Curation Information

Publication
The effect of zinc limitation on the transcriptome of Pseudomonas protegens Pf-5.;Lim CK, Hassan KA, Penesyan A, Loper JE, Paulsen IT;Environmental microbiology 2013 Mar; 15(3):702-15 [22900619]
TF
Zur [Q4KKK3, view regulon]
Reported TF sp.
Pseudomonas protegens Pf-5
Reported site sp.
Pseudomonas protegens Pf-5
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE32921) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32921.

Experimental Process

Differentially expressed genes in response to zinc-limiting conditions were identified by microarrays experiments. The microarray data were validated by qRT-PCR. Zur binding sites upstream of these genes were identified by using MEME algorithm.

Transcription Factor Binding Sites


TTGTTATAATATAACAT
ATGTTATATTATAACAA
ATGTTATATTATAACAA
TTGTTATAATATAACAT
ATGTTATATTGTATCAA
ATGTGATCTTATAACAA
TTGTTATAAGATCACAT
ATGTTATATTGTTTCAA
ATGTTATTGTATAACGC
ATGATATGTTATTACAT
ATGTTACTTTATAACGC
TCGTTATATAGTAACGA
TTGTTATAATATAACAT
ATGTTATATTATAACAA
ATGTTATATTATAACAA
TTGTTATAATATAACAT
ATGTTATATTGTATCAA
ATGTGATCTTATAACAA
TTGTTATAAGATCACAT
ATGTTATATTGTTTCAA
ATGTTATTGTATAACGC
ATGATATGTTATTACAT
ATGTTACTTTATAACGC
TCGTTATATAGTAACGA

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
TTGTTATAATATAACAT PFL_6174,
... ... PFL_6174 PFL_6173 PFL_6172 PFL_6171 PFL_6175
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTTATATTATAACAA PFL_6175,
... ... PFL_6175 PFL_6174 PFL_6173 PFL_6172 PFL_6171
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTTATATTATAACAA amiC,
... ... amiC PFL_6177 mntA mntB mntC hisI2 PFL_6182 PFL_6183 thrS_2
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTGTTATAATATAACAT PFL_6177,
... ... PFL_6177 amiC mntA mntB mntC hisI2 PFL_6182 PFL_6183 thrS_2
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTTATATTGTATCAA PFL_4911,
... ... PFL_4911 PFL_4910 PFL_4912
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTGATCTTATAACAA PFL_5527,
... ... PFL_5527 PFL_5528 PFL_5529 PFL_5530 PFL_5531
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTGTTATAAGATCACAT PFL_5528,
... ... PFL_5528 PFL_5527 PFL_5529 PFL_5530 PFL_5531
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTTATATTGTTTCAA PFL_0932,
... ... PFL_0932 PFL_0931
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTTATTGTATAACGC rpmE_1
... ... rpmE_1
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGATATGTTATTACAT rpmJ
... ... rpmJ
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATGTTACTTTATAACGC PFL_0646,
... ... PFL_0646 PFL_0645 PFL_0644 PFL_0643 PFL_0642
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TCGTTATATAGTAACGA PFL_6194,
... ... PFL_6194 PFL_6193 PFL_6192 cadA_2 PFL_6190 PFL_6189 PFL_6188 PFL_6187 PFL_6195 PFL_6196 PFL_6197 PFL_6198 PFL_6199 cdsA_2
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified