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Susorov D, Echeverria D, Khvorova A, Korostelev AA. mRNA-specific readthrough of nonsense codons by antisense oligonucleotides (R-ASOs). Nucleic Acids Res 2024:gkae624. [PMID: 39011883 DOI: 10.1093/nar/gkae624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/14/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
Nonsense mutations account for >10% of human genetic disorders, including cystic fibrosis, Alagille syndrome, and Duchenne muscular dystrophy. A nonsense mutation results in the expression of a truncated protein, and therapeutic strategies aim to restore full-length protein expression. Most strategies under development, including small-molecule aminoglycosides, suppressor tRNAs, or the targeted degradation of termination factors, lack mRNA target selectivity and may poorly differentiate between nonsense and normal stop codons, resulting in off-target translation errors. Here, we demonstrate that antisense oligonucleotides can stimulate readthrough of disease-causing nonsense codons, resulting in high yields of full-length protein in mammalian cellular lysate. Readthrough efficiency depends on the sequence context near the stop codon and on the precise targeting position of an oligonucleotide, whose interaction with mRNA inhibits peptide release to promote readthrough. Readthrough-inducing antisense oligonucleotides (R-ASOs) enhance the potency of non-specific readthrough agents, including aminoglycoside G418 and suppressor tRNA, enabling a path toward target-specific readthrough of nonsense mutations in CFTR, JAG1, DMD, BRCA1 and other mutant genes. Finally, through systematic chemical engineering, we identify heavily modified fully functional R-ASO variants, enabling future therapeutic development.
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Affiliation(s)
- Denis Susorov
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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2
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Rodríguez-Vargas A, Collins K. Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein. Nucleic Acids Res 2024; 52:6571-6585. [PMID: 38499488 PMCID: PMC11194090 DOI: 10.1093/nar/gkae194] [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: 12/26/2023] [Revised: 02/08/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
Eukaryotic retrotransposons encode a reverse transcriptase that binds RNA to template DNA synthesis. The ancestral non-long terminal repeat (non-LTR) retrotransposons encode a protein that performs target-primed reverse transcription (TPRT), in which the nicked genomic target site initiates complementary DNA (cDNA) synthesis directly into the genome. The best understood model system for biochemical studies of TPRT is the R2 protein from the silk moth Bombyx mori. The R2 protein selectively binds the 3' untranslated region of its encoding RNA as template for DNA insertion to its target site in 28S ribosomal DNA. Here, binding and TPRT assays define RNA contributions to RNA-protein interaction, template use for TPRT and the fidelity of template positioning for TPRT cDNA synthesis. We quantify both sequence and structure contributions to protein-RNA interaction. RNA determinants of binding affinity overlap but are not equivalent to RNA features required for TPRT and its fidelity of template positioning for full-length TPRT cDNA synthesis. Additionally, we show that a previously implicated RNA-binding protein surface of R2 protein makes RNA binding affinity dependent on the presence of two stem-loops. Our findings inform evolutionary relationships across R2 retrotransposon RNAs and are a step toward understanding the mechanism and template specificity of non-LTR retrotransposon mobility.
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Affiliation(s)
- Anthony Rodríguez-Vargas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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3
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Gordon BH, Blackford N, Silvers R. Deciphering the Binding of 5' Stem Loop RNA to the La Domain of Human LARP6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598414. [PMID: 38915490 PMCID: PMC11195269 DOI: 10.1101/2024.06.11.598414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
La-related protein 6 regulates the highly organized biosynthesis of type I procollagen polypeptides and affects proper assembly of procollagen peptides into heterotrimers of type I procollagen. LARP6-mediated regulation of collagen biosynthesis is mediated through interaction with the 5' stem loop motif found in type I and III collagen mRNA. Recent studies highlight the involvement of HsLARP6 in fibroproliferative diseases and its potential as a target for therapeutic intervention. The intrinsic instability of the La domain of HsLARP6 hampers studies probing the molecular basis of biologically- and disease-relevant structure-function relationship, particularly when high concentrations are required. This work provides detailed procedures to produce milligram amounts of RNase-free and functional La domain of HsLARP6. Furthermore, we investigated the effect of the construct length as well as RNA binding on protein stability. N- and C-terminal extensions greatly impact stability based on interactions with the core domain and modulation of the pI. When in complex with its cognate 5'SL RNA, the La domain shows unprecedented stability compared to the aggregation-prone unbound state. The protein-RNA complex remains stable for at least 50x longer than the unbound state, under identical conditions, likely due to a global change in conformational plasticity upon RNA binding. These results provide a foundation for further studies of the molecular recognition of 5'SL by HsLARP6 as well as a platform for refining potential antifibrotic therapeutics.
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Affiliation(s)
- Blaine H. Gordon
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Nolan Blackford
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Robert Silvers
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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4
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Weber F, Motzkus NA, Brandl L, Möhler M, Alempijevic A, Jäschke A. Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes. Nucleic Acids Res 2024; 52:5438-5450. [PMID: 38716860 PMCID: PMC11162767 DOI: 10.1093/nar/gkae353] [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: 06/13/2023] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 06/11/2024] Open
Abstract
In recent years, several noncanonical RNA caps derived from cofactors and metabolites have been identified. Purine-containing RNA caps have been extensively studied, with multiple decapping enzymes identified and efficient capture and sequencing protocols developed for nicotinamide adenine dinucleotide (NAD)-RNA, which allowed for a stepwise elucidation of capping functions. Despite being identified as an abundant noncanonical RNA-cap, UDP-sugar-capped RNA remains poorly understood, which is partly due to its complex in vitro preparation. Here, we describe a scalable synthesis of sugar-capped uridine-guanosine dinucleotides from readily available protected building blocks and their enzymatic conversion into several cell wall precursor-capped dinucleotides. We employed these capped dinucleotides in T7 RNA polymerase-catalyzed in vitro transcription reactions to efficiently generate RNAs capped with uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), its N-azidoacetyl derivative UDP-GlcNAz, and various cell wall precursors. We furthermore identified four enzymes capable of processing UDP-GlcNAc-capped RNA in vitro: MurA, MurB and MurC from Escherichia coli can sequentially modify the sugar-cap structure and were used to introduce a bioorthogonal, clickable moiety, and the human Nudix hydrolase Nudt5 was shown to efficiently decap UDP-GlcNAc-RNA. Our findings underscore the importance of efficient synthetic methods for capped model RNAs. Additionally, we provide useful enzymatic tools that could be utilized in the development and application of UDP-GlcNAc capture and sequencing protocols. Such protocols are essential for deepening our understanding of the widespread yet enigmatic GlcNAc modification of RNA and its physiological significance.
