RegulonDB RegulonDB 11.1: Operon Form
   

aspA-dcuA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: dcuA
Gene(s): dcuA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Golby P., et al., 1998
Promoter
Name: dcuAp1
+1: 4366843
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 70
Sequence: aagcgaacagtaatcgtacagggtagtacaaataaaaaaggcacgtcagatgacgtgcctTttttcttgtgagcagtaact
                             -35                   -10      +1                   
Note(s): dcuAp was validated experimentally in anaerobic conditions Chung D,2013.
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Chung D., et al., 2013
[1] Golby P., et al., 1998


Transcription unit          
Name: aspA
Synonym(s): OP00219
Gene(s): aspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Nitrate represses the expression of the aspA-dcuA operon when NarL is present. NarL binds a region from positions -60 to -115 upstream of the transcriptional start site of the aspA gene, where three consensus sequences of the NarL-binding sites were identified Goh EB,2005.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Golby P., et al., 1998
[3] Woods SA., et al., 1986
Promoter
Name: aspAp
+1: 4368432
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 105
Sequence: accgacacttaaagtgatccagattacggtagaaatcctcaagcagcatatgatctcgggTattcggtcgatgcaggggat
                             -35                      -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Golby P., et al., 1998
[4] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: acaagaaaaaAGGCACGTCATCTGACGTGCCttttttattt
Reference(s): [5] Takagi JS., et al., 1985
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
proximal CRP-cyclic-AMP activator aspAp 4368512 4368534 -90.5 agtaatcccaAAGCGGTGATCTATTTCACAAATtaataattaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [6], [8], [9]
[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 aspAp 4368499 4368516 -75.0 atctatttcaCAAATTAATAATTAAGGGgtaaaaaccg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
remote DcuR-phosphorylated activator aspAp 4368585 4368602 -161.0 cgaatcgcgtTTAGCTTATATTGTGGTCattagcaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
[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 aspAp 4368466 4368479 -40.5 gacacttaaaGTGATCCAGATTACggtagaaatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
[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
proximal NarL-phosphorylated repressor aspAp 4368496 4368502 -67.0 ttaataattaAGGGGTAaaaaccgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]
proximal NarL-phosphorylated repressor aspAp 4368505 4368511 -76.0 tttcacaaatTAATAATtaaggggtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]
remote NarL-phosphorylated repressor aspAp 4368541 4368547 -112.0 aactatttttGGTAGTAatcccaaagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]


Transcription unit          
Name: aspA-dcuA
Synonym(s): OP00219
Gene(s): dcuA, aspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Nitrate represses the expression of the aspA-dcuA operon when NarL is present. NarL binds a region from positions -60 to -115 upstream of the transcriptional start site of the aspA gene, where three consensus sequences of the NarL-binding sites were identified Goh EB,2005.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [7] Goh EB., et al., 2005
[1] Golby P., et al., 1998
Promoter
Name: aspAp
+1: 4368432
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 105
Sequence: accgacacttaaagtgatccagattacggtagaaatcctcaagcagcatatgatctcgggTattcggtcgatgcaggggat
                             -35                      -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Golby P., et al., 1998
[4] Huerta AM., et al., 2003
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
proximal CRP-cyclic-AMP activator aspAp 4368512 4368534 -90.5 agtaatcccaAAGCGGTGATCTATTTCACAAATtaataattaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [6], [8], [9]
[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 aspAp 4368499 4368516 -75.0 atctatttcaCAAATTAATAATTAAGGGgtaaaaaccg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
remote DcuR-phosphorylated activator aspAp 4368585 4368602 -161.0 cgaatcgcgtTTAGCTTATATTGTGGTCattagcaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
[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 aspAp 4368466 4368479 -40.5 gacacttaaaGTGATCCAGATTACggtagaaatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
[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
proximal NarL-phosphorylated repressor aspAp 4368496 4368502 -67.0 ttaataattaAGGGGTAaaaaccgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]
proximal NarL-phosphorylated repressor aspAp 4368505 4368511 -76.0 tttcacaaatTAATAATtaaggggtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]
remote NarL-phosphorylated repressor aspAp 4368541 4368547 -112.0 aactatttttGGTAGTAatcccaaagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.6 4366836 4366867 tacaaataaaAAAGGCACGTCAGATGACGTGCCTTTTTTCTtgtgagcagt
  anti-terminator -11.5 4366862 4366932 gatgcacccgGCTTACAAAGCAAAACGCTATACTGATGAAAGCGAACAGTAATCGTACAGGGTAGTACAAATAAAAAAGGcacgtcagat
  anti-anti-terminator -5.6 4366899 4366954 atattttctcCGTACAGAATCTGATGCACCCGGCTTACAAAGCAAAACGCTATACTGATGAAAGCgaacagtaat
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    

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

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

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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


Reference(s)    

 [1] 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

 [2] Chung D., Park D., Myers K., Grass J., Kiley P., Landick R., Keles S., 2013, dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data., PLoS Comput Biol 9(10):e1003246

 [3] Woods SA., Miles JS., Roberts RE., Guest JR., 1986, Structural and functional relationships between fumarase and aspartase. Nucleotide sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli K12., Biochem J 237(2):547-57

 [4] 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

 [5] Takagi JS., Ida N., Tokushige M., Sakamoto H., Shimura Y., 1985, Cloning and nucleotide sequence of the aspartase gene of Escherichia coli W., Nucleic Acids Res 13(6):2063-74

 [6] 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

 [7] Goh EB., Bledsoe PJ., Chen LL., Gyaneshwar P., Stewart V., Igo MM., 2005, Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system., J Bacteriol 187(14):4890-9

 [8] Gosset G., Zhang Z., Nayyar S., Cuevas WA., Saier MH., 2004, Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli., J Bacteriol 186(11):3516-24

 [9] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

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

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