Curation Information

Publication: Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage.;Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA;Molecular microbiology 2009 Mar; 71(5):1071-87 [19210620]
TF: DinJ [Q47149, view regulon], [Q47150, view regulon]
Reported TF sp.: Escherichia coli str. K-12 substr. MG1655
Reported site sp.: Escherichia coli str. K-12 substr. MG1655
Created by: Erill Lab
Curation notes: -

Experimental Process

EMSA was used to prove that the DinJ-YafQ complex binds the palindrome upstream of the dinJ-yafQ operon.

The paper reports that TF forms complex with other proteins for binding with reported sites.

Manuscript reports only binding of complex DinJ-YafQ, not individual units.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

CTGAATAAATATACAG

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence	Regulated genes	Gene diagram	Experimental techniques	TF function	TF type
CTGAATAAATATACAG			Experimental technique details EMSA (ECO:0001807) EMSA - ECO:0001807 Electro-mobility shift-assays (or gel retardation assays) are a standard way of assessing TF-binding. A fragment of DNA of interest is amplified and labeled with a fluorophore. The fragment is left to incubate in a solution containing abundant TF and non-specific DNA (e.g. randomly cleaved DNA from salmon sperm, of all things) and then a gel is run with the incubated sample and a control (sample that has not been in contact with the TF). If the TF has bound the sample, the complex will migrate more slowly than unbound DNA through the gel, and this retarded band can be used as evidence of binding. The unspecific DNA ensures that the binding is specific to the fragment of interest and that any non-specific DNA-binding proteins left-over in the TF purification will bind there, instead of on the fragment of interest. EMSAs are typically carried out in a bunch of fragments, shown as multiple double (control+experiment) lanes in a wide picture. Certain additional controls are run in at least one of the fragments to ascertain specificity. In the most basic of these, specific competitor (the fragment of interest or a known positive control, unlabelled) is added to the reaction. This should sequester the TF and hence make the retardation band disappear, proving that the binding is indeed specific -	repressor	dimer