RhizoBindingSites v2.0 is a bioinformatic database of DNA motifs potentially involved in transcriptional regulation deduced from sites of the itself genome

Abstract

RhizoBindingSites is ade novodepurified database of conserved DNA motifs potentially involved in the transcriptional regulation of theRhizobium,Sinorhizobium,Bradyrhizobium,Azorhizobium,andMesorhizobiumrepresentative 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 greater number of transcription factors (TFs) in the vicinity than O-matrices, corresponding to a more significant genomic coverage for S-matrices. 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 ofRhizobium etliCFN42,R. leguminosarumbv.viciae3841, andSinorhizobium meliloti1021. These data were deposited in RhizoBindingSites and the RhizoBindingSites v2.0 database (http://rhizobindingsites.ccg.unam.mx/).