Curation Information

Publication
Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus.;Li Y, Gao H, Qin L, Li B, Han Y, Guo Z, Song Y, Zhai J, Du Z, Wang X, Zhou D, Yang R;BMC genomics 2008 Mar 27; 9():143 [18366809]
TF
PhoP [A0A0B6P4W3, view regulon]
Reported TF sp.
Yersinia pestis biovar Microtus strain 201
Reported site sp.
Yersinia pestis biovar Microtus strain 201
Created by
Erill Lab
Curation notes
-
External databases
NCBI GEO (GSE9279) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9279.

Experimental Process

DNA-array results from PMID: 16061330. EMSA for all up/downregulated genes i) responsible for stress-adaptive or regulatory function; and ii) with a homologue of E. coli PhoP box sequence in their promoter-proximal regions (with a cutoff of 2 bp mismatch). Further corroboration of binding site by DNAse footprinting.

Transcription Factor Binding Sites


TGTTTAAGTATTGTTTAA
TAATTAAATGATATTGAA
TGTTCAATAACACATCAA
ATTTAACTGTATGCTTAT
TTTTTATATTTTTGTTGT
CGTTTAACGATAGGCAAA
TGTTTATAAATGGTTTTA
GGGTTTTTTACCGTTTAT
TGTCTATAGCCTGTTTAT
TGTTTAAGTATTGTTTAA
TAATTAAATGATATTGAA
TGTTCAATAACACATCAA
ATTTAACTGTATGGTTAT
TTTTTATATTTTTGTTGT
CGTTTAACGATAGGCAAA
TGTTTATAAATGGTTTTA
GGGTTTTTTACCGTTTAT
TGTCTATAGCCTGTTTAT

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
TGTTTAAGTATTGTTTAA
... ... cheM YPO1659
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TAATTAAATGATATTGAA sodA,
... ... sodA fdhD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TGTTCAATAACACATCAA sodB,
... ... sodB YPO2385
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTTAACTGTATGGTTAT sodB,
... ... sodB YPO2385
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TTTTTATATTTTTGTTGT sodB,
... ... sodB YPO2385
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGTTTAACGATAGGCAAA ahpC,
... ... ahpC YPO3193
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TGTTTATAAATGGTTTTA YPO2174,
... ... YPO2174 YPO2173
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GGGTTTTTTACCGTTTAT oppA,
... ... oppA YPO2181
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TGTCTATAGCCTGTTTAT
... ... tnp YPO0542
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer