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Barth KM, Hiller DA, Belem de Andrade G, Kavita K, Fernando CM, Breaker RR, Strobel SA. Decoding the Complex Functional Landscape of the ykkC Riboswitches. Biochemistry 2025; 64:1983-1995. [PMID: 40254862 DOI: 10.1021/acs.biochem.4c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
Abstract
The ykkC class is the most diverse riboswitch class to date, recognizing structurally and chemically diverse ligands using only minor changes in sequence and structure. Structural studies have demonstrated how sequence changes correspond to altered specificity; however, they are insufficient to define the requirements for functional riboswitch specificity. Here, we report an extensive mutational analysis of the ppGpp riboswitch to investigate the functional role in transcriptional control for this variant riboswitch. Disruption of the terminator hairpin at a single base pair is sufficient to abolish nearly all function, highlighting the fine-tuning of the terminator hairpin to its corresponding aptamer domain. This fine-tuning has been observed in other riboswitches, suggesting that high levels of tunability may be a common feature of riboswitches. Additionally, mutational analysis shows that the previously reported binding site position, G93, does not necessarily correspond to PRPP-driven function as expected. Phylogenetic analysis of natural riboswitches that contain G93 revealed an additional ykkC subclass that binds to both XMP and GMP. This variant subclass is associated with genes for de novo GMP synthesis. Identification of this variant class provides further evidence for small sequence changes corresponding to altered ligand specificity.
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Affiliation(s)
- Kathryn M Barth
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, United States
| | - David A Hiller
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, United States
| | - Gabriel Belem de Andrade
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, United States
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, United States
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Scott A Strobel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, United States
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Jagodnik J, Tjaden B, Ross W, Gourse R. Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA. Nucleic Acids Res 2023; 51:852-869. [PMID: 36617997 PMCID: PMC9881157 DOI: 10.1093/nar/gkac1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/30/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Ligand-binding RNAs (RNA aptamers) are widespread in the three domains of life, serving as sensors of metabolites and other small molecules. When aptamers are embedded within RNA transcripts as components of riboswitches, they can regulate gene expression upon binding their ligands. Previous methods for biochemical validation of computationally predicted aptamers are not well-suited for rapid screening of large numbers of RNA aptamers. Therefore, we utilized DRaCALA (Differential Radial Capillary Action of Ligand Assay), a technique designed originally to study protein-ligand interactions, to examine RNA-ligand binding, permitting rapid screening of dozens of RNA aptamer candidates concurrently. Using this method, which we call RNA-DRaCALA, we screened 30 ykkC family subtype 2a RNA aptamers that were computationally predicted to bind (p)ppGpp. Most of the aptamers bound both ppGpp and pppGpp, but some strongly favored only ppGpp or pppGpp, and some bound neither. Expansion of the number of biochemically verified sites allowed construction of more accurate secondary structure models and prediction of key features in the aptamers that distinguish a ppGpp from a pppGpp binding site. To demonstrate that the method works with other ligands, we also used RNA DRaCALA to analyze aptamer binding by thiamine pyrophosphate.
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Affiliation(s)
- Jonathan Jagodnik
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Brian Tjaden
- Department of Computer Science, Wellesley College, Wellesley, MA 02481, USA
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
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Hamal Dhakal S, Panchapakesan SSS, Slattery P, Roth A, Breaker RR. Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine. Proc Natl Acad Sci U S A 2022; 119:e2120246119. [PMID: 35622895 PMCID: PMC9295807 DOI: 10.1073/pnas.2120246119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
- Siddhartha Hamal Dhakal
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | | | - Paul Slattery
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT 06520-8103
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
- HHMI, Yale University, New Haven, CT 06520-8103
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103
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Knappenberger A, Hiller D. How Do Bacteria "See" Molecules Inside Themselves? FRONTIERS FOR YOUNG MINDS 2022; 10:686804. [PMID: 36909261 PMCID: PMC9997733 DOI: 10.3389/frym.2022.686804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
RNA, like its close cousin DNA, is used to store information in the cell. Unlike DNA, it is really good at folding up into interesting shapes, which makes it good at lots of other important jobs. Some kinds of RNA, called riboswitches, can sense what is going on inside a cell. Each riboswitch fits a specific small molecule. When the riboswitch and small molecule interact it changes what the cell does. For example, if the small molecule is harmful the cell might start making a protein that will get rid of it. Recently, scientists discovered some riboswitches that look very similar to each other but recognize very different small molecules. We used X-ray crystallography to get pictures of these riboswitches. We saw how changing just one piece of the riboswitch changed which small molecule it recognized. This shows us how RNA can gain new functions as an organism evolves.
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Affiliation(s)
- Andrew Knappenberger
- Scott Strobel lab, Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA.,Address change: Pfizer, Inc, San Diego, CA, USA
| | - David Hiller
- Scott Strobel lab, Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
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Trachman RJ, Ferré-D'Amaré AR. An uncommon [K +(Mg 2+) 2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch. RNA (NEW YORK, N.Y.) 2021; 27:1257-1264. [PMID: 34257148 PMCID: PMC8457001 DOI: 10.1261/rna.078824.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The widespread ykkC-I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the Burkholderia sp. TJI49 ykkC-I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from Dickeya dadantii and Sulfobacillus acidophilus, our Burkholderia structure reveals a chelated K+ ion adjacent to two Mg2+ ions in the guanidine-binding pocket. Thermal melting analysis shows that K+ chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K+(Mg2+)2] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of ykkC-I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K+ chelation in the Burkholderia Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg2+ ion binding in place of the K+ ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among ykkC-I riboswitches.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
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Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology. Biochem Soc Trans 2021; 48:1941-1951. [PMID: 32869842 PMCID: PMC7609027 DOI: 10.1042/bst20191060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
Abstract
Structured cis-regulatory RNAs have evolved across all domains of life, highlighting the utility and plasticity of RNA as a regulatory molecule. Homologous RNA sequences and structures often have similar functions, but homology may also be deceiving. The challenges that derive from trying to assign function to structure and vice versa are not trivial. Bacterial riboswitches, viral and eukaryotic IRESes, CITEs, and 3′ UTR elements employ an array of mechanisms to exert their effects. Bioinformatic searches coupled with biochemical and functional validation have elucidated some shared and many unique ways cis-regulators are employed in mRNA transcripts. As cis-regulatory RNAs are resolved in greater detail, it is increasingly apparent that shared homology can mask the full spectrum of mRNA cis-regulator functional diversity. Furthermore, similar functions may be obscured by lack of obvious sequence similarity. Thus looking beyond homology is crucial for furthering our understanding of RNA-based regulation.
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