Curation Information

Publication: Characterization of the Burkholderia thailandensis SOS response using whole transcriptome shotgun sequencing.;Ulrich RL, Deshazer D, Kenny TA, Ulrich MP, Moravusova A, Opperman T, Bavari S, Bowlin TL, Moir DT, Panchal RG;Applied and environmental microbiology 2013 Jul 19; (): [23872555]
TF: LexA [Q2SVP7, view regulon]
Reported TF sp.: Burkholderia thailandensis E264
Reported site sp.: Burkholderia thailandensis E264
Created by: Erill Lab
Curation notes: -

Experimental Process

RNA-seq with w-t and a recA mutant. Genes induced only in w-t with mit-C or ciprofloxacin assumed to be LexA regulated. Putative sites identified by search with Gammaproteobacteria LexA-binding consensus.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

CTGTATTTTTATACAG
CTGTGTTTTTGTACAG
CTGTTTTTTTATACAG
CTGGTTCGACGGCCAG

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	Experimental techniques	TF function	TF type
CTGTATTTTTATACAG	lexA,	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	repressor	dimer
CTGTGTTTTTGTACAG	BTH_I1859,	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	repressor	dimer
CTGTTTTTTTATACAG	recA, recX,	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	repressor	dimer
CTGGTTCGACGGCCAG	dnaE2,	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	repressor	dimer