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Affiliation(s)
- Frederik Weber
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Nikolas Alexander Motzkus
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Leona Brandl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Marvin Möhler
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Andrijana Alempijevic
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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5
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Zhang Y, Xu Z, Xiao Y, Jiang H, Zuo X, Li X, Fang X. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST. Nat Commun 2024; 15:4206. [PMID: 38760339 PMCID: PMC11101630 DOI: 10.1038/s41467-024-48478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore-quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric "A"-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore-quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST-tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.
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Affiliation(s)
- Yufan Zhang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China
| | - Zhonghe Xu
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Xiao
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haodong Jiang
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Xing Li
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Xianyang Fang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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6
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Kompatscher M, Bartosik K, Erharter K, Plangger R, Juen F, Kreutz C, Micura R, Westhof E, Erlacher M. Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons. Nucleic Acids Res 2024; 52:1374-1386. [PMID: 38050960 PMCID: PMC10853795 DOI: 10.1093/nar/gkad1136] [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: 09/13/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
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Affiliation(s)
- Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Raphael Plangger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Fabian Sebastian Juen
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Matthias D Erlacher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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7
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Tidwell ED, Kilde IR, Leskaj S, Koutmos M. Fluorescent Ligand Equilibrium Displacement: A High-Throughput Method for Identification of FMN Riboswitch-Binding Small Molecules. Int J Mol Sci 2024; 25:735. [PMID: 38255809 PMCID: PMC11154562 DOI: 10.3390/ijms25020735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Antibiotic resistance remains a pressing global concern, with most antibiotics targeting the bacterial ribosome or a limited range of proteins. One class of underexplored antibiotic targets is bacterial riboswitches, structured RNA elements that regulate key biosynthetic pathways by binding a specific ligand. We developed a methodology termed Fluorescent Ligand Equilibrium Displacement (FLED) to rapidly discover small molecules that bind the flavin mononucleotide (FMN) riboswitch. FLED leverages intrinsically fluorescent FMN and the quenching effect on RNA binding to create a label-free, in vitro method to identify compounds that can bind the apo population of riboswitch in a system at equilibrium. The response difference between known riboswitch ligands and controls demonstrates the robustness of the method for high-throughput screening. An existing drug discovery library that was screened using FLED resulted in a final hit rate of 0.67%. The concentration response of each hit was determined and revealed a variety of approximate effective concentration values. Our preliminary screening data support the use of FLED to identify small molecules for medicinal chemistry development as FMN riboswitch-targeted antibiotic compounds. This robust, label-free, and cell-free method offers a strong alternative to other riboswitch screening methods and can be adapted to a variety of laboratory setups.
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Affiliation(s)
| | - Ingrid R. Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Markos Koutmos
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA;
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
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8
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Haslecker R, Pham VV, Glänzer D, Kreutz C, Dayie TK, D'Souza VM. Extending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA. Nat Commun 2023; 14:8422. [PMID: 38110450 PMCID: PMC10728113 DOI: 10.1038/s41467-023-44254-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
RNA performs a wide range of functions regulated by its structure, dynamics, and often post-transcriptional modifications. While NMR is the leading method for understanding RNA structure and dynamics, it is currently limited by the inability to reduce spectral crowding by efficient segmental labeling. Furthermore, because of the challenging nature of RNA chemistry, the tools being developed to introduce site-specific modifications are increasingly complex and laborious. Here we use a previously designed Tgo DNA polymerase mutant to present SegModTeX - a versatile, one-pot, copy-and-paste approach to address these challenges. By precise, stepwise construction of a diverse set of RNA molecules, we demonstrate the technique to be superior to RNA polymerase driven and ligation methods owing to its substantially high yield, fidelity, and selectivity. We also show the technique to be useful for incorporating some fluorescent- and a wide range of other probes, which significantly extends the toolbox of RNA biology in general.
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Affiliation(s)
- Raphael Haslecker
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Vincent V Pham
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Glänzer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20782, USA
| | - Victoria M D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
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9
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Li H, Zhu D, Yang Y, Ma Y, Chen Y, Xue P, Chen J, Qin M, Xu D, Cai C, Cheng H. Restricted tRNA methylation by intermolecular disulfide bonds in DNMT2/TRDMT1. Int J Biol Macromol 2023; 251:126310. [PMID: 37579906 DOI: 10.1016/j.ijbiomac.2023.126310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Reportedly, DNMT2/TRDMT1 mainly methylates tRNAs at C38 and prevents them from the cleavage under stress. It also plays an essential role in the survival and physiological homeostasis of organisms. Nevertheless, DNMT2/TRDMT1 exhibits much weaker tRNA methylation activity in vitro than other tRNA methyltransferases, TrmD and Trm5. Here, we explored the restricted tRNA methylation mechanism by DNMT2/TRDMT1. In the current study, the optimized buffer C at 37 °C was the best condition for DNMT2/TRDMT1 activation. Of note, Dithiothreitol (DTT) was an indispensable component for this enzyme catalysis. Moreover, reductants took similar effects on the conformation change and oligomeric formation of DNMT2/TRDMT1. Ultimately, LC-MS/MS result revealed that C292-C292 and C292-C287 were predominant intermolecular disulfide bonds in recombinant DNMT2/TRDMT1. Notably, DNMT2/TRDMT1 existed primarily as dimers via intermolecular disulfide bonds C79-C24, C292-C292, and C222-C24 in HEK293T cells. GSSG stress enhanced tRNA methylation level in the early stage of stress, whereas the DNMT2/TRDMT1 activity might be unfavorable along with this enzyme accumulation in the nucleus. Excitingly, GSH stress downregulated the DNMT2/TRDMT1 expression and promoted tRNA methylation in cells, probably through breaking intermolecular disulfide bonds in this enzyme. Thus, our findings demonstrated restricted tRNA methylation by disulfide bonds in DNMT2/TRDMT1, and will provide important implications for redox stress related-diseases.
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Affiliation(s)
- Huari Li
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China.
