Curation Information

Publication
The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus.;Zhan L, Han Y, Yang L, Geng J, Li Y, Gao H, Guo Z, Fan W, Li G, Zhang L, Qin C, Zhou D, Yang R;Infection and immunity 2008 Nov; 76(11):5028-37 [18710863]
TF
CRP [Q7CFV3, view regulon]
Reported TF sp.
Yersinia pestis biovar Microtus strain 201
Reported site sp.
Yersinia pestis biovar Microtus strain 201
Created by
Patrick O'Neill
Curation notes
this curation just the contains positively regulated CRP sites listed in the paper. The genome listed in this curation is not the exact strain used, but a closely related strain whose gene names the authors use to report sites.

Experimental Process

Determination of binding by DNAse footprinting and EMSA verified by PSSM search. Determination of regulation by qt-PCR in WT and crp^- mutant.

Transcription Factor Binding Sites


AATGTATGATCGAGATCACTTTT
AATGTTTGATTGCCGTCACGTTT
AACTTTTGACTGACATCACAAAA
GAGATGTGACTTTTATCACAACA
AAATCGTGATCCTAATCACTGTT
AAACTGTGATTTGACTCACTCTG
AATATTTGATCATGATCACTTCC
AAACTGTGATGCAGATCACTATA
AAATAGTGATGTATATCTCAACC
AGATTGTGACTTGTCTCTCAATT
AAACAGTGAGTTATAGCACATAT
TATCTGTGATTGCTCTCACACTT
AAAGTTTGATGTAGCTAACGCTA
GAAATGCGATGCTACTCACGGTT
AATATGTGCTGGATATAACAGTT
AAATAGTGAGCCAAGTAACAAAA
GTTATGTGATGCAGATCAAATGT
ATTTTGTGACGTAGGTCACTGTA
ATTGTGTGAATCATGTCACATTG
AAACTGTGATTCTGATCAAGGTT
AATATGTGGGTTATATCACTTTT
AATGTATGATCGAGATCACTTTT
AATGTTTGATTGCCGTCACGTTT
AACTTTTGACTGACATCACAAAA
GAGATGTGACTTTTATCACAACA
AAATCGTGATCCTAATCACTGTT
AAACTGTGATTTGACTCACTCTG
AATATTTGATCATGATCACTTCC
AAACTGTGATGCAGATCACTATA
AAATAGTGATGTATATCTCAACC
AGATTGTGACTTGTCTCTCAATT
AAACAGTGAGTTATAGCACATAT
TATCTGTGATTGCTCTCACACTT
AAAGTTTGATGTAGCTAACGCTA
GAAATGCGATGCTACTCACGGTT
AATATGTGCTGGATATAACAGTT
AAATAGTGAGCCAAGTAACAAAA
GTTATGTGATGCAGATCAAATGT
ATTTTGTGACGTAGGTCACTGTA
ATTGTGTGAATCATGTCACATTG
AAACTGTGATTCTGATCAAGGTT
AATATGTGGGTTATATCACTTTT

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
AATGTATGATCGAGATCACTTTT yfiA,
... ... yfiA yfiO
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AATGTTTGATTGCCGTCACGTTT ptsG,
... ... ptsG YPO1607 holB tmk yceG
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AACTTTTGACTGACATCACAAAA araF,
... ... araF araB
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
GAGATGTGACTTTTATCACAACA
... ... YPO3953 gntM
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAATCGTGATCCTAATCACTGTT sdhC,
... ... sdhC gltA sdhD sdhA sdhB
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAACTGTGATTTGACTCACTCTG cydA,
... ... cydA sucD sucC cydB
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AATATTTGATCATGATCACTTCC pepT,
... ... pepT cobB
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAACTGTGATGCAGATCACTATA idnO,
... ... idnO YPO2538 gntV
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAATAGTGATGTATATCTCAACC fadD,
... ... fadD YPO2073
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AGATTGTGACTTGTCTCTCAATT dadA,
... ... dadA YPO2145 YPO2148
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAACAGTGAGTTATAGCACATAT ompC,
... ... ompC micF
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
TATCTGTGATTGCTCTCACACTT aspA,
... ... aspA fxsA
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAAGTTTGATGTAGCTAACGCTA cspD,
... ... cspD clpS clpA
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
GAAATGCGATGCTACTCACGGTT aas,
... ... aas ygeD bisC
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AATATGTGCTGGATATAACAGTT YPO0400,
... ... YPO0400 YPO0399 YPO0398 YPO0401 YPO0402
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAATAGTGAGCCAAGTAACAAAA YPO0819,
... ... YPO0819 YPO0820
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
GTTATGTGATGCAGATCAAATGT YPO2436,
... ... YPO2436 marC
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
ATTTTGTGACGTAGGTCACTGTA YPO2536,
... ... YPO2536 YPO2537
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
ATTGTGTGAATCATGTCACATTG YPO2795,
... ... YPO2795 YPO2794 YPO2793 YPO2792 yapC
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAACTGTGATTCTGATCAAGGTT YPO3151,
... ... YPO3151 ybaV
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AATATGTGGGTTATATCACTTTT YPO3647,
... ... YPO3647 pcp
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer