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PMID: 28396576 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Riboswitch diversity and distribution.

RNA (New York, N.Y.) ·Vol. 23 ·No. 7 ·2017-00-00 ·Pages 995-1011

McCown PJ, Corbino KA, Stav S, Sherlock ME, Breaker RR

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.

Keywords
RNA World aptamer coenzyme ligand noncoding RNA
MeSH Terms
Bacteria/genetics Consensus Sequence Models, Molecular Nucleic Acid Conformation Phylogeny RNA, Bacterial/chemistry,genetics RNA, Untranslated/chemistry Riboswitch Sequence Analysis, RNA/methods
Chemicals
RNA, Bacterial RNA, Untranslated Riboswitch
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
McCown Phillip J ORCID
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
Corbino Keith A
Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA.
Stav Shira
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
Sherlock Madeline E ORCID
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA.
Breaker Ronald R ORCID
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.
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Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1469-9001
DOI
10.1261/rna.061234.117
Published
2017-00-00
Epub
2017-00-10
Pages
995-1011
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC5473149
Subset
IM
Grants
NIGMS NIH HHS · T32 GM007223 · United States
Howard Hughes Medical Institute · United States
NCRR NIH HHS · S10 RR019895 · United States
NIGMS NIH HHS · P01 GM022778 · United States
NIGMS NIH HHS · T32 GM007499 · United States
External Links
PubMed source DOI: 10.1261/rna.061234.117 PMC Full Text View journal details
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