1
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Li B, Liu S, Zheng W, Liu A, Yu P, Wu D, Zhou J, Zhang P, Liu C, Lin Q, Ye J, He S, Huang Q, Zhou H, Chen J, Qu L, Yang J. RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators. Nat Biotechnol 2024; 42:119-131. [PMID: 37037902 DOI: 10.1038/s41587-023-01749-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/13/2023] [Indexed: 04/12/2023]
Abstract
A kink-turn (K-turn) is a three-dimensional RNA structure that exists in all three primary phylogenetic domains. In this study, we developed the RIP-PEN-seq method to identify the full-length sequences of RNAs bound by the K-turn binding protein 15.5K and discovered a previously uncharacterized class of RNAs with backward K-turn motifs (bktRNAs) in humans and mice. All bktRNAs share two consensus sequence motifs at their fixed terminal position and have complex folding properties, expression and evolution patterns. We found that a highly conserved bktRNA1 guides the methyltransferase fibrillarin to install RNA methylation of U12 small nuclear RNA in humans. Depletion of bktRNA1 causes global splicing dysregulation of U12-type introns by impairing the recruitment of ZCRB1 to the minor spliceosome. Most bktRNAs regulate the splicing of local introns by interacting with the 15.5K protein. Taken together, our findings characterize a class of small RNAs and uncover another layer of gene expression regulation that involves crosstalk among bktRNAs, RNA splicing and RNA methylation.
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Affiliation(s)
- Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wujian Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Anrui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Peng Yu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Di Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Ping Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiao Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jiayi Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Simeng He
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Qiaojuan Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
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2
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Li M, Deng J, Peng X, Wang J, Wilson TJ, Huang L, Lilley DMJ. Structure and ion-dependent folding of k-junctions. RNA (NEW YORK, N.Y.) 2023; 29:1411-1422. [PMID: 37311599 PMCID: PMC10573300 DOI: 10.1261/rna.079678.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly.
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Affiliation(s)
- Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jia Wang
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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3
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Matoušková E, Dršata T, Pfeifferová L, Šponer J, Réblová K, Lankaš F. RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems. Biophys J 2022; 121:705-714. [PMID: 35122735 PMCID: PMC8943727 DOI: 10.1016/j.bpj.2022.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/23/2021] [Accepted: 01/28/2022] [Indexed: 11/02/2022] Open
Abstract
Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.
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Affiliation(s)
- Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Dršata
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Lucie Pfeifferová
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Kamila Réblová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Centre of Molecular Biology and Genetics, University Hospital Brno, Czech Republic.
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic.
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4
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Liu D, Shao Y, Piccirilli JA, Weizmann Y. Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. SCIENCE ADVANCES 2021; 7:eabf4459. [PMID: 34550747 PMCID: PMC8457670 DOI: 10.1126/sciadv.abf4459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid–based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable one-stranded tiles for x-ray crystallographic determination. We solved three structures to near-atomic resolution: a 2D parallelogram, a 3D nanobracelet unexpectedly formed from an RNA designed for a nanocage, and, eventually, a bona fide 3D nanocage designed with the guidance of the two previous structures. Structural details of their constituent motifs, such as kissing loops, branched kissing loops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed, providing insights into those natural motifs. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanoarchitectural design and suggests a route to investigate RNA motif structures by configuring them into nanoarchitectures.
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Affiliation(s)
- Di Liu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Yossi Weizmann
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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5
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Huang L, Liao X, Li M, Wang J, Peng X, Wilson TJ, Lilley DMJ. Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules. Nucleic Acids Res 2021; 49:5916-5924. [PMID: 33978763 PMCID: PMC8191799 DOI: 10.1093/nar/gkab333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/13/2021] [Accepted: 05/09/2021] [Indexed: 01/25/2023] Open
Abstract
k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1). We have analyzed the ion-dependence of folding of the four k-turns using fluorescence resonance energy transfer, and determined the conformation of two of them using X-ray crystallography. We find that the experimental data fully conform to both the predicted folding and conformational properties. We conclude that our folding rules are robust, and can be applied to new k-turns of unknown characteristics with confidence.
