title: Riboswitch diversity and distribution.
abstract: Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands. Some riboswitch classes are very common and are present in bacteria from nearly all lineages, whereas others are exceedingly rare and appear in only a few species whose DNA has been sequenced. Presented herein are the consensus sequences, structural models, and phylogenetic distributions for all validated riboswitch classes. Based on our findings, we predict that there are potentially many thousands of distinct bacterial riboswitch classes remaining to be discovered, but that the rarity of individual undiscovered classes will make it increasingly difficult to find additional examples of this RNA-based sensory and gene control mechanism.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Phillip J
authors.identifier: 0000-0002-8012-1931
authors.initials: PJ
authors.lastname: McCown
authors.affiliation: Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Corbino
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Shira
authors.initials: S
authors.lastname: Stav
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Madeline E
authors.identifier: 0000-0002-6471-4243
authors.initials: ME
authors.lastname: Sherlock
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.|Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA.|Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA.
authors.forename: Ronald R
authors.identifier: 0000-0002-2165-536X
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D001419:Bacteria / Q000235:genetics*; D016384:Consensus Sequence; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D022661:RNA, Untranslated / Q000737:chemistry; D058928:Riboswitch; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated; D058928:Riboswitch
keywords: RNA World; aptamer; coenzyme; ligand; noncoding RNA