RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: tonB
Synonym(s): OP00228
Gene(s): tonB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Expression of tonB, along with that of other genes also regulated by Fur, is reduced under Zn excess Xu Z,2019.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Postle K., et al., 1983
[2] Young GM., et al., 1994
Promoter
Name: tonBp
+1: 1311054
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: ttcactgatcctgatcgtcttgccttattgaatatgattgctatttgcatttaaaatcgaGacctggtttttctactgaaa
                            -35                     -10     +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Lisser S., et al., 1993
[1] Postle K., et al., 1983
Terminator(s)
Type: rho-independent
Sequence: gtaagcagaaAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTattactcaac
Reference(s): [1] Postle K., et al., 1983
TF binding sites (TFBSs)
[Fur,+] 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 Fur-Fe2+ activator tonBp 1311020 1311038 -25.0 gtcttgccttATTGAATATGATTGCTATTtgcatttaaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]
[Fur,-] 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 Fur-Fe2+ repressor tonBp 1311026 1311044 -19.0 ccttattgaaTATGATTGCTATTTGCATTtaaaatcgag nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]
proximal Fur-Fe2+ repressor tonBp 1311030 1311048 -15.0 attgaatatgATTGCTATTTGCATTTAAAatcgagacct nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]
proximal Fur-Fe2+ repressor tonBp 1311070 1311088 26.0 gtttttctacTGAAATGATTATGACTTCAatgacccttg nd [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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

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


Reference(s)    

 [1] Postle K., Good RF., 1983, DNA sequence of the Escherichia coli tonB gene., Proc Natl Acad Sci U S A 80(17):5235-9

 [2] Young GM., Postle K., 1994, Repression of tonB transcription during anaerobic growth requires Fur binding at the promoter and a second factor binding upstream., Mol Microbiol 11(5):943-54

 [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] Lisser S., Margalit H., 1993, Compilation of E. coli mRNA promoter sequences., Nucleic Acids Res 21(7):1507-16

 [5] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

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