Curation Information

Publication: Analysis of promoter elements involved in the transcriptional initiation of RpoS-dependent Borrelia burgdorferi genes.;Eggers CH, Caimano MJ, Radolf JD;Journal of bacteriology 2004 Nov; 186(21):7390-402 [15489451]
TF: RpoS [O51712, view regulon]
Reported TF sp.: Borrelia burgdorferi strain 297
Reported site sp.: Borrelia burgdorferi 297
Created by: Erill Lab
Curation notes: -

Experimental Process

The RpoS-dependent expression of promoter ospC was assessed through beta-galactosidase assays. An extended -10 site for the RpoS promoter was predicted based on similarity to the known E. coli consensus and verified through site-directed mutagenesis coupled with beta-gal assays.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

TGGACTAATAAT

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
TGGACTAATAAT	ospC,		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 Site directed mutagenesis (ECO:0005667) Site directed mutagenesis - ECO:0005667 Target-specific mutation, as opposed to non-specific mutation. In the context of TF-binding sites, site-directed mutagenesis is typically used to establish/confirm the specific sequence and location of a site, often in tandem with EMSA. Different positions of a putative binding site are mutated to non-consensus (or random) bases and binding to the mutated site is evaluated through EMSA or other means. Often implemented only in conserved motif positions or serially through all positions of a site. -	activator	monomer