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Affiliation(s)
- Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Xinli Liao
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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6
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Lai SM, Gopalan V. Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs. Methods Mol Biol 2021; 2167:147-169. [PMID: 32712919 DOI: 10.1007/978-1-0716-0716-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kink-turns are important RNA structural modules that facilitate long-range tertiary interactions and form binding sites for members of the L7Ae family of proteins. Present in a wide variety of functional RNAs, kink-turns play key organizational roles in many RNA-based cellular processes, including translation, modification, and tRNA biogenesis. It is important to determine the contribution of kink-turns to the overall architecture of resident RNAs, as these modules dictate ribonucleoprotein (RNP) assembly and function. This chapter describes a site-directed, hydroxyl radical-mediated footprinting strategy that utilizes L7Ae-tethered chemical nucleases to experimentally validate computationally identified kink-turns in any RNA and under a wide variety of conditions. The work plan described here uses the catalytic RNase P RNA as an example to provide a blueprint for using this footprinting method to map RNA-protein interactions in other RNP complexes.
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Affiliation(s)
- Stella M Lai
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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7
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Füchtbauer AF, Wranne MS, Bood M, Weis E, Pfeiffer P, Nilsson JR, Dahlén A, Grøtli M, Wilhelmsson LM. Interbase FRET in RNA: from A to Z. Nucleic Acids Res 2019; 47:9990-9997. [PMID: 31544922 PMCID: PMC6821158 DOI: 10.1093/nar/gkz812] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 01/22/2023] Open
Abstract
Interbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tCO and the non-emissive acceptor tCnitro. The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA structural changes is demonstrated by monitoring the transition from A- to Z-form RNA. Finally, the measured FRET data were compared with theoretical FRET patterns obtained from two previously reported Z-RNA PDB structures, to shed new light on this elusive RNA conformation.
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Affiliation(s)
- Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden.,Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Erik Weis
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden.,Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Anders Dahlén
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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8
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Ashraf S, Huang L, Lilley DMJ. Effect of methylation of adenine N 6 on kink turn structure depends on location. RNA Biol 2019; 16:1377-1385. [PMID: 31234702 PMCID: PMC6779385 DOI: 10.1080/15476286.2019.1630797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 12/22/2022] Open
Abstract
N6-methyladenine is the most common covalent modification in cellular RNA species, with demonstrated functional consequences. At the molecular level this methylation could alter local RNA structure, and/or modulate the binding of specific proteins. We have previously shown that trans-Hoogsteen-sugar (sheared) A:G base pairs can be completely disrupted by methylation, and that this occurs in a sub-set ofD/D k-turn structures. In this work we have investigated to what extent sequence context affects the severity with which inclusion of N6-methyladenine into different A:G base pairs of a standard k-turn affects RNA folding and L7Ae protein binding. We find that local sequence has a major influence, ranging from complete absence of folding and protein binding to a relatively mild effect. We have determined the crystal structure of one of these species both free and protein-bound, showing the environment of the methyl group and the way the modification is accommodated into the k-turn structure.
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Affiliation(s)
- Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, U.K
| | - Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, U.K
| | - David M. J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, U.K
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9
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Abstract
The kink-turn (k-turn) is a widespread structural motif found in functional RNA species. It typically comprises a three-nucleotide bulge followed by tandem trans sugar edge-Hoogsteen G:A base pairs. It introduces a sharp kink into the axis of duplex RNA, juxtaposing the minor grooves. Cross-strand H-bonds form at the interface, accepted by the conserved adenine nucleobases of the G:A basepairs. Alternative acceptors for one of these divides the k-turns into two conformational classes N3 and N1. The base pair that follows the G:A pairs (3b:3n) determines which conformation is adopted by a given k-turn. k-turns often mediate tertiary contacts in folded RNA species and frequently bind proteins. Common k-turn binding proteins include members of the L7Ae family, such as the human 15·5k protein. A recognition helix within these proteins binds in the widened major groove on the outside of the k-turn, that makes specific H-bonds with the conserved guanine nucleobases of the G:A pairs. L7Ae binds with extremely high affinity, and single-molecule data are consistent with folding by conformational selection. The standard, simple k-turn can be elaborated in a variety of ways, that include the complex k-turns and the k-junctions. In free solution in the absence of added metal ions or protein k-turns do not adopt the tightly-kinked conformation. They undergo folding by the binding of proteins, by the formation of tertiary contacts, and some (but not all) will fold on the addition of metal ions. Whether or not folding occurs in the presence of metal ions depends on local sequence, including the 3b:3n position, and the -1b:-1n position (5' to the bulge). In most cases -1b:-1n = C:G, so that the 3b:3n position is critical since it determines both folding properties and conformation. In general, the selection of these sequence matches a given k-turn to its biological requirements. The k-turn structure is now very well understood, to the point at which they can be used as a building block for the formation of RNA nano-objects, including triangles and squares.
