RegulonDB RegulonDB 11.1: Operon Form
   

dinJ-yafQ operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: dinJ-yafQ
Gene(s): yafQ, dinJ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The dinJ gene is repressed by both DnaA and LexA in an independent manner, but the actions of these two proteins are additive during the SOS response Wurihan,2018 The sites position for both regulators were not shown Wurihan,2018
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: dinJp
+1: 246615
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 113
Sequence: gtatcccggatcgtttctgaacaaacttaataaaccattattataaaattaacatatataTttcagttaattatgtaaaaa
                      -35                        -10        +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[DinJ-YafQ,-] 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
remote DinJ-YafQ repressor dinJp 246519 246535 89.5 tacaattcaaGCTGAATAAATATACAGcacaggagat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
[LexA,-] 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
remote LexA repressor dinJp 246517 246536 89.5 ctacaattcaAGCTGAATAAATATACAGCAcaggagatac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences


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] Lewis LK., Harlow GR., Gregg-Jolly LA., Mount DW., 1994, Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli., J Mol Biol 241(4):507-23

 [3] Ruangprasert A., Maehigashi T., Miles SJ., Giridharan N., Liu JX., Dunham CM., 2014, Mechanisms of toxin inhibition and transcriptional repression by Escherichia coli DinJ-YafQ., J Biol Chem 289(30):20559-69

 [4] Prysak MH., Mozdzierz CJ., Cook AM., Zhu L., Zhang Y., Inouye M., Woychik NA., 2009, Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage., Mol Microbiol 71(5):1071-87

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