Curation Information

Publication: Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens.;Krushkal J, Juárez K, Barbe JF, Qu Y, Andrade A, Puljic M, Adkins RM, Lovley DR, Ueki T;Gene 2010 Dec 1; 469(1-2):31-44 [20708667]
TF: PilR [Q74D24, view regulon]
Reported TF sp.: Geobacter sulfurreducens PCA
Reported site sp.: Geobacter sulfurreducens PCA
Created by: Erill Lab
Curation notes: -

Experimental Process

Computational search used to predict PilR sites genome-wide using previous known consensus from Pseudomonas. Site upstream of pilA shown to be functional by luciferase assays with constructs containing or not the site, but maintaining the RpoN site.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

GGCAAAATTTGGCATG

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
GGCAAAATTTGGCATG	pilA-N,		Experimental technique details Luciferase reporter assay (ECO:0005648) Luciferase reporter assay - ECO:0005648 A type of reporter assay . The idea is identical to a betagalactosidase assay, but here fluorescence of luciferase gene product is used as the reporter. - Experimental technique details Regular expression search (ECO:0005662) Regular expression search - ECO:0005662 Similar to a PSSM search, a regular expression search looks for patterns in DNA, by making use of "degenerate" symbols and parenthetic constructs. For instance, [ATA (N:4–6) STGTC] indicates a pattern of ATA followed by 4 to 6 variable characters (N) and a suffix starting with a "strong" (S=G or C) base and the sequence TGTC. -	activator	not specified