Database Commons

a catalog of worldwide biological databases

RhizoBindingSites is a depurified database of conserved DNA motifs potentially involved in the transcriptional regulation of the , , , , and genera covering 9 representative symbiotic species, deduced from the upstream regulatory sequences of orthologous genes (O-matrices) from the Rhizobiales taxon. The sites collected with O-matrices per gene per genome from RhizoBindingSites were used to deduce matrices using the dyad-Regulatory Sequence Analysis Tool (RSAT) method, giving rise to novel S-matrices for the construction of the RizoBindingSites v2.0 database. A comparison of the S-matrix logos showed a greater frequency and/or re-definition of specific-position nucleotides found in the O-matrices. Moreover, S-matrices were better at detecting genes in the genome, and there was a more significant number of transcription factors (TFs) in the vicinity than O-matrices, corresponding to a more significant genomic coverage for S-matrices. O-matrices of 3187 TFs and S-matrices of 2754 TFs from 9 species were deposited in RhizoBindingSites and RhizoBindingSites v2.0, respectively. The homology between the matrices of TFs from a genome showed inter-regulation between the clustered TFs. In addition, matrices of AraC, ArsR, GntR, and LysR ortholog TFs showed different motifs, suggesting distinct regulation. Benchmarking showed 72%, 68%, and 81% of common genes per regulon for O-matrices and approximately 14% less common genes with S-matrices of CFN42, bv. 3841, and 1021. These data were deposited in RhizoBindingSites and the RhizoBindingSites v2.0 database (http://rhizobindingsites.ccg.unam.mx/).

Basic knowledge of transcriptional regulation is needed to understand the mechanisms governing biological processes, i.e., nitrogen fixation by Rhizobiales bacteria in symbiosis with leguminous plants. The RhizoBindingSites database is a computer-assisted framework providing motif-gene-associated conserved sequences potentially implicated in transcriptional regulation in nine symbiotic species. A dyad analysis algorithm was used to deduce motifs in the upstream regulatory region of orthologous genes, and only motifs also located in the gene seed promoter with a p-value of 1e-4 were accepted. A genomic scan analysis of the upstoream sequences with these motifs was performed. These predicted binding sites were categorized according to low, medium and high homology between the matrix and the upstream regulatory sequence. On average, 62.7% of the genes had a motif, accounting for 80.44% of the genes per genome, with 19613 matrices (a matrix is a representation of a motif). The RhizoBindingSites database provides motif and gene information, motif conservation in the order Rhizobiales, matrices, motif logos, regulatory networks constructed from theoretical or experimental data, a criterion for selecting motifs and a guide for users. The RhizoBindingSites database is freely available online at rhizobindingsites.ccg.unam.mx.