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10
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Polaski JT, Kletzien OA, Drogalis LK, Batey RT. A functional genetic screen reveals sequence preferences within a key tertiary interaction in cobalamin riboswitches required for ligand selectivity. Nucleic Acids Res 2019; 46:9094-9105. [PMID: 29945209 PMCID: PMC6158498 DOI: 10.1093/nar/gky539] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/30/2018] [Indexed: 01/14/2023] Open
Abstract
Riboswitches are structured mRNA sequences that regulate gene expression by directly binding intracellular metabolites. Generating the appropriate regulatory response requires the RNA rapidly and stably acquire higher-order structure to form the binding pocket, bind the appropriate effector molecule and undergo a structural transition to inform the expression machinery. These requirements place riboswitches under strong kinetic constraints, likely restricting the sequence space accessible by recurrent structural modules such as the kink turn and the T-loop. Class-II cobalamin riboswitches contain two T-loop modules: one directing global folding of the RNA and another buttressing the ligand binding pocket. While the T-loop module directing folding is highly conserved, the T-loop associated with binding is substantially less so, with no clear consensus sequence. To further understand the functional role of the binding-associated module, a functional genetic screen of a library of riboswitches with the T-loop and its interacting nucleotides was used to build an experimental phylogeny comprised of sequences that possess a wide range of cobalamin-dependent regulatory activity. Our results reveal conservation patterns of the T-loop and its interaction with the binding core that allow for rapid tertiary structure formation and demonstrate its importance for generating strong ligand-dependent repression of mRNA expression.
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Affiliation(s)
- Jacob T Polaski
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Otto A Kletzien
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Lea K Drogalis
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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11
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Bhattacharya S, Jhunjhunwala A, Halder A, Bhattacharyya D, Mitra A. Going beyond base-pairs: topology-based characterization of base-multiplets in RNA. RNA (NEW YORK, N.Y.) 2019; 25:573-589. [PMID: 30792229 PMCID: PMC6467009 DOI: 10.1261/rna.068551.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/18/2019] [Indexed: 05/17/2023]
Abstract
Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of "n" nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-based nomenclature rules for quartets, which are extendable to higher multiplets. We also demonstrate the utility of our approach toward the identification and annotation of higher order RNA multiplets, by investigating the occurrence contexts of selected examples in order to gain insights regarding their probable functional roles.
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Affiliation(s)
- Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF, Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
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12
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Åsman AKM, Curtis BA, Archibald JM. Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae. Genome Biol Evol 2019; 11:1117-1134. [PMID: 30949682 PMCID: PMC6461891 DOI: 10.1093/gbe/evz064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2019] [Indexed: 12/27/2022] Open
Abstract
The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived “nucleomorph” genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2′-O methylation of rRNA (but not snRNA). In B. natans, we found the previously undetected 5S rRNA as well as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18–21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.
