Journal
RNA BIOLOGY
Volume 15, Issue 3, Pages 377-390Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/15476286.2017.1403002
Keywords
Aptamer; comparative sequence analysis; gene regulation; metabolite; noncoding RNA; signaling molecule
Categories
Funding
- National Institute of General Medical Sciences (NIGMS) [GM022778, DE022340]
- NIH [T32GM007223, F32GM116426]
- National Science Foundation Graduate Research Fellowship Program [IDGE1122492]
- HHMI Investigator support
- Division Of Physics
- Direct For Mathematical & Physical Scien [1522467] Funding Source: National Science Foundation
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Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn2+, and the metabolites guanidine and PRPP. Such studies also yield useful linkages between the ligands sensed by the riboswitches and numerous biochemical pathways. In the current report, we describe the known characteristics of 30 distinct classes of orphan riboswitch candidates - some of which have remained unsolved for over a decade. We also discuss the prospects for uncovering novel biological insights via focused studies on these RNAs. Lastly, we make recommendations for experimental objectives along the path to finding ligands for these mysterious RNAs.
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