Curation Information

Publication: Role of sigma54 in the regulation of genes involved in type I and type IV pili biogenesis in Xylella fastidiosa.;da Silva Neto JF, Koide T, Abe CM, Gomes SL, Marques MV;Archives of microbiology 2008 Mar; 189(3):249-61 [17985115]
TF: 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. Promoter regions of the differentially expressed genes were searched for potential RpoN binding sites by identifying matches with the σ54-binding consensus. Microarray results were validated by qRT-PCR. The transcriptional start site of pilA1 was determined by primer extension analysis. Also, a good consensus for binding of the integration host factor (IHF) was identified between positions −45 and −80.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

TGGCACACCTTCTGC

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
TGGCACACCTTCTGC	XF2542,		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 DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level. - Experimental technique details qRT-PCR [RNA] (ECO:0001808) qRT-PCR [RNA] - ECO:0001808 Quantitative Reverse-Transcription PCR is a modification of PCR in which RNA is first reverse transcribed into cDNA and this is amplified measuring the product (qPCR) in real time. It therefore allows one to analyze transcription by directly measuring the product (RNA) of a gene's transcription. If the gene is transcribed more, the starting product for PCR is larger and the corresponding volume of amplification is also larger. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	activator	not specified