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Affiliation(s)
- Anna K M Åsman
- Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada.,Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Bruce A Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada
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13
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Huang L, Ashraf S, Lilley DMJ. The role of RNA structure in translational regulation by L7Ae protein in archaea. RNA (NEW YORK, N.Y.) 2019; 25:60-69. [PMID: 30327333 PMCID: PMC6298567 DOI: 10.1261/rna.068510.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/07/2018] [Indexed: 05/03/2023]
Abstract
A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem-loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem-loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
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14
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Lee J, Park EB, Min J, Sung SE, Jang Y, Shin JS, Chun D, Kim KH, Hwang J, Lee MK, Go YY, Kwon D, Kim M, Kang SJ, Choi BS. Systematic editing of synthetic RIG-I ligands to produce effective antiviral and anti-tumor RNA immunotherapies. Nucleic Acids Res 2018; 46:1635-1647. [PMID: 29373735 PMCID: PMC5829749 DOI: 10.1093/nar/gky039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/17/2018] [Indexed: 12/25/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) recognizes double-stranded viral RNAs (dsRNAs) containing two or three 5' phosphates. A few reports of 5'-PPP-independent RIG-I agonists have emerged, but little is known about the molecular principles underlying their recognition. We recently found that the bent duplex RNA from the influenza A panhandle promoter activates RIG-I even in the absence of a 5'-triphosphate moiety. Here, we report that non-canonical synthetic RNA oligonucleotides containing G-U wobble base pairs that form a bent helix can exert RIG-I-mediated antiviral and anti-tumor effects in a sequence- and site-dependent manner. We present synthetic RNAs that have been systematically modified to enhance their efficacy and we outline the basic principles for engineering RIG-I agonists applicable to immunotherapy.
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Affiliation(s)
- Janghyun Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Eun-Byeol Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jiyoun Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Si-Eun Sung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Yejin Jang
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, South Korea
| | - Jin Soo Shin
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, South Korea
| | - Dongmin Chun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Ki-Hun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jihyun Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Mi-Kyung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Yun Young Go
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, South Korea
| | - Dohyeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Meehyein Kim
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, South Korea
| | - Suk-Jo Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
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15
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Ashraf S, Huang L, Lilley DMJ. Sequence determinants of the folding properties of box C/D kink-turns in RNA. RNA (NEW YORK, N.Y.) 2017; 23:1927-1935. [PMID: 28956757 PMCID: PMC5689011 DOI: 10.1261/rna.063453.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 05/20/2023]
Abstract
Folding properties differ markedly between kink-turns (k-turns) that have different biological functions. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. In contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.
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Affiliation(s)
- Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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16
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Lai LB, Tanimoto A, Lai SM, Chen WY, Marathe IA, Westhof E, Wysocki VH, Gopalan V. A novel double kink-turn module in euryarchaeal RNase P RNAs. Nucleic Acids Res 2017; 45:7432-7440. [PMID: 28525600 PMCID: PMC5499556 DOI: 10.1093/nar/gkx388] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/25/2017] [Indexed: 01/18/2023] Open
Abstract
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns. Mutagenesis of each of the putative K-turns singly or in combination decreased the number of bound L7Ae copies, and either eliminated or changed the L7Ae footprint on the mutant RPRs. In addition, our results support an unprecedented ‘double K-turn’ module in type A and type M archaeal RPR variants.