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yapeng Yang
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yunfei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yong Chen
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Pingfang Xue
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Juan Chen
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Mian Qin
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Dandan Xu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Chao Cai
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Hongjing Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
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10
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Nouri S, Boudet J, Dreher-Teo H, Allain FHT, Glockshuber R, Salmon L, Giese C. Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy. Angew Chem Int Ed Engl 2023; 62:e202305120. [PMID: 37248171 DOI: 10.1002/anie.202305120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
In NMR spectroscopy, residual dipolar couplings (RDCs) have emerged as one of the most exquisite probes of biological structure and dynamics. The measurement of RDCs relies on the partial alignment of the molecule of interest, for example by using a liquid crystal as a solvent. Here, we establish bacterial type 1 pili as an alternative liquid-crystalline alignment medium for the measurement of RDCs. To achieve alignment at pilus concentrations that allow for efficient NMR sample preparation, we elongated wild-type pili by recombinant overproduction of the main structural pilus subunit. Building on the extraordinary stability of type 1 pili against spontaneous dissociation and unfolding, we show that the medium is compatible with challenging experimental conditions such as high temperature, the presence of detergents, organic solvents or very acidic pH, setting it apart from most established alignment media. Using human ubiquitin, HIV-1 TAR RNA and camphor as spectroscopic probes, we demonstrate the applicability of the medium for the determination of RDCs of proteins, nucleic acids and small molecules. Our results show that type 1 pili represent a very useful alternative to existing alignment media and may readily assist the characterization of molecular structure and dynamics by NMR.
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Affiliation(s)
- Sirine Nouri
- Centre de RMN à Très Hauts Champs, CNRS, ENSL, UCBL, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Hiang Dreher-Teo
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, CNRS, ENSL, UCBL, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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11
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Imai S, Suzuki H, Fujiyoshi Y, Shimada I. Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor. Nat Commun 2023; 14:4977. [PMID: 37640715 PMCID: PMC10462655 DOI: 10.1038/s41467-023-40582-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/27/2023] [Indexed: 08/31/2023] Open
Abstract
Many RNA viruses employ internal ribosome entry sites (IRESs) in their genomic RNA to commandeer the host's translational machinery for replication. The IRES from encephalomyocarditis virus (EMCV) interacts with eukaryotic translation initiation factor 4 G (eIF4G), recruiting the ribosomal subunit for translation. Here, we analyze the three-dimensional structure of the complex composed of EMCV IRES, the HEAT1 domain fragment of eIF4G, and eIF4A, by cryo-electron microscopy. Two distinct eIF4G-interacting domains on the IRES are identified, and complex formation changes the angle therebetween. Further, we explore the dynamics of these domains by using solution NMR spectroscopy, revealing conformational equilibria in the microsecond to millisecond timescale. In the lowly-populated conformations, the base-pairing register of one domain is shifted with the structural transition of the three-way junction, as in the complex structure. Our study provides insights into the viral RNA's sophisticated strategy for optimal docking to hijack the host protein.
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Affiliation(s)
- Shunsuke Imai
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Hiroshi Suzuki
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Ichio Shimada
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
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12
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Schweibenz BD, Solotchi M, Hanpude P, Devarkar S, Patel S. RIG-I recognizes metabolite-capped RNAs as signaling ligands. Nucleic Acids Res 2023; 51:8102-8114. [PMID: 37326006 PMCID: PMC10450190 DOI: 10.1093/nar/gkad518] [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: 10/06/2022] [Accepted: 06/12/2023] [Indexed: 06/17/2023] Open
Abstract
The innate immune receptor RIG-I recognizes 5'-triphosphate double-stranded RNAs (5' PPP dsRNA) as pathogenic RNAs. Such RNA-ends are present in viral genomes and replication intermediates, and they activate the RIG-I signaling pathway to produce a potent interferon response essential for viral clearance. Endogenous mRNAs cap the 5' PPP-end with m7G and methylate the 2'-O-ribose to evade RIG-I, preventing aberrant immune responses deleterious to the cell. Recent studies have identified RNAs in cells capped with metabolites such as NAD+, FAD and dephosphoCoA. Whether RIG-I recognizes these metabolite-capped RNAs has not been investigated. Here, we describe a strategy to make metabolite-capped RNAs free from 5' PPP dsRNA contamination, using in vitro transcription initiated with metabolites. Mechanistic studies show that metabolite-capped RNAs have a high affinity for RIG-I, stimulating the ATPase activity at comparable levels to 5' PPP dsRNA. Cellular signaling assays show that the metabolite-capped RNAs potently stimulate the innate antiviral immune response. This demonstrates that RIG-I can tolerate diphosphate-linked, capped RNAs with bulky groups at the 5' RNA end. This novel class of RNAs that stimulate RIG-I signaling may have cellular roles in activating the interferon response and may be exploited with proper functionalities for RIG-I-related RNA therapeutics.
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Affiliation(s)
- Brandon D Schweibenz
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at the Robert Wood Johnson Medical School of Rutgers University, USA
| | - Mihai Solotchi
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at the Robert Wood Johnson Medical School of Rutgers University, USA
| | - Pranita Hanpude
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Swapnil C Devarkar
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at the Robert Wood Johnson Medical School of Rutgers University, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
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13
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DasGupta S, Zhang S, Szostak JW. Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly. ACS CENTRAL SCIENCE 2023; 9:1670-1678. [PMID: 37637737 PMCID: PMC10451029 DOI: 10.1021/acscentsci.3c00547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Indexed: 08/29/2023]
Abstract
Catalytic RNAs or ribozymes are considered to be central to primordial biology. Most ribozymes require moderate to high concentrations of divalent cations such as Mg2+ to fold into their catalytically competent structures and perform catalysis. However, undesirable effects of Mg2+ such as hydrolysis of reactive RNA building blocks and degradation of RNA structures are likely to undermine its beneficial roles in ribozyme catalysis. Further, prebiotic cell-like compartments bounded by fatty acid membranes are destabilized in the presence of Mg2+, making ribozyme function inside prebiotically relevant protocells a significant challenge. Therefore, we sought to identify conditions that would enable ribozymes to retain activity at low concentrations of Mg2+. Inspired by the ability of ribozymes to function inside crowded cellular environments with <1 mM free Mg2+, we tested molecular crowding as a potential mechanism to lower the Mg2+ concentration required for ribozyme-catalyzed RNA assembly. Here, we show that the ribozyme-catalyzed ligation of phosphorimidazolide RNA substrates is significantly enhanced in the presence of the artificial crowding agent polyethylene glycol. We also found that molecular crowding preserves ligase activity under denaturing conditions such as alkaline pH and the presence of urea. Additionally, we show that crowding-induced stimulation of RNA-catalyzed RNA assembly is not limited to phosphorimidazolide ligation but extends to the RNA-catalyzed polymerization of nucleoside triphosphates. RNA-catalyzed RNA ligation is also stimulated by the presence of prebiotically relevant small molecules such as ethylene glycol, ribose, and amino acids, consistent with a role for molecular crowding in primordial ribozyme function and more generally in the emergence of RNA-based cellular life.
