RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: aldA
Gene(s): aldA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene aldA is enhanced under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Baldoma L., et al., 1988
[2] Chen YM., et al., 1987
[3] Pellicer MT., et al., 1999
Promoter
Name: aldAp
+1: 1488190
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 42
Sequence: cccttcacagaattgtcctttcacgattccgtctctctgatgattgatgttaattaacaaTgtattcaccgaaaacaaaca
                           -35                     -10      +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[5] Limon A., et al., 1997
[6] Pellicer MT., et al., 1999
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
remote ArcA-phosphorylated repressor aldAp 1488026 1488040 -157.0 aaagtcgctcGTTACGTTAAAAATTgcccgtttgt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
remote ArcA-phosphorylated repressor aldAp 1488046 1488060 -137.0 aaattgcccgTTTGTGAACCACTTGtttgcaaacg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
proximal ArcA-phosphorylated repressor aldAp 1488178 1488192 -5.0 gatgattgatGTTAATTAACAATGTattcaccgaa nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [10]
proximal ArcA-phosphorylated repressor aldAp 1488184 1488198 2.0 tgatgttaatTAACAATGTATTCACcgaaaacaaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
proximal ArcA-phosphorylated repressor aldAp 1488195 1488209 13.0 aacaatgtatTCACCGAAAACAAACatataaatca nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]
[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 aldAp 1488120 1488141 -59.5 ttacacttgtTTTTATGAAGCCCTTCACAGAAttgtcctttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [5]
[DnaA,-] 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 DnaA-ATP repressor aldAp 1488178 1488186 -7.5 gatgattgatGTTAATTAAcaatgtattc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
[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 repressor aldAp 1488173 1488186 -10.5 tctctgatgaTTGATGTTAATTAAcaatgtattc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]
[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
remote MarA activator aldAp 1488019 1488038 -161.0 gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[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
remote Rob activator aldAp 1488019 1488038 -161.0 gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[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
remote SoxS activator aldAp 1488019 1488038 -161.0 gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence

 [EXP-IMP-SITE-MUTATION] Site mutation

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

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

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


Reference(s)    

 [1] Baldoma L., Aguilar J., 1988, Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation., J Bacteriol 170(1):416-21

 [2] Chen YM., Zhu Y., Lin EC., 1987, NAD-linked aldehyde dehydrogenase for aerobic utilization of L-fucose and L-rhamnose by Escherichia coli., J Bacteriol 169(7):3289-94

 [3] Pellicer MT., Fernandez C., Badia J., Aguilar J., Lin EC., Baldom L., 1999, Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter., J Biol Chem 274(3):1745-52

 [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] Limon A., Hidalgo E., Aguilar J., 1997, The aldA gene of Escherichia coli is under the control of at least three transcriptional regulators., Microbiology 143 ( Pt 6):2085-95

 [6] Pellicer MT., Lynch AS., De Wulf P., Boyd D., Aguilar J., Lin EC., 1999, A mutational study of the ArcA-P binding sequences in the aldA promoter of Escherichia coli., Mol Gen Genet 261(1):170-6

 [7] Martin RG., Rosner JL., 2002, Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data., Mol Microbiol 44(6):1611-24

 [8] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [9] Ozaki T., Kumaki Y., Kitagawa R., Ogawa T., 2001, Anomalous DnaA protein binding to the regulatory region of the Escherichia coli aldA gene., Microbiology 147(Pt 1):153-9

 [10] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

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