Challenges of ligand identification for the second wave of orphan riboswitch candidates
Autor: | Shira Stav, Kenneth I Brewer, Kimberly A. Harris, Gayan Mirihana Arachchilage, Sarah N. Malkowski, Etienne B Greenlee, Ruben M Atilho, Kevin R. Perkins, Ronald R. Breaker, Madeline E. Sherlock |
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Rok vydání: | 2018 |
Předmět: |
0301 basic medicine
Riboswitch Models Molecular Aptamer Amino Acid Motifs Computational biology Biology Bioinformatics Ligands 03 medical and health sciences Yeasts RNA Messenger Molecular Biology 030102 biochemistry & molecular biology Bacteria Ligand RNA Fungal Cell Biology Experimental validation Aptamers Nucleotide Non-coding RNA RNA Bacterial 030104 developmental biology Nucleic Acid Conformation Identification (biology) Function (biology) Research Paper |
DOI: | 10.6084/m9.figshare.5598436.v2 |
Popis: | 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. |
Databáze: | OpenAIRE |
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