Curation Information

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon.;da Silva Neto JF, Koide T, Gomes SL, Marques MV;BMC microbiology 2010 Aug 28; 10():231 [20799976]
RpoN [Q9PDH1, view regulon]
Reported TF sp.
Xylella fastidiosa J1a12
Reported site sp.
Xylella fastidiosa J1a12
Created by
Dinara Sagitova
Curation notes

Experimental Process

DNA microarray experiments were used to reveal the global transcriptional profile of X. fastidiosa under nitrogen starvation conditions. To identify other members of the σ54 regulon undetected by microarray analysis, an in silico search was performed to locate potential RpoN-binding sites in X. fastidiosa genome. The intergenic regions of the complete genome sequence of X. fastidiosa were scored against a strong position-specific weight matrix derived from 186 known σ54-binding sites of 44 different bacterial species. glnA transcription start site was identified by primer extension assays. RpoN binding site withing glnA promoter region was identified by visual inspection.

Transcription Factor Binding Sites


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
... ... XF1842 uppP XF1843 XF1844
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Visual sequence inspection (nan) - activator not specified