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Affiliation(s)
- Saurja DasGupta
- Department
of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Howard
Hughes Medical Institute, Massachusetts General
Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Stephanie Zhang
- Department
of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Jack W. Szostak
- Department
of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Howard
Hughes Medical Institute, Massachusetts General
Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
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14
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Liu T, Patel S, Pyle AM. Making RNA: Using T7 RNA polymerase to produce high yields of RNA from DNA templates. Methods Enzymol 2023; 691:185-207. [PMID: 37914446 DOI: 10.1016/bs.mie.2023.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
RNA is playing an ever-growing role in molecular biology and biomedicine due to the many ways it influences gene expression and its increasing use in modern therapeutics. Hence, production of RNA molecules in large quantity and high purity has become essential for advancing basic scientific research and for developing next-generation therapeutics. T7 RNA polymerase (RNAP) is a DNA-dependent RNA polymerase of bacteriophage origin and it is the most widely-utilized tool enzyme for producing RNA. Here we describe a set of robust methods for in vitro transcribing RNA molecules from DNA templates using T7 RNAP, along with a set of subsequent RNA purification schemes. In the first part of this chapter, we provide the general method for T7 RNAP-based in vitro transcription and technical notes for troubleshooting failed or inefficient transcription. We also provide modified protocols for preparing specialized RNA transcripts. In the second part, we provide two purification methods using either gel-based denaturing purification or size exclusion column-based non-denaturing purification for isolating high-purity RNA products from transcription reaction mixtures and preparing them for downstream applications. This chapter is designed to provide researchers with versatile ways to efficiently generate RNA molecules of interest and a troubleshooting guide should they encounter problems while working with in vitro transcription using T7 RNAP.
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Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Shivali Patel
- Department of Molecular Biophysics and Biochemistry, New Haven, CT, United States
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States; Howard Hughes Medical Institute, Yale University, New Haven, CT, United States.
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15
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Watson ZL, Knudson IJ, Ward FR, Miller SJ, Cate JHD, Schepartz A, Abramyan AM. Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates. Nat Chem 2023:10.1038/s41557-023-01226-w. [PMID: 37308707 DOI: 10.1038/s41557-023-01226-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/28/2023] [Indexed: 06/14/2023]
Abstract
As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi-Dunitz angle of 76-115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Isaac J Knudson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Fred R Ward
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA
| | - Scott J Miller
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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16
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Fricke R, Swenson CV, Roe LT, Hamlish NX, Shah B, Zhang Z, Ficaretta E, Ad O, Smaga S, Gee CL, Chatterjee A, Schepartz A. Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-α-amino acids in vitro and in vivo. Nat Chem 2023:10.1038/s41557-023-01224-y. [PMID: 37264106 DOI: 10.1038/s41557-023-01224-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.
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Affiliation(s)
- Riley Fricke
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Cameron V Swenson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Leah Tang Roe
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Noah Xue Hamlish
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Bhavana Shah
- Process Development, Amgen, Thousand Oaks, CA, USA
| | | | - Elise Ficaretta
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Sarah Smaga
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Abhishek Chatterjee
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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17
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Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
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Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
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18
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Ma X, Bakhtina M, Shulgina I, Cantara WA, Kuzmishin Nagy A, Goto Y, Suga H, Foster MP, Musier-Forsyth K. Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain. Nucleic Acids Res 2023; 51:3988-3999. [PMID: 36951109 PMCID: PMC10164551 DOI: 10.1093/nar/gkad192] [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: 11/30/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
High fidelity tRNA aminoacylation by aminoacyl-tRNA synthetases is essential for cell viability. ProXp-ala is a trans-editing protein that is present in all three domains of life and is responsible for hydrolyzing mischarged Ala-tRNAPro and preventing mistranslation of proline codons. Previous studies have shown that, like bacterial prolyl-tRNA synthetase, Caulobacter crescentus ProXp-ala recognizes the unique C1:G72 terminal base pair of the tRNAPro acceptor stem, helping to ensure deacylation of Ala-tRNAPro but not Ala-tRNAAla. The structural basis for C1:G72 recognition by ProXp-ala is still unknown and was investigated here. NMR spectroscopy, binding, and activity assays revealed two conserved residues, K50 and R80, that likely interact with the first base pair, stabilizing the initial protein-RNA encounter complex. Modeling studies are consistent with direct interaction between R80 and the major groove of G72. A third key contact between A76 of tRNAPro and K45 of ProXp-ala was essential for binding and accommodating the CCA-3' end in the active site. We also demonstrated the essential role that the 2'OH of A76 plays in catalysis. Eukaryotic ProXp-ala proteins recognize the same acceptor stem positions as their bacterial counterparts, albeit with different nucleotide base identities. ProXp-ala is encoded in some human pathogens; thus, these results have the potential to inform new antibiotic drug design.
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Affiliation(s)
- Xiao Ma
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Mark P Foster
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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19
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Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z. Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Nat Catal 2023. [DOI: 10.1038/s41929-023-00934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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20
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Jia X, Zhang C, Luo B, Frandsen JK, Watkins AM, Li K, Zhang M, Wei X, Yang Y, Henkin TM, Su Z. Cryo-EM-guided engineering of T-box-tRNA modules with enhanced selectivity and sensitivity in translational regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530422. [PMID: 36909519 PMCID: PMC10002618 DOI: 10.1101/2023.02.28.530422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Riboswitches are non-coding RNA elements that play vital roles in regulating gene expression. Their specific ligand-dependent structural reorganization facilitates their use as templates for design of engineered RNA switches for therapeutics, nanotechnology and synthetic biology. T-box riboswitches bind tRNAs to sense aminoacylation and control gene expression via transcription attenuation or translation inhibition. Here we determine the cryo-EM structure of the wild-type Mycobacterium smegmatis ileS T-box in complex with its cognate tRNA Ile . This structure shows a very flexible antisequestrator region that tolerates both 3'-OH and 2',3'-cyclic phosphate modification at the 3' end of tRNA Ile . Elongation of one helical turn (11-base pair) in both the tRNA acceptor arm and T-box Stem III maintains T-box-tRNA complex formation and increases the selectivity for tRNA 3' end modification. Moreover, elongation of Stem III results in ∼6-fold tighter binding to tRNA, which leads to increased sensitivity of downstream translational regulation indicated by precedent translation. Our results demonstrate that cryo-EM can guide RNA engineering to design improved riboswitch modules for translational regulation, and potentially a variety of additional functions.
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21
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General Strategies for RNA X-ray Crystallography. Molecules 2023; 28:molecules28052111. [PMID: 36903357 PMCID: PMC10004510 DOI: 10.3390/molecules28052111] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
An extremely small proportion of the X-ray crystal structures deposited in the Protein Data Bank are of RNA or RNA-protein complexes. This is due to three main obstacles to the successful determination of RNA structure: (1) low yields of pure, properly folded RNA; (2) difficulty creating crystal contacts due to low sequence diversity; and (3) limited methods for phasing. Various approaches have been developed to address these obstacles, such as native RNA purification, engineered crystallization modules, and incorporation of proteins to assist in phasing. In this review, we will discuss these strategies and provide examples of how they are used in practice.
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22
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Han L, Luo Z, Ju Y, Chen B, Zou T, Wang J, Xu J, Gu Q, Yang XL, Schimmel P, Zhou H. The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements. SCIENCE ADVANCES 2023; 9:eadf1027. [PMID: 36753552 PMCID: PMC9908026 DOI: 10.1126/sciadv.adf1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
As a class of essential enzymes in protein translation, aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are organized into two classes of 10 enzymes each, based on two conserved active site architectures. The (αβ)2 glycyl-tRNA synthetase (GlyRS) in many bacteria is an orphan aaRS whose sequence and unprecedented X-shaped structure are distinct from those of all other aaRSs, including many other bacterial and all eukaryotic GlyRSs. Here, we report a cocrystal structure to elucidate how the orphan GlyRS kingdom specifically recognizes its substrate tRNA. This structure is sharply different from those of other aaRS-tRNA complexes but conforms to the clash-free, cross-class aaRS-tRNA docking found with conventional structures and reinforces the class-reconstruction paradigm. In addition, noteworthy, the X shape of orphan GlyRS is condensed with the largest known spatial rearrangement needed by aaRSs to capture tRNAs, which suggests potential nonactive site targets for aaRS-directed antibiotics, instead of less differentiated hard-to-drug active site locations.
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Affiliation(s)
- Lu Han
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingchen Ju
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bingyi Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Taotao Zou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Junjian Wang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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23
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Xu L, Xiao Y, Zhang J, Fang X. Structural insights into translation regulation by the THF-II riboswitch. Nucleic Acids Res 2023; 51:952-965. [PMID: 36620887 PMCID: PMC9881143 DOI: 10.1093/nar/gkac1257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF) riboswitch in response to specific binding of THF and its derivatives. Recently, a second class of THF riboswitches, named THF-II, was identified in Gram-negative bacteria, which exhibit distinct architecture from the previously characterized THF-I riboswitches found in Gram-positive bacteria. Here, we present the crystal structures of the ligand-bound THF-II riboswitch from Mesorhizobium loti. These structures exhibit a long rod-like fold stabilized by continuous base pair and base triplet stacking across two helices of P1 and P2 and their interconnecting ligand-bound binding pocket. The pterin moiety of the ligand docks into the binding pocket by forming hydrogen bonds with two highly conserved pyrimidines in J12 and J21, which resembles the hydrogen-bonding pattern at the ligand-binding site FAPK in the THF-I riboswitch. Using small-angle X-ray scattering and isothermal titration calorimetry, we further characterized the riboswitch in solution and reveal that Mg2+ is essential for pre-organization of the binding pocket for efficient ligand binding. RNase H cleavage assay indicates that ligand binding reduces accessibility of the ribosome binding site in the right arm of P1, thus down-regulating the expression of downstream genes. Together, these results provide mechanistic insights into translation regulation by the THF-II riboswitch.
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Affiliation(s)
| | | | - Jie Zhang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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24
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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25
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Sapkota KP, Li S, Zhang J. Cotranscriptional Assembly and Native Purification of Large RNA-RNA Complexes for Structural Analyses. Methods Mol Biol 2023; 2568:1-12. [PMID: 36227558 DOI: 10.1007/978-1-0716-2687-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recent technological developments such as cryogenic electron microscopy (Cryo-EM) and X-ray free electron lasers (XFEL) have significantly expanded the available toolkit to visualize large, complex noncoding RNAs and their complexes. Consequently, the quality of the RNA sample, as measured by its chemical monodispersity and conformational homogeneity, has become the bottleneck that frequently precludes effective structural analyses. Here we describe a general RNA sample preparation protocol that combines cotranscriptional RNA folding and RNA-RNA complex assembly, followed by native purification of stoichiometric complexes. We illustrate and discuss the utility of this versatile method in overcoming RNA misfolding and enabling the structural and mechanistic elucidations of the T-box riboswitch-tRNA complexes.
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Affiliation(s)
- Krishna P Sapkota
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Shuang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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26
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Díaz-Casado L, Santana AG, Gómez-Pinto I, Villacampa A, Corzana F, Jiménez-Barbero J, González C, Asensio JL. Binding-driven reactivity attenuation enables NMR identification of selective drug candidates for nucleic acid targets. Commun Chem 2022; 5:137. [PMID: 36697799 PMCID: PMC9814457 DOI: 10.1038/s42004-022-00755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 01/28/2023] Open
Abstract
NMR methods, and in particular ligand-based approaches, are among the most robust and reliable alternatives for binding detection and consequently, they have become highly popular in the context of hit identification and drug discovery. However, when dealing with DNA/RNA targets, these techniques face limitations that have precluded widespread application in medicinal chemistry. In order to expand the arsenal of spectroscopic tools for binding detection and to overcome the existing difficulties, herein we explore the scope and limitations of a strategy that makes use of a binding indicator previously unexploited by NMR: the perturbation of the ligand reactivity caused by complex formation. The obtained results indicate that ligand reactivity can be utilised to reveal association processes and identify the best binders within mixtures of significant complexity, providing a conceptually different reactivity-based alternative within NMR screening methods.
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Affiliation(s)
- Laura Díaz-Casado
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Andrés G. Santana
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Irene Gómez-Pinto
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Alejandro Villacampa
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Francisco Corzana
- grid.119021.a0000 0001 2174 6969Dept. Química and Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26005 La Rioja, Spain
| | - Jesús Jiménez-Barbero
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC-bioGUNE). Derio, 48160 Bizkaia, Spain
| | - Carlos González
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Juan Luis Asensio
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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27
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Liu Y, Munsayac A, Hall I, Keane SC. Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA. J Mol Biol 2022; 434:167688. [PMID: 35717998 PMCID: PMC9474619 DOI: 10.1016/j.jmb.2022.167688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/22/2022]
Abstract
The miR-17 ∼ 92a polycistron, also known as oncomiR-1, is commonly overexpressed in multiple cancers and has several oncogenic properties. OncomiR-1 encodes six constituent microRNAs (miRs), each enzymatically processed with different efficiencies. However, the structural mechanism that regulates this differential processing remains unclear. Chemical probing of oncomiR-1 revealed that the Drosha cleavage sites of pri-miR-92a are sequestered in a four-way junction. NPSL2, an independent stem loop element, is positioned just upstream of pri-miR-92a and sequesters a crucial part of the sequence that constitutes the basal helix of pri-miR-92a. Disruption of the NPSL2 hairpin structure could promote the formation of a pri-miR-92a structure that is primed for processing by Drosha. Thus, NPSL2 is predicted to function as a structural switch, regulating pri-miR-92a processing. Here, we determined the solution structure of NPSL2 using solution NMR spectroscopy. This is the first high-resolution structure of an oncomiR-1 element. NPSL2 adopts a hairpin structure with a large, but highly structured, apical and internal loops. The 10-bp apical loop contains a pH-sensitive A+·C mismatch. Additionally, several adenosines within the apical and internal loops have elevated pKa values. The protonation of these adenosines can stabilize the NPSL2 structure through electrostatic interactions. Our study provides fundamental insights into the secondary and tertiary structure of an important RNA hairpin proposed to regulate miR biogenesis.
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Affiliation(s)
- Yaping Liu
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/YapingLiu5
| | - Aldrex Munsayac
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Ian Hall
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/ihallu14
| | - Sarah C Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
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28
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Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O'Donoghue P, Söll D, Tharp JM. Ancestral Archaea Expanded the Genetic Code with Pyrrolysine. J Biol Chem 2022; 298:102521. [PMID: 36152750 DOI: 10.1016/j.jbc.2022.102521] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
The pyrrolysyl-tRNA synthetase (PylRS) facilitates the co-translational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain highly active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Ca. Methanomethylophilus alvus. We show that, compared to the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency, but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 tRNAPyl sequences from diverse anaerobic archaea and bacteria. This analysis suggests that the PylRS•tRNAPyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the co-evolutionary history of PylRS and tRNAPyl and reveal the emergence of tRNAPyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNAPyl species with the more common G73-containing tRNAPyl will enable future efforts to engineer PylRS systems for further genetic code expansion.
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Affiliation(s)
- Li-Tao Guo
- Department of Molecular Biophysics & Biochemistry
| | - Kazuaki Amikura
- Department of Molecular Biophysics & Biochemistry; Department of Interdisciplinary Space Science, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Kanagawa, Japan
| | - Han-Kai Jiang
- Institute of Biological Chemistry; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Xian Fu
- BGI-Shenzhen, Shenzhen, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yane-Shih Wang
- Institute of Biological Chemistry; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Canada; Department of Chemistry, The University of Western Ontario, London, Canada
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry; Department of Chemistry, Yale University, New Haven, CT, USA
| | - Jeffery M Tharp
- Department of Molecular Biophysics & Biochemistry; Department of Chemistry, The University of Western Ontario, London, Canada.
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29
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Knox HJ, Rego Campello H, Lester HA, Gallagher T, Dougherty DA. Characterization of Binding Site Interactions and Selectivity Principles in the α3β4 Nicotinic Acetylcholine Receptor. J Am Chem Soc 2022; 144:16101-16117. [PMID: 36006801 DOI: 10.1021/jacs.2c06495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) play an important role in neurotransmission and are also involved in addiction and several disease states. There is significant interest in therapeutic targeting of nAChRs; however, achieving selectivity for one subtype over others has been a longstanding challenge, given the close structural similarities across the family. Here, we characterize binding interactions in the α3β4 nAChR subtype via structure-function studies involving noncanonical amino acid mutagenesis and two-electrode voltage clamp electrophysiology. We establish comprehensive binding models for both the endogenous neurotransmitter ACh and the smoking cessation drug cytisine. We also use a panel of C(10)-substituted cytisine derivatives to probe the effects of subtle changes in the ligand structure on binding. By comparing our results to those obtained for the well-studied α4β2 subtype, we identify several features of both the receptor and agonist structure that can be utilized to enhance selectivity for either α3β4 or α4β2. Finally, we characterize binding interactions of the α3β4-selective partial agonist AT-1001 to determine factors that contribute to its selectivity. These results shed new light on the design of selective nAChR-targeted ligands and can be used to inform the design of improved therapies with minimized off-target effects.
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Affiliation(s)
- Hailey J Knox
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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30
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Radmehr M, Adebayo TS. Does health expenditure matter for life expectancy in Mediterranean countries? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60314-60326. [PMID: 35420335 PMCID: PMC9008298 DOI: 10.1007/s11356-022-19992-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
This research assesses the effect of health expenditure and sanitation on life expectancy in Mediterranean countries. We also consider other drivers of life expectancy, such as CO2 emissions and economic growth. The study covers the period 2000-2018, and the recently developed method of moments quantile regression (MMQR) approach was utilised to assess these interconnections. This method is immune to outliers and creates an asymmetric interrelationship between variables. The outcomes from the MMQR unveiled that economic growth, health expenditure, and sanitation enhanced life expectancy in all quantiles (0.1-0.90). Furthermore, in all quantiles (0.1-0.90), the effect of CO2 emissions on life expectancy was negative. Moreover, as a robustness check, the FMOLS, DOLS, and FE-OLS long-run estimators were applied, and the outcomes validated the MMQR outcomes. Based on the results generated, policymakers in these nations should implement effective environmental and public health measures that will pay off in the long run through improved health as a result of lower emissions of CO2, as well as increased economic expansion and productivity.
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Affiliation(s)
- Mehrshad Radmehr
- Faculty of Economics and Administrative Science, Department of Business Administration, Cyprus International University, Mersin 10, Nicosia, Northern Cyprus Turkey
| | - Tomiwa Sunday Adebayo
- Faculty of Economics and Administrative Science, Department of Business Administration, Cyprus International University, Mersin 10, Nicosia, Northern Cyprus Turkey
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31
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Feyrer H, Gurdap CO, Marušič M, Schlagnitweit J, Petzold K. Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR. PLoS One 2022; 17:e0264662. [PMID: 35802676 PMCID: PMC9269771 DOI: 10.1371/journal.pone.0264662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods represent an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.
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Affiliation(s)
- Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Cenk Onur Gurdap
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Maja Marušič
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana, Slovenia
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Centre de RMN à Très Hauts Champs de Lyon, UMR5082 CNRS/ENS-Lyon/Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- * E-mail:
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32
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Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
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Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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33
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tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch. CRYSTALS 2022. [DOI: 10.3390/cryst12050694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RNAs are prone to misfolding and are often more challenging to crystallize and phase than proteins. Here, we demonstrate that tRNA fusion can streamline the crystallization and structure determination of target RNA molecules. This strategy was applied to the T-box riboswitch system to capture a dynamic interaction between the tRNA 3′-UCCA tail and the T-box antiterminator, which senses aminoacylation. We fused the T-box antiterminator domain to the tRNA anticodon arm to capture the intended interaction through crystal packing. This approach drastically improved the probability of crystallization and successful phasing. Multiple structure snapshots captured the antiterminator loop in an open conformation with some resemblance to that observed in the recent co-crystal structures of the full-length T box riboswitch–tRNA complex, which contrasts the resting, closed conformation antiterminator observed in an earlier NMR study. The anticipated tRNA acceptor–antiterminator interaction was captured in a low-resolution crystal structure. These structures combined with our previous success using prohead RNA–tRNA fusions demonstrates tRNA fusion is a powerful method in RNA structure determination.