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Affiliation(s)
- Lien B Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Akiko Tanimoto
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Stella M Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Yi Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ila A Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Westhof
- Université de Strasbourg, Centre National de la Recherche Scientifique, Architecture et Réactivité de l'ARN, UPR9002, F-67084, Strasbourg, France
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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17
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Bayrak CS, Kim N, Schlick T. Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. Nucleic Acids Res 2017; 45:5414-5422. [PMID: 28158755 PMCID: PMC5435971 DOI: 10.1093/nar/gkx045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/22/2017] [Indexed: 12/15/2022] Open
Abstract
Kink turns are widely occurring motifs in RNA, located in internal loops and associated with many biological functions including translation, regulation and splicing. The associated sequence pattern, a 3-nt bulge and G-A, A-G base-pairs, generates an angle of ∼50° along the helical axis due to A-minor interactions. The conserved sequence and distinct secondary structures of kink-turns (k-turn) suggest computational folding rules to predict k-turn-like topologies from sequence. Here, we annotate observed k-turn motifs within a non-redundant RNA dataset based on sequence signatures and geometrical features, analyze bending and torsion angles, and determine distinct knowledge-based potentials with and without k-turn motifs. We apply these scoring potentials to our RAGTOP (RNA-As-Graph-Topologies) graph sampling protocol to construct and sample coarse-grained graph representations of RNAs from a given secondary structure. We present graph-sampling results for 35 RNAs, including 12 k-turn and 23 non k-turn internal loops, and compare the results to solved structures and to RAGTOP results without special k-turn potentials. Significant improvements are observed with the updated scoring potentials compared to the k-turn-free potentials. Because k-turns represent a classic example of sequence/structure motif, our study suggests that other such motifs with sequence signatures and unique geometrical features can similarly be utilized for RNA structure prediction and design.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Namhee Kim
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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18
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Huang L, Ashraf S, Wang J, Lilley DM. Control of box C/D snoRNP assembly by N 6-methylation of adenine. EMBO Rep 2017; 18:1631-1645. [PMID: 28623187 PMCID: PMC5579392 DOI: 10.15252/embr.201743967] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/03/2023] Open
Abstract
N6-methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N6-methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N6-methylation of adenine prevents the formation of trans Hoogsteen-sugar A·G base pairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A·G base pairs (but not Watson-Crick base pairs) are more susceptible to disruption by N6mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared base pair with guanine and mediates a key tertiary interaction.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
| | - David Mj Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK
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19
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Kimura M. Structural basis for activation of an archaeal ribonuclease P RNA by protein cofactors. Biosci Biotechnol Biochem 2017; 81:1670-1680. [PMID: 28715256 DOI: 10.1080/09168451.2017.1353404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5'-leader sequence of precursor tRNA (pre-tRNA) in all phylogenetic domains. We have found that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. Biochemical characterizations over the past 10 years have revealed that PhoPop5 and PhoRpp30 fold into a heterotetramer and cooperate to activate a catalytic domain (C-domain) in PhopRNA, whereas PhoRpp21 and PhoRpp29 form a heterodimer and function together to activate a specificity domain (S-domain) in PhopRNA. PhoRpp38 plays a role in elevation of the optimum temperature of RNase P activity, binding to kink-turn (K-turn) motifs in two stem-loops in PhopRNA. This review describes the structural and functional information on P. horikoshii RNase P, focusing on the structural basis for the PhopRNA activation by the five RNase P proteins.
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Affiliation(s)
- Makoto Kimura
- a Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School , Kyushu University , Fukuoka , Japan
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20
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Gu X, Park SY, Tonelli M, Cornilescu G, Xia T, Zhong D, Schroeder SJ. NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions. J Phys Chem Lett 2016; 7:3841-3846. [PMID: 27631837 PMCID: PMC5762182 DOI: 10.1021/acs.jpclett.6b01465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.
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Affiliation(s)
- Xiaobo Gu
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sun-Young Park
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Marco Tonelli
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Tianbing Xia
- Department of Molecular and Cell Biology, University of Texas, Dallas, Texas 75080, United States
| | - Dongping Zhong
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Susan J. Schroeder
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Corresponding Author.
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21
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Lee MK, Kim HE, Park EB, Lee J, Kim KH, Lim K, Yum S, Lee YH, Kang SJ, Lee JH, Choi BS. Structural features of influenza A virus panhandle RNA enabling the activation of RIG-I independently of 5'-triphosphate. Nucleic Acids Res 2016; 44:8407-16. [PMID: 27288441 PMCID: PMC5041458 DOI: 10.1093/nar/gkw525] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/10/2016] [Accepted: 05/29/2016] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) recognizes specific molecular patterns of viral RNAs for inducing type I interferon. The C-terminal domain (CTD) of RIG-I binds to double-stranded RNA (dsRNA) with the 5'-triphosphate (5'-PPP), which induces a conformational change in RIG-I to an active form. It has been suggested that RIG-I detects infection of influenza A virus by recognizing the 5'-triphosphorylated panhandle structure of the viral RNA genome. Influenza panhandle RNA has a unique structure with a sharp helical bending. In spite of extensive studies of how viral RNAs activate RIG-I, whether the structural elements of the influenza panhandle RNA confer the ability to activate RIG-I signaling has been poorly explored. Here, we investigated the dynamics of the influenza panhandle RNA in complex with RIG-I CTD using NMR spectroscopy and showed that the bending structure of the panhandle RNA negates the requirement of a 5'-PPP moiety for RIG-I activation.
