期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2022
卷号：119
期号：22
DOI：10.1073/pnas.2120246119
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance
Numerous purines and their metabolic derivatives must be monitored for proper control of relevant metabolic pathways. In certain bacteria, some metabolic steps related to purine production or degradation are catalyzed by proteins whose production is under direct regulatory control by purine-sensing riboswitches. Four riboswitch classes selective for guanine, adenine, and 2′-deoxyguanosine (two classes) reported previously exploit a common architecture involving a three-stem junction. Here, we describe three additional classes based on this same scaffold that sense xanthine, guanine, or 2′-deoxyguanosine. Thus, some riboswitches can diversify their ligand-sensing and gene-control functions without the need to evolve entirely novel structures, which highlights a capability that could have also been exploited by ancient forms of life during the RNA World.
The aptamer portions of previously reported riboswitch classes that sense guanine, adenine, or 2′-deoxyguanosine are formed by a highly similar three-stem junction with distinct nucleotide sequences in the regions joining the stems. The nucleotides in these joining regions form the major features of the selective ligand-binding pocket for each aptamer. Previously, we reported the existence of additional, rare variants of the predominant guanine-sensing riboswitch class that carry nucleotide differences in the ligand-binding pocket, suggesting that these RNAs have further diversified their structures and functions. Herein, we report the discovery and analysis of three naturally occurring variants of guanine riboswitches that are narrowly distributed across Firmicutes. These RNAs were identified using comparative sequence analysis methods, which also revealed that some of the gene associations for these variants are atypical for guanine riboswitches or their previously known natural variants. Binding assays demonstrate that the newfound variant riboswitch representatives recognize xanthine, guanine, or 2′-deoxyguanosine, with the guanine class exhibiting greater discrimination against related purines than the more common guanine riboswitch class reported previously. These three additional variant classes, together with the four previously discovered riboswitch classes that employ the same three-stem junction architecture, reveal how a simple structural framework can be diversified to expand the range of purine-based ligands sensed by RNA.
