Curation Information

Publication
A LuxR-type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes.;Pappas KM, Winans SC;Molecular microbiology 2003 May; 48(4):1059-73 [12753196]
TF
TraR [P54294, view regulon]
Reported TF sp.
Agrobacterium fabrum str. C58
Reported site sp.
Agrobacterium tumefaciens strain R10
Created by
Joe Sparenberg
Curation notes
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Experimental Process

lacZ assays with promoter fragments of different lengths showed that TraR activates the expression of the repABC operon. EMSA showed direct binding to tra boxes 2 and 3. DNase I footprinting confirmed that the sequences were, in fact, tra boxes 2 and 3. Additionally, site-directed mutagenesis experiment validated the functionality of the tra box III.

Transcription Factor Binding Sites


ATGTGCAGATCTGCACGT
ATGTGCAAATCTGCACTT
TTGTGCAGATCTGCACTT
TTGTGCAGATCTGCACTT

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
TTGTGCAGATCTGCACTT repA, repB,
... ... repA repB traI trbB trbC trbD trbE trbJ trbK trbL trbF trbG trbH trbI Atu6030
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - activator dimer
TTGTGCAGATCTGCACTT repA, repB,
... ... repA repB traI trbB trbC trbD trbE trbJ trbK trbL trbF trbG trbH trbI Atu6030
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator dimer