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Affiliation(s)
- Mi-Kyung Lee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea Disease Target Structure Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Hee-Eun Kim
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Eun-Byeol Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Janghyun Lee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Ki-Hun Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Kyungeun Lim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Seoyun Yum
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Young-Hoon Lee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Suk-Jo Kang
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Byong-Seok Choi
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
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22
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Huang L, Lilley DMJ. A quasi-cyclic RNA nano-scale molecular object constructed using kink turns. NANOSCALE 2016; 8:15189-95. [PMID: 27506301 PMCID: PMC5058347 DOI: 10.1039/c6nr05186c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/01/2016] [Indexed: 05/25/2023]
Abstract
k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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23
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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24
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Huang L, Wang J, Lilley DMJ. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function. Nucleic Acids Res 2016; 44:5390-8. [PMID: 27016741 PMCID: PMC4914095 DOI: 10.1093/nar/gkw201] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/08/2016] [Accepted: 03/14/2016] [Indexed: 11/20/2022] Open
Abstract
k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Shi X, Huang L, Lilley DMJ, Harbury PB, Herschlag D. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nat Chem Biol 2016; 12:146-52. [PMID: 26727239 PMCID: PMC4755865 DOI: 10.1038/nchembio.1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022]
Abstract
With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.
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Affiliation(s)
- Xuesong Shi
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Lin Huang
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - David M J Lilley
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Pehr B Harbury
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
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Huang L, Lilley DMJ. The Kink Turn, a Key Architectural Element in RNA Structure. J Mol Biol 2016; 428:790-801. [PMID: 26522935 PMCID: PMC5061560 DOI: 10.1016/j.jmb.2015.09.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/24/2015] [Indexed: 01/03/2023]
Abstract
Kink turns (k-turns) are widespread structural elements that introduce an axial bend into duplex RNA with an included angle of 50°. These mediate key tertiary interactions and bind specific proteins including members of the L7Ae family. The standard k-turn comprises a three-nucleotide bulge followed by G·A and A·G pairs. The RNA kinks by an association of the two minor grooves, stabilized by the formation of a number of key cross-strand hydrogen bonds mostly involving the adenine bases of the G·A and A·G pairs. The k-turns may be divided into two conformational classes, depending on the receptor for one of these hydrogen bonds. k-turns become folded by one of three different processes. Some, but not all, k-turns become folded in the presence of metal ions. Whether or not a given k-turn is folded under these conditions is determined by its sequence. We present a set of rules for the prediction of folding properties and the structure adopted on local sequence.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom.
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Hardin JW, Warnasooriya C, Kondo Y, Nagai K, Rueda D. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET. Nucleic Acids Res 2015; 43:10963-74. [PMID: 26503251 PMCID: PMC4678811 DOI: 10.1093/nar/gkv1011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/24/2015] [Indexed: 11/13/2022] Open
Abstract
In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions as an assembly scaffold as well as a critical catalytic component. Protein binding to the RNA scaffold can induce structural changes, which in turn modulate subsequent binding of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 and U6 snRNAs, Snu13, Prp31, Prp3 and Prp4, seven Sm and seven LSm proteins. We have studied successive binding of all protein components to the snRNA duplex during di-snRNP assembly by electrophoretic mobility shift assay and accompanying conformational changes in the U4/U6 RNA 3-way junction by single-molecule FRET. Stems I and II of the duplex were found to co-axially stack in free RNA and function as a rigid scaffold during the entire assembly, but the U4 snRNA 5' stem-loop adopts alternative orientations each stabilized by Prp31 and Prp3/4 binding accounting for altered Prp3/4 binding affinities in presence of Prp31.