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34
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Herzel L, Stanley JA, Yao CC, Li GW. Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome. Nucleic Acids Res 2022; 50:5029-5046. [PMID: 35524564 PMCID: PMC9122600 DOI: 10.1093/nar/gkac295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
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Affiliation(s)
- Lydia Herzel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Julian A Stanley
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Chun-Chen Yao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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35
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Bou-Nader C, Zhang J. Rational engineering enables co-crystallization and structural determination of the HIV-1 matrix-tRNA complex. STAR Protoc 2022; 3:101056. [PMID: 35005638 PMCID: PMC8715211 DOI: 10.1016/j.xpro.2021.101056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Host tRNAs specifically interact with the matrix domain (MA) of HIV-1 major structural polyprotein, Gag, to control its membrane localization and virion assembly. In this protocol, we describe the purification and engineering of HIV-1 MA and tRNA, and the co-crystallization and structure determination of the complex using X-ray crystallography. Rational engineering of the tRNA surface created tRNA-tRNA packing contacts that drove the formation of diffraction-quality co-crystals. This protocol can be adapted to solve other ribonucleoprotein complex structures containing structured RNAs. For complete details on the use and execution of this protocol, please refer to Bou-Nader et al. (2021).
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
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36
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Peters JK, Tibble RW, Warminski M, Jemielity J, Gross JD. Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis. Structure 2022; 30:721-732.e4. [PMID: 35290794 PMCID: PMC9081138 DOI: 10.1016/j.str.2022.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/30/2021] [Accepted: 02/16/2022] [Indexed: 01/06/2023]
Abstract
Poxviruses encode decapping enzymes that remove the protective 5' cap from both host and viral mRNAs to commit transcripts for decay by the cellular exonuclease Xrn1. Decapping by these enzymes is critical for poxvirus pathogenicity by means of simultaneously suppressing host protein synthesis and limiting the accumulation of viral double-stranded RNA (dsRNA), a trigger for antiviral responses. Here we present a high-resolution structural view of the vaccinia virus decapping enzyme D9. This Nudix enzyme contains a domain organization different from other decapping enzymes in which a three-helix bundle is inserted into the catalytic Nudix domain. The 5' mRNA cap is positioned in a bipartite active site at the interface of the two domains. Specificity for the methylated guanosine cap is achieved by stacking between conserved aromatic residues in a manner similar to that observed in canonical cap-binding proteins VP39, eIF4E, and CBP20, and distinct from eukaryotic decapping enzyme Dcp2.
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37
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Knezic B, Keyhani-Goldau S, Schwalbe H. Mapping the conformational landscape of the neutral network of RNA sequences that connect two functional distinctly different ribozymes. Chembiochem 2022; 23:e202200022. [PMID: 35112772 PMCID: PMC9305247 DOI: 10.1002/cbic.202200022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/02/2022] [Indexed: 11/08/2022]
Abstract
During evolution of an RNA world, the development of enzymatic function was essential. Such enzymatic function was linked to RNA sequences capable of adopting specific RNA folds that possess catalytic pockets to promote catalysis. Within this primordial RNA world, initially evolved self-replicating ribozymes presumably mutated to ribozymes with new functions. In 2000, Schultes and Bartel investigated such conversion from one ribozyme to a new ribozyme with distinctly different catalytic functions. Within a neutral network that linked these two prototype ribozymes, a single RNA chain could be identified that exhibited both enzymatic functions. This system serves as a paradigm for an evolutionary system that allows neutral drifts by stepwise mutation from one ribozyme into a different ribozyme without loss of intermittent function. Here, we investigated this complex functional diversification by analyzing several RNA sequences within this neutral network between two ribozymes with class III ligase activity and with self-cleavage reactivity. We utilized rapid RNA sample preparation for NMR spectroscopic studies together with SHAPE analysis and in-line probing to characterize secondary structure changes within the neutral network. Our investigations allowed delineation of the 2 nd structure space and by comparison with the previously determined catalytic function allowed correlation of the structure-function relation of ribozyme function in this neutral network.
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Affiliation(s)
- Bozana Knezic
- Goethe-Universitat Frankfurt am Main, Biochemistry, Chemistry, and Pharmacy, GERMANY
| | - Sara Keyhani-Goldau
- Goethe-Universitat Frankfurt am Main, Biochemistry, Chemistry, and Pharmacy, GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main, Institut für Organische Chemie und Chemische Biologie, Max-von-Laue-Str. 7, 60438, Frankfurt, GERMANY
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38
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Jones CP, Ferré-D'Amaré AR. Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot. RNA (NEW YORK, N.Y.) 2022; 28:239-249. [PMID: 34845084 PMCID: PMC8906546 DOI: 10.1261/rna.078825.121] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/04/2021] [Indexed: 05/30/2023]
Abstract
SARS-CoV-2 produces two long viral protein precursors from one open reading frame using a highly conserved RNA pseudoknot that enhances programmed -1 ribosomal frameshifting. The 1.3 Å-resolution X-ray structure of the pseudoknot reveals three coaxially stacked helices buttressed by idiosyncratic base triples from loop residues. This structure represents a frameshift-stimulating state that must be deformed by the ribosome and exhibits base-triple-adjacent pockets that could be targeted by future small-molecule therapeutics.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
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39
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Narayan C, Veeramani S, Thiel WH. Optimization of RNA Aptamer SELEX Methods: Improved Aptamer Transcript 3'-End Homogeneity, PAGE Purification Yield, and Target-Bound Aptamer RNA Recovery. Nucleic Acid Ther 2022; 32:74-80. [PMID: 34757856 PMCID: PMC8817694 DOI: 10.1089/nat.2021.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Since its inception in the early 1990s, SELEX remains the gold standard for discovering RNA aptamers specific for proteins and small molecules. The SELEX process has undergone countless modifications and now encompasses a breadth of innovative selection schemes to pare an aptamer library toward target-specific aptamers. Common to all these RNA aptamer SELEX processes are the steps for the preparation of DNA template and in vitro transcription of aptamer RNA. These steps have remained mostly unchanged over the past three decades and would benefit from optimization. We focused on three key areas: improving the homogeneity of in vitro transcribed aptamer RNA, increasing the efficiency of in vitro transcribed aptamer RNA purification by PAGE, and improving the quality of target-bound aptamer RNA recovered during SELEX. Together, these optimizations contribute toward a more efficient SELEX process and are applicable to both protein-based and cell-based RNA aptamer selections.
