RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: torCAD
Synonym(s): OP00297, tor
Gene(s): torC, torA, torD   Genome Browser M3D Gene expression COLOMBOS
Note(s): Cells have increased variability in torCAD transcription in response to oxygen via repressing expression of the trimethylamine oxide (TMAO) receptor, TorT, and the sensor kinase, TorS, which are part of the signaling system regulating the torCAD operon Carey JN,2018
Reference(s): [1] Iobbi-Nivol C., et al., 1996
[2] Jourlin C., et al., 1996
Promoter
Name: torCp
+1: 1058056
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: gccgtaagccgttcatcctgaccagtgccgctgttcatatttgctcattaagatcgcttcActaaaccataattctacagg
                         -35                     -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Mejean V., et al., 1994
TF binding sites (TFBSs)
[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
nd NarL-phosphorylated repressor torCp nd nd nd nd nd [EXP-IMP] W [8]
[TorR,+] 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 TorR-phosphorylated activator torCp 1057973 1057982 -78.5 tttactcattCTGTTCATATctgttcatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
proximal TorR-phosphorylated activator torCp 1057983 1057992 -68.5 ctgttcatatCTGTTCATATtctgccgtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [6], [7]
proximal TorR-phosphorylated activator torCp 1058002 1058011 -49.5 ttctgccgtaAGCCGTTCATcctgaccagt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
proximal TorR-phosphorylated activator torCp 1058026 1058035 -25.5 accagtgccgCTGTTCATATttgctcatta nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd


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

 [EXP-IMP] Inferred from mutant phenotype

 [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-GSELEX] high throughput Genomic SELEX-chip evidence

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Iobbi-Nivol C., Pommier J., Simala-Grant J., Mejean V., Giordano G., 1996, High substrate specificity and induction characteristics of trimethylamine-N-oxide reductase of Escherichia coli., Biochim Biophys Acta 1294(1):77-82

 [2] Jourlin C., Simon G., Pommier J., Chippaux M., Mejean V., 1996, The periplasmic TorT protein is required for trimethylamine N-oxide reductase gene induction in Escherichia coli., J Bacteriol 178(4):1219-23

 [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] Mejean V., Iobbi-Nivol C., Lepelletier M., Giordano G., Chippaux M., Pascal MC., 1994, TMAO anaerobic respiration in Escherichia coli: involvement of the tor operon., Mol Microbiol 11(6):1169-79

 [5] Ansaldi M., Simon G., Lepelletier M., Mejean V., 2000, The TorR high-affinity binding site plays a key role in both torR autoregulation and torCAD operon expression in Escherichia coli., J Bacteriol 182(4):961-6

 [6] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [7] Simon G., Jourlin C., Ansaldi M., Pascal MC., Chippaux M., Mejean V., 1995, Binding of the TorR regulator to cis-acting direct repeats activates tor operon expression., Mol Microbiol 17(5):971-80

 [8] Iuchi S., Lin EC., 1987, The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli., Proc Natl Acad Sci U S A 84(11):3901-5

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