RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: adiA
Gene(s): adiA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Stim KP., et al., 1993
Promoter
Name: adiAp
+1: 4340556
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: ttcaaaaatgtttgtttttcacgcgctttacagcccgaaaaggccggaagatacttgcccGcaacgaagattccttcataa
                                -35                    -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Stim KP., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: aaggccaggcGGCGTAATGTTATTTAAACAATTACGCCttcagcggaa
Reference(s): [1] Stim KP., et al., 1993
TF binding sites (TFBSs)
[AdiY,+] 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 AdiY activator adiAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4]
[H-NS,-] 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 H-NS repressor adiAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[IHF,+] 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 IHF activator adiAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION] W [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.9 4340527 4340563 ccggaagataCTTGCCCGCAACGAAGATTCCTTCATAACCGGGTAAgcaatgatga
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-HINF] Inferred by a human based on computational evidence

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

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

 [EXP-IMP] Inferred from mutant phenotype

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Stim KP., Bennett GN., 1993, Nucleotide sequence of the adi gene, which encodes the biodegradative acid-induced arginine decarboxylase of Escherichia coli., J Bacteriol 175(5):1221-34

 [2] 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

 [3] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [4] Stim-Herndon KP., Flores TM., Bennett GN., 1996, Molecular characterization of adiY, a regulatory gene which affects expression of the biodegradative acid-induced arginine decarboxylase gene (adiA) of Escherichia coli., Microbiology 142 ( Pt 5):1311-20

 [5] Shi X., Waasdorp BC., Bennett GN., 1993, Modulation of acid-induced amino acid decarboxylase gene expression by hns in Escherichia coli., J Bacteriol 175(4):1182-6

RegulonDB