Curation Information

Publication: Characterization and functional analysis of the poxB gene, which encodes pyruvate oxidase in Lactobacillus plantarum.;Lorquet F, Goffin P, Muscariello L, Baudry JB, Ladero V, Sacco M, Kleerebezem M, Hols P;Journal of bacteriology 2004 Jun; 186(12):3749-59 [15175288]
TF: CcpA [F9UQH6, view regulon]
Reported TF sp.: Lactobacillus plantarum LM3
Reported site sp.: Lactobacillus plantarum LM3
Created by: Dinara Sagitova
Curation notes: -

Experimental Process

The transcription start site of the poxB gene was mapped by primer extension analysis. A putative CcpA binding site was identified by visual inspection of the poxB promoter. Primer extension experiments in the wild type and ccpA mutant strains identified that poxB transcription was repressed by CcpA. An in vivo footprinting analysis showed that there was a CcpA-dependent protection of the CcpA binding site in the poxB promoter sequence.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

TGTAAGCGTTTGCT

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
TGTAAGCGTTTGCT	pox5		Experimental technique details Premethylation interference footprinting (ECO:0005656) Premethylation interference footprinting - ECO:0005656 A variation of DNAse footprinting in which certain residues are methylated to evidence their role in binding. Similar to site-directed mutagenesis in its ability to designate specific residues as being essential for binding. - Experimental technique details Primer Extension assay (ECO:0005657) Primer Extension assay - ECO:0005657 Primer Extension Assay is a simple method of assessing expression levels. The total RNA produced by the culture is isolated. A short synthetic oligonucleotide primer (complementary to a short sequence on the target RNA) is radiolabelled (usually with 32P) and the primer anneals to the RNA. Reverse transcriptase then extends the RNA producing cDNA. The cDNA is analyzed on a polyacrylamide gel. The amount of cDNA in a band on the gel is proportional to the amount of initial RNA, thus providing expression levels of RNA from the culture. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	repressor	not specified