RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: tynA
Gene(s): tynA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of tynA is activated in carbon- and nitrogen-limited cells in the presence of a FeaR coactivator Zeng J,2013.
During carbon limitation in the presence of the FeaR coactivators (glycerol medium plus tyramine/PEA), both tynA and feaB are upregulated Zeng J,2013. On the other hand, it has been observed that aldehydes derived from some amines (PEA, Tyra, DA, Trypta), instead of the amines themselves, activate tynA expression in a FeaR- dependent way Rottinghaus AG, Xi C, Amrofell MB, Yi H, Moon TS,2022
tynA, feaB, and fliA promoters are strongly repressed when the nsrR start codon from the wild-type GUG is changed to AUG Chhabra S,2015
Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR negatively controlling the tynA gene has been identified Partridge JD,2009 However, this site is far from the tynA promoter, at -138666 bp from the TSS.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: tynAp
+1: 1451409
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 60
Sequence: gccaaacaacctggcaggtgcaggcaatcccctttgcatcagtactgataatgtgaacctGactaaaccgcccacagagcg
                                -35                 -10     +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
[2] Zeng J., et al., 2013
TF binding sites (TFBSs)
[FeaR,+] 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 FeaR activator tynAp 1451442 1451462 -43.0 cctgccaaacAACCTGGCAGGTGCAGGCAATcccctttgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2]
proximal FeaR activator tynAp 1451463 1451484 -64.0 cactgtatgaAAAGCTGGCACACCTGCCAAACaacctggcag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.3 1451555 1451586 tcggtgaatgAAGGGCAACGGCGAATAGTTGCCCTTTTATTtcactaagtt
  anti-terminator -6.9 1451575 1451618 tggccaggcaGCACGGTGATTTTGTCGATTAATCGGTGAATGAAGGGCAACGGcgaatagttg
  anti-anti-terminator -7.3 1451612 1451650 cccggtggcgCTGTATTCAATTCTGACGCTGGTGGCCAGGCAGCACGGtgattttgtc
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

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

 [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-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] 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

 [2] Zeng J., Spiro S., 2013, Finely tuned regulation of the aromatic amine degradation pathway in Escherichia coli., J Bacteriol 195(22):5141-50

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