RegulonDB RegulonDB 11.1: Operon Form
   

kbl-tdh operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: kbl-tdh
Synonym(s): OP00316, tdh
Gene(s): tdh, kbl   Genome Browser M3D Gene expression COLOMBOS
Note(s): The kbl-tdh operon, coding for two enzymes of the threonine degradation pathway (threonine dehydrogenase and 2-amino-3-ketobutyrate lyase), is positively regulated by Lrp, dependent on leucine Rex JH,1991. Fraenkel YM,1995
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for tdh. This structure could regulate the expression of the gene, 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.
Reference(s): [1] Landgraf JR., et al., 1994
Promoter
Name: kblp
+1: 3792577
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: tttgcagaagtgttaacgcgttatctcgtcgcgacctataagtttgggtaatatgtgctgGaatttgccctgtctggagaa
                            -35                       -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Aronson BD., et al., 1988
[3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[Lrp,+] 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 Lrp activator kblp 3792636 3792650 -66.5 gttacacgttATTTATCCTGAATTTtgcagaagtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Lrp activator kblp 3792647 3792661 -77.0 agagacatcaAGTTACACGTTATTTatcctgaatt nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd nd


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.4 3792745 3792782 caactgagatAGGAAAAATGATGCTTTGGCATCATTTTTTCTTTTTAtatcaatgca
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-AINF] Inferred computationally without human oversight

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

 [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] Landgraf JR., Levinthal M., Danchin A., 1994, The role of H-NS in one carbon metabolism., Biochimie 76(10-11):1063-70

 [2] Aronson BD., Ravnikar PD., Somerville RL., 1988, Nucleotide sequence of the 2-amino-3-ketobutyrate coenzyme A ligase (kbl) gene of E. coli., Nucleic Acids Res 16(8):3586

 [3] 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

 [4] Rex JH., Aronson BD., Somerville RL., 1991, The tdh and serA operons of Escherichia coli: mutational analysis of the regulatory elements of leucine-responsive genes., J Bacteriol 173(19):5944-53

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