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Affiliation(s)
- John W Hardin
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chandani Warnasooriya
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Yasushi Kondo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Rueda
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
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28
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Wostenberg C, Ceres P, Polaski JT, Batey RT. A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol 2015; 427:3473-3490. [PMID: 26343759 DOI: 10.1016/j.jmb.2015.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/24/2023]
Abstract
RNA folding in vivo is significantly influenced by transcription, which is not necessarily recapitulated by Mg(2+)-induced folding of the corresponding full-length RNA in vitro. Riboswitches that regulate gene expression at the transcriptional level are an ideal system for investigating this aspect of RNA folding as ligand-dependent termination is obligatorily co-transcriptional, providing a clear readout of the folding outcome. The folding of representative members of the SAM-I family of riboswitches has been extensively analyzed using approaches focusing almost exclusively upon Mg(2+) and/or S-adenosylmethionine (SAM)-induced folding of full-length transcripts of the ligand binding domain. To relate these findings to co-transcriptional regulatory activity, we have investigated a set of structure-guided mutations of conserved tertiary architectural elements of the ligand binding domain using an in vitro single-turnover transcriptional termination assay, complemented with phylogenetic analysis and isothermal titration calorimetry data. This analysis revealed a conserved internal loop adjacent to the SAM binding site that significantly affects ligand binding and regulatory activity. Conversely, most single point mutations throughout key conserved features in peripheral tertiary architecture supporting the SAM binding pocket have relatively little impact on riboswitch activity. Instead, a secondary structural element in the peripheral subdomain appears to be the key determinant in observed differences in regulatory properties across the SAM-I family. These data reveal a highly coupled network of tertiary interactions that promote high-fidelity co-transcriptional folding of the riboswitch but are only indirectly linked to regulatory tuning.
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Affiliation(s)
- Christopher Wostenberg
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Pablo Ceres
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Jacob T Polaski
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA.
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29
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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Zhang J, Ferré-D'Amaré AR. Structure and mechanism of the T-box riboswitches. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:419-33. [PMID: 25959893 DOI: 10.1002/wrna.1285] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 01/11/2023]
Abstract
In most Gram-positive bacteria, including many clinically devastating pathogens from genera such as Bacillus, Clostridium, Listeria, and Staphylococcus, T-box riboswitches sense and regulate intracellular availability of amino acids through a multipartite messenger RNA (mRNA)-transfer RNA (tRNA) interaction. The T-box mRNA leaders respond to nutrient starvation by specifically binding cognate tRNAs and sensing whether the bound tRNA is aminoacylated, as a proxy for amino acid availability. Based on this readout, T-boxes direct a transcriptional or translational switch to control the expression of downstream genes involved in various aspects of amino acid metabolism: biosynthesis, transport, aminoacylation, transamidation, and so forth. Two decades after its discovery, the structural and mechanistic underpinnings of the T-box riboswitch were recently elucidated, producing a wealth of insights into how two structured RNAs can recognize each other with robust affinity and exquisite selectivity. The T-box paradigm exemplifies how natural noncoding RNAs can interact not just through sequence complementarity but can add molecular specificity by precisely juxtaposing RNA structural motifs, exploiting inherently flexible elements and the biophysical properties of post-transcriptional modifications, ultimately achieving a high degree of shape complementarity through mutually induced fit. The T-box also provides a proof-of-principle that compact RNA domains can recognize minute chemical changes (such as tRNA aminoacylation) on another RNA. The unveiling of the structure and mechanism of the T-box system thus expands our appreciation of the range of capabilities and modes of action of structured noncoding RNAs, and hints at the existence of networks of noncoding RNAs that communicate through both, structural and sequence specificity.
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Affiliation(s)
- Jinwei Zhang
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
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31
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Halder A, Bhattacharya S, Datta A, Bhattacharyya D, Mitra A. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs. Phys Chem Chem Phys 2015; 17:26249-63. [DOI: 10.1039/c5cp04894j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ab initio computations and bioinformatics studies reveal that stabilization of some important RNA structural motifs might involve N7 protonation of guanine.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | | | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
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