Curation Information

Publication
Characterization of Zur-dependent genes and direct Zur targets in Yersinia pestis.;Li Y, Qiu Y, Gao H, Guo Z, Han Y, Song Y, Du Z, Wang X, Zhou D, Yang R;BMC microbiology 2009 Jun 25; 9(9):128 [19552825]
TF
Zur [Q0WJZ2, view regulon]
Reported TF sp.
Yersinia pestis biovar microtus strain 201
Reported site sp.
Yersinia pestis biovar microtus strain 201
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE15183) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15183.

Experimental Process

Microarray analysis was done to identify Zur-regulated genes. Microarray data was validated by real-time RT-PCR. EMSAs validated that Zur bound the promoters of the identified genes. The effect of Zur on the promoter activity of znuCB, znuA and ykgM-rpmJ2 was further validated by constructing lacZ reporter fusion analyses. DNase I footprinting assay was used to precisely determine the Zur binding sites on its target promoters.

Transcription Factor Binding Sites


GATGTTACATTATAACATA
AATGTTATAATATTACGCT
GATGTTACATTATAACATA
AATGTTATAATATTACGCT

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
GATGTTACATTATAACATA rpmJ,
... ... rpmJ rpmE2 acrB2 acrA3 acrR2 dsrE2
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
AATGTTATAATATTACGCT znuC, znuA,
... ... znuC znuA znuB ruvB nlpD3
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer