Curation Information

Publication: Structural organization, nucleotide sequence, and regulation of the Haemophilus influenzae rec-1+ gene.;Zulty JJ, Barcak GJ;Journal of bacteriology 1993 Nov; 175(22):7269-81 [8226674]
TF: LexA [P44858, view regulon]
Reported TF sp.: Haemophilus influenzae Rd KW20
Reported site sp.: Haemophilus influenzae Rd KW20
Created by: Kathryn Cronise
Curation notes: -

Experimental Process

A search using the consensus sequence from the LexA motif in E. coli was used to identify the site. Induction with mit-C was validated with primer extension assay and beta-gal assays.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

CTGTACATCAATACAG

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
CTGTACATCAATACAG	recA,		Experimental technique details Beta-gal reporter assay Beta-gal reporter assay Reporter assay using the beta-galactosidase (lacZ) gene. The lacZ gene is typically fused to the promoter of interest. Differential regulation of the promoter mediated by the TF is assessed by induction of the system and evaluation of lacZ expression. Bacteria expressing lacZ appear blue when grown on a X-gal medium. The assay is often performed using a plasmid borne construction on a lacZ(def) strain. - 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 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. -	repressor	dimer