title: Challenges of ligand identification for riboswitch candidates.
abstract: Expanding DNA sequence databases and improving methods for comparative analysis are being exploited to identify numerous noncoding RNA elements including riboswitches. Ligands for many riboswitch classes usually can be inferred based on the genomic contexts of representative RNAs, and complex formation or genetic regulation subsequently demonstrated experimentally. However, there are several candidate riboswitches for which ligands have not been identified. In this report, we discuss three of the most compelling riboswitch candidates: the ykkC/ykkD, yybP/ykoY and pfl RNAs. Each of these RNAs is numerous, phylogenetically widespread, and carries features that are hallmarks of metabolite-binding riboswitches, such as a well-conserved aptamer-like structure and apparent interactions with gene regulation elements such as ribosome binding sites or intrinsic transcription termination stems. These RNAs likely represent only a small sampling of the challenging motifs that researchers will encounter as new noncoding RNAs are identified.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Meyer
authors.forename: Ming C
authors.initials: MC
authors.lastname: Hammond
authors.forename: Yasmmyn
authors.initials: Y
authors.lastname: Salinas
authors.forename: Adam
authors.initials: A
authors.lastname: Roth
authors.forename: Narasimhan
authors.initials: N
authors.lastname: Sudarsan
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D052157:Aptamers, Nucleotide / Q000378:metabolism; D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D016384:Consensus Sequence; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D008024:Ligands; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011687:Purines / Q000096:biosynthesis; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D058928:Riboswitch / Q000235:genetics*; D013728:Terminator Regions, Genetic
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D011687:Purines; D012329:RNA, Bacterial; D058928:Riboswitch; C030985:purine