Curation Information

Publication
Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis.;Gao H, Zhang Y, Han Y, Yang L, Liu X, Guo Z, Tan Y, Huang X, Zhou D, Yang R;BMC microbiology 2011 Feb 23; 11(1):39 [21345178]
TF
OmpR [Q7CFX0, view regulon]
Reported TF sp.
Yersinia pestis biovar Microtus str. 201
Reported site sp.
Yersinia pestis biovar Microtus str. 201
Created by
Grace Chandler
Curation notes
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Experimental Process

Standard cDNA microarray analysis revealed 224 genes affected by a OmpR knockout mutant. known OmpR binding sites from S. enterica and E. coli were aligned to form a PSSM. A PSSM search using this motif on the 224 regulated genes, using a score threshold of 7, identified 14 putative binding sites. real-time RT-PCR analysis validated the role of OmpR in differential expression of the 14 OmpR gene targets. ompC, ompF and ompX activation was also confirmed by qRT-PCR. LacZ fusion assays confirmed this result. Dnase I footprinting localized the binding sites for these genes. LacZ fusion demonstrated auto-activation of ompR. DNase I footprinting localized this binding site.

Transcription Factor Binding Sites


AAAACATTTTATTACATTTA
AAAACATTTTATTACATTTA
ATAAATACTTGTTGCAATTT
TTTACATTTTGTAACACATA
TTTAAATGTTGTAACAATTT
TTAACACTTAAATTCATTTT
CATACTCTGCGTAACATTTT
AGCACAGTTTATTACATCTC
GATCAGTTTTGTAACATTTG
GATCAGTTTTGTAACATTTG
TTTACCCATGATTTCATCTT
TGTACTCAACGTATCATCTA
AATAAGCTTTGTAACAATTT
GAAATTCTTTGTTACATGAA
AAAACATTTTATTACATTTA
AAAACATTTTATTACATTTA
ATAAATACTTGTTGCAATTT
TTTACATTTTGTAACACATA
TTTAAATGTTGTAACAATTT
TTAACACTTAAATTCATTTT
CATACTCTGCGTAACATTTT
AGCACAGTTTATTACATCTC
GATCAGTTTTGTAACATTTG
GATCAGTTTTGTAACATTTG
TTTACCCATGATTTCATCTT
TGTACTCAACGTATCATCTA
AATAAGCTTTGTAACAATTT
GAAATTCTTTGTTACATGAA

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
AAAACATTTTATTACATTTA YP_2927,
... ... YP_2927 bglX2 YP_2933 malG5 malF5 ugpB4 purR10 YP_2928 yapF YP_2925 YP_2926
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
AAAACATTTTATTACATTTA YP_2926,
... ... YP_2926 bglX2 YP_2933 malG5 malF5 ugpB4 purR10 YP_2928 YP_2927 yapF YP_2925
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATAAATACTTGTTGCAATTT ompC1
... ... ompC1
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 PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTTACATTTTGTAACACATA ompC2
... ... ompC2
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 PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTTAAATGTTGTAACAATTT phoP,
... ... phoP phoQ YP_1762
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTAACACTTAAATTCATTTT ampD3
... ... ampD3
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CATACTCTGCGTAACATTTT sfcA2
... ... sfcA2
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
AGCACAGTTTATTACATCTC rplU,
... ... rplU ispB rpmA rhaT3 obgE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
GATCAGTTTTGTAACATTTG hcp7,
... ... hcp7 YP_3068 YP_3067 YP_3066 YP_3065
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
GATCAGTTTTGTAACATTTG YP_3068,
... ... YP_3068 YP_3067 YP_3066 YP_3065 hcp7
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTTACCCATGATTTCATCTT cysM2,
... ... cysM2 hutU hutH apt2 rhaT14 accC1
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TGTACTCAACGTATCATCTA
... ... apt2 rhaT14 accC1
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
AATAAGCTTTGTAACAATTT ompR,
... ... ompR envZ
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 PSSM site search (ECO:0005659) - activator not specified
GAAATTCTTTGTTACATGAA ompX,
... ... ompX rhaT11 rimI1 tam
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 PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified