title: Conserved regulatory motifs in bacteria: riboswitches and beyond.
abstract: We present a computational approach that identifies regulatory elements conserved across phylogenetically distant organisms. Intergenic regulatory regions were clustered by orthology of the adjacent genes, and an iterative process was applied to search for significant motifs, enabling new elements of the putative regulon to be added in each cycle. With this approach, we identified highly conserved riboswitches and the Gram positive T-box. Interestingly, we identified many other regulatory systems that appear to depend on conserved RNA structures.
authors.affiliation: Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, 62210 Morelos, México.
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
authors.forename: Nancy
authors.initials: N
authors.lastname: Ontiveros-Palacios
authors.forename: Ricardo
authors.initials: R
authors.lastname: Ciria
authors.forename: Enrique
authors.initials: E
authors.lastname: Merino
mesh_terms: D001419:Bacteria / Q000235:genetics*; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics*; D030541:Databases, Genetic; D005809:Genes, Regulator / Q000235:genetics*; D010802:Phylogeny; D012313:RNA / Q000235:genetics*
chemical_list: D012313:RNA