Curation Information

Publication
Genetic composition of the Bacillus subtilis SOS system.;Au N, Kuester-Schoeck E, Mandava V, Bothwell LE, Canny SP, Chachu K, Colavito SA, Fuller SN, Groban ES, Hensley LA, O'Brien TC, Shah A, Tierney JT, Tomm LL, O'Gara TM, Goranov AI, Grossman AD, Lovett CM;Journal of bacteriology 2005 Nov; 187(22):7655-66 [16267290]
TF
LexA [P31080, view regulon]
Reported TF sp.
Bacillus subtilis YB886
Reported site sp.
Bacillus subtilis YB886
Created by
Erill Lab
Curation notes
B. subtilis YB886 is a prophage-cured derivative of B. subtilis 168

Experimental Process

Computer search for sites with experimental validation of binding with EMSA (quantitative), followed with DNA array analysis of induction with Mit-C in w.t. and recA(def) strains The apparent Kd values for these genes were determined as the concentration of LexA that binds to one half of the total DNA sites.

Transcription Factor Binding Sites


AGAACATTTGTTCC
AGAACTCATGTTCG
CGAACATGAGTTCT
AGAACATTCGTTCT
AGAACGTATGTTTT
AGAACGTACATTCC
AGAACGTGCATTCG
AGAACAAACGTTCC
GGAACGTTTGTTCT
AGAACACACGTTCG
CGAACGTATGTTTG
CGAATATGCGTTCG
CGAACAAACGTTCT
GGAATGTTTGTTCG
CGAACAAACGTTTC
CGAACCTATGTTTG
CAAACATACGTTCT
CGAACTTTTGTTCT
GGAACGTTTGTTCT
AGAACACTTGTTCC
AGAACAAACGTTCT
GGAATATTCGTTCG
AGAACATAAATTCG
CGAACATACTTTCG
CGAACATAAGTTCT
CAAACTTTTGTTCT
AGAACGATTGTTCT
CGAACATATGTTAA
AAAACAAACGTTCG
AGAACATTTGTTTC
CGAACTTTAGTTCG
AGAACAAGTGTTCT
CGAACGTATGTTTG
CGAACGTATATTCC
AAAACGTAAGTTCG
CGAACATGTTTTCG
CGAAACTTTGTTCG
AGAACATAGGTTCC
CGAACATAAGTTTT
GAAACTTGTGTTCG
AGAACATTTGTTCC
AGAACTCATGTTCG
CGAACATGAGTTCT
AGAACATTCGTTCT
AGAACGTATGTTTT
AGAACGTACATTCC
AGAACGTGCATTCG
AGAACAAACGTTCC
GGAACGTTTGTTCT
AGAACAAACGTTCG
CGAACGTATGTTTG
CGAATATGCGTTCG
CGAACAAACGTTCT
GGAATGTTTGTTCG
CGAACAAACGTTTC
CGAACCTATGTTTG
CAAACATACGTTCT
CGAACTTTTGTTCT
GGAACGTTTGTTCT
AGAACACTTGTTCC
AGAACAAACGTTCT
GGAATATTCGTTCG
AGAACATAAATTCG
CGAACATACTTTCG
CGAACATAAGTTCT
CAAACTTTTGTTCT
AGAACGATTGTTCT
CGAACATATGTTAA
AAAACAAACGTTCG
AGAACATTTGTTTC
CGAACTTTAGTTCG
AGAACAAGTGTTCT
CGAACGTATGTTTG
CGAACGTATATTCC
AAAACGTAAGTTCG
CGAACATGTTTTCG
CGAAACTTTGTTCG
AGAACATAGGTTCC
CGAACATAAGTTTT
GAAACTTGTGTTCG

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
AGAACATTTGTTCC ybaK,
... ... ybaK ybaJ
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACTCATGTTCG dinB, ydgH,
... ... dinB ydgH ydgG
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACATGAGTTCT dinB,
... ... dinB ydgG ydgH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACATTCGTTCT ydiO, ydiP,
... ... ydiO ydiP ydzV ydzU
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACGTATGTTTT pcrA, ligA, yerH,
... ... pcrA ligA yerH pcrB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACGTACATTCC yhaZ,
... ... yhaZ yheA yhaX
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACGTGCATTCG yhaO, yhaN,
... ... yhaO yhaN natB natA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACAAACGTTCC yhjD, yhjE,
... ... yhjD yhjE sipV
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GGAACGTTTGTTCT yhjD, yhjE,
... ... yhjD yhjE sipV
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACAAACGTTCG
... ... xkdA yjqC xre
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACGTATGTTTG ykzR,
... ... ykzR ykvQ ykvR
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAATATGCGTTCG recA,
... ... recA cinA pgsA ymfM
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACAAACGTTCT aprX,
... ... aprX ymzE ymzE
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GGAATGTTTGTTCG lexA, yneA, yneB
... ... lexA yneA yneB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACAAACGTTTC lexA, yneA, yneB
... ... lexA yneA yneB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACCTATGTTTG lexA, yneA, yneB
... ... lexA yneA yneB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CAAACATACGTTCT parE, parC,
... ... parE parC yneT
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACTTTTGTTCT
... ... yolD uvrX yolC yolB yolA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GGAACGTTTGTTCT
... ... yozL yozK yobH yozM yobI
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACACTTGTTCC
... ... yorB yorA yoqZ
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACAAACGTTCT
... ... yolD uvrX yolC yolB yolA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GGAATATTCGTTCG
... ... hbs spoIVA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACATAAATTCG
... ... ypuD sipS
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACATACTTTCG yqjW,
... ... yqjW yqjX yqzH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACATAAGTTCT yqjW, yqjX,
... ... yqjW yqjX yqzH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CAAACTTTTGTTCT
... ... yqxL yqhB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACGATTGTTCT
... ... yqeG yqeH aroE yqeI nadD yqeK yqeL yqeM sda
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACATATGTTAA ruvA, ruvB,
... ... ruvA ruvB yrzS queA tgt yajC bofC csbX
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AAAACAAACGTTCG uvrC,
... ... uvrC trxA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACATTTGTTTC
... ... dnaE ytrH ytrI
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACTTTAGTTCG uvrB, uvrA,
... ... uvrB uvrA csbA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACAAGTGTTCT tagC,
... ... tagC tagB tagA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACGTATGTTTG tagC,
... ... tagC tagB tagA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACGTATATTCC vpr,
... ... vpr ywcI sacT ywcJ ywcH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AAAACGTAAGTTCG
... ... fliP fliZ cheY fliY fliM fliL ylzI flgG flgD fliK ylxF fliJ fliI fliH fliQ fliR flhB flhA flhF ylxH cheB cheA cheW cheC cheD sigD ylxL
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACATGTTTTCG
... ... rpe yloQ prkC prpC yloN rsmB fmt def priA coaBC thiN
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAAACTTTGTTCG
... ... sigH yacP rlmB mrnC cysS cysE rpmG secE
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AGAACATAGGTTCC
... ... ylbC ylbB ylbD ylbE
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
CGAACATAAGTTTT
... ... yonT yoyJ yonU yonS
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GAAACTTGTGTTCG
... ... yqkA yqkB yqkC yqkD yqjZ yqjY
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - repressor dimer