Curation Information

Publication: Role of a Fur homolog in iron metabolism in Nitrosomonas europaea.;Vajrala N, Sayavedra-Soto LA, Bottomley PJ, Arp DJ;BMC microbiology 2011 Feb 21; 11(3):37 [21338516]
TF: Fur [Q820Q2, view regulon]
Reported TF sp.: Nitrosomonas europaea ATCC 19718
Reported site sp.: Nitrosomonas europaea ATCC 19718
Created by: Dinara Sagitova
Curation notes: -

Experimental Process

An in silico search with N. europaea Fur consensus sequence identified a potential Fur box in the NE0616 promoter. FURTA confirmed that the predicted Fur box was functional.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

TAATAATACGTATCTTTAT

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
TAATAATACGTATCTTTAT	fur1,		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 FURTA (ECO:0005633) FURTA - ECO:0005633 A technique used to locate and isolate Fur sites via cloning. The genome of a target organism is digested with restriction enzymes, and ligated into high copy plasmids to create a plasmid library, which is then cloned into a cell line with a fur-repressed reporter. In cells where the introduced high copy plasmid contains a fur site, fur will be titrated away from it's binding site on the reporter (and throughout the genome), marking the colony. The cell can then be isolated, the plasmid extracted and sequenced for further study. -	repressor	not specified