 [COMP-AINF] Inferred computationally without human oversight

 [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.

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

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

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IPI] Inferred from physical interaction


Reference(s)    

 [1] Taliaferro LP., Keen EF., Sanchez-Alberola N., Wolf RE., 2012, Transcription Activation by Escherichia coli Rob at Class II Promoters: Protein-Protein Interactions between Rob's N-Terminal Domain and the σ(70) Subunit of RNA Polymerase., J Mol Biol 419(3-4):139-57

 [2] Jair KW., Yu X., Skarstad K., Thony B., Fujita N., Ishihama A., Wolf RE., 1996, Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication., J Bacteriol 178(9):2507-13

 [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] Cunningham L., Gruer MJ., Guest JR., 1997, Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli., Microbiology 143 ( Pt 12):3795-805

 [7] 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

 [8] Chen YP., Lin HH., Yang CD., Huang SH., Tseng CP., 2012, Regulatory role of cAMP receptor protein over Escherichia coli fumarase genes., J Microbiol 50(3):426-33

 [9] Gillette WK., Martin RG., Rosner JL., 2000, Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation., J Mol Biol 299(5):1245-55

 [10] Pomposiello PJ., Bennik MH., Demple B., 2001, Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate., J Bacteriol 183(13):3890-902

 [11] Benov L., Fridovich I., 2002, Induction of the soxRS regulon of Escherichia coli by glycolaldehyde., Arch Biochem Biophys 407(1):45-8

 [12] Jair KW., Martin RG., Rosner JL., Fujita N., Ishihama A., Wolf RE., 1995, Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters., J Bacteriol 177(24):7100-4

 [13] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [14] Fuentes AM., Diaz-Mejia JJ., Maldonado-Rodriguez R., Amabile-Cuevas CF., 2001, Differential activities of the SoxR protein of Escherichia coli: SoxS is not required for gene activation under iron deprivation., FEMS Microbiol Lett 201(2):271-5

 [15] 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

 [16] Miles JS., Guest JR., 1984, Complete nucleotide sequence of the fumarase gene fumA, of Escherichia coli., Nucleic Acids Res 12(8):3631-42

 [17] Miles JS., Guest JR., 1984, Nucleotide sequence and transcriptional start point of the phosphomannose isomerase gene (manA) of Escherichia coli., Gene 32(1-2):41-8

 [18] Surmann K., Stopp M., Worner S., Dhople VM., Volker U., Unden G., Hammer E., 2020, Fumarate dependent protein composition under aerobic and anaerobic growth conditions in Escherichia coli., J Proteomics 212:103583

 [19] 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

 [20] Masse E., Gottesman S., 2002, A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli., Proc Natl Acad Sci U S A 99(7):4620-5

 [21] Masse E., Vanderpool CK., Gottesman S., 2005, Effect of RyhB small RNA on global iron use in Escherichia coli., J Bacteriol 187(20):6962-71

 [22] Prevost K., Desnoyers G., Jacques JF., Lavoie F., Masse E., 2011, Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage., Genes Dev 25(4):385-96

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