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Affiliation(s)
- Chandan Narayan
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA
| | - Suresh Veeramani
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Department of Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: Suresh Veeramani, DVM, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William H. Thiel
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: William H. Thiel, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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40
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Abstract
In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.
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41
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Amikura K, Hibi K, Shimizu Y. Efficient and Precise Protein Synthesis in a Cell-Free System Using a Set of In Vitro Transcribed tRNAs with Nucleotide Modifications. Methods Mol Biol 2022; 2433:151-168. [PMID: 34985743 DOI: 10.1007/978-1-0716-1998-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Reconstitution of a complicated system with a minimal set of components is essential for understanding the mechanisms of how the input is reflected in the output, which is fundamental for further engineering of the corresponding system. We have recently developed a reconstituted cell-free protein synthesis system equipped only with 21 in vitro transcribed tRNAs, one of the minimal systems for understanding the genetic code decoding mechanisms. Introduction of several nucleotide modifications to the transcribed tRNAs showed improvement of both protein synthesis efficiency and its fidelity, suggesting various combinations of tRNAs and their modifications can be evaluated in the developed system. In this chapter, we describe how to prepare this minimal system. Methods for preparing the transcribed tRNAs, their modifications, and the protein production using the set of prepared tRNAs are shown.
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Affiliation(s)
- Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keita Hibi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics research (BDR), Osaka, Japan.
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42
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Kotar A, Ma S, Keane SC. pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31. Biophys Chem 2022; 283:106763. [DOI: 10.1016/j.bpc.2022.106763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022]
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43
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Nagano M, Ishida S, Suga H. Inner residues of macrothiolactone in autoinducer peptides-I/IV circumvents S-to-O acyl transfer to the upstream serine residue. RSC Chem Biol 2022; 3:295-300. [PMID: 35359496 PMCID: PMC8905530 DOI: 10.1039/d1cb00225b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/23/2022] [Indexed: 11/21/2022] Open
Abstract
Autoinducing peptides I and IV (AIP-I/IV) are naturally occurring cyclic thiodepsipeptides (CTPs) bearing a Ser–Thr–Cys–Asp/Tyr (STC[D/Y]) tetrapeptide motif, where the Cys thiol (HSC) in the side-chain is linked to the Met C-terminal carboxylic acid (MCOOH) to form 5-residue macrothiolactones,−SC(D/Y)FIMCO−. We have recently reported that CTPs containing SX1CX2 motifs spontaneously undergo macrolactonization to yield cyclic depsipeptides (CDPs) by an unprecedented rapid S-to-O acyl transfer to the upstream Ser hydroxyl group. Interestingly, even though the STC[D/Y] motif in AIP-I/IV is a member of the SX1CX2 motif family, it maintains the CTP form. This suggests that AIP-I/IV have a structural or chemical motive for avoiding such an S-to-O acyl transfer, thus retaining the CTP form intact. Here we have used genetic code reprogramming to ribosomally synthesize various AIP-I analogs and studied what the determinant is to control the formation of CTP vs. CDP products. The study revealed that a Gly substitution of the inner Asp/Tyr or Met residues in the thiolactone drastically alters the resistance to the promotion of the S-to-O acyl transfer, giving the corresponding CDP product. This suggests that the steric hindrances originating from the α-substituted sidechain in these two amino acids in the AIP-I/IV thiolactone likely play a critical role in controlling the resistance against macrolactone rearrangement to the upstream Ser residue. In AIP-I/IV, single Gly mutation at the thiolactone induces S-to-O acyl shift to yield a corresponding ring-expanded lactone form.![]()
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Affiliation(s)
- Masanobu Nagano
- Graduate School of Science, The University of Tokyo 113-0033 Japan
| | - Satoshi Ishida
- Graduate School of Science, The University of Tokyo 113-0033 Japan
| | - Hiroaki Suga
- Graduate School of Science, The University of Tokyo 113-0033 Japan
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44
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Shen S, Naganuma M, Tomari Y, Tadakuma H. Revisiting the Glass Treatment for Single-Molecule Analysis of ncRNA Function. Methods Mol Biol 2022; 2509:209-231. [PMID: 35796966 DOI: 10.1007/978-1-0716-2380-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-molecule imaging is a powerful method for unveiling precise molecular mechanisms. Particularly, single-molecule analysis with total internal reflection fluorescence (TIRF ) microscopy has been successfully applied to the characterization of molecular mechanisms in ncRNA studies. Tracing interactions at the single-molecule level have elucidated the intermediate states of the reaction, which are hidden by ensemble averaging in combinational biochemical approaches, and clarified the key steps of the interaction. However, applying a single-molecule technique to ncRNA analysis still remains a challenge, requiring laborious trial and error to identify a suitable glass surface passivation method. In this chapter, we revisit the major glass surface passivation methods using polyethylene glycol (PEG) treatment and summarize a detailed protocol for single-molecule analysis of the dicing process of Dcr-2, which may apply piRNA studies in the future.
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Affiliation(s)
- Shuting Shen
- School of Life Science and Technology & Gene Editing Center, ShanghaiTech University, Shanghai, China
| | - Masahiro Naganuma
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Tadakuma
- School of Life Science and Technology & Gene Editing Center, ShanghaiTech University, Shanghai, China.
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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45
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Obi P, Chen YG. The design and synthesis of circular RNAs. Methods 2021; 196:85-103. [PMID: 33662562 PMCID: PMC8670866 DOI: 10.1016/j.ymeth.2021.02.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs distinguished by their single-stranded, covalently-closed topology. Although initially perceived as rare byproducts of aberrant splicing, circRNAs are now recognized as ubiquitously expressed and functionally significant. These discoveries have led to a growing need for ways to model circRNAs in living cells to advance our understanding of their biogenesis, regulation, and function, and to adopt them as new technologies for application within research and medicine. In this review, we provide an updated summary of approaches used to produce circRNAs in vitro and in vivo, the latter of which has grown considerably in recent years. Given increased interest in the unique functions carried out by individual circRNAs, we further dedicate a section on how to customize synthesized circRNAs for specific biological roles. We focus on the most common applications, including designing circRNAs for protein delivery, to target miRNAs and proteins, to act as fluorescent reporters, and to modulate cellular immunity.
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Affiliation(s)
- Prisca Obi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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46
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Li H, Zhu D, Wu J, Ma Y, Cai C, Chen Y, Qin M, Dai H. New substrates and determinants for tRNA recognition of RNA methyltransferase DNMT2/TRDMT1. RNA Biol 2021; 18:2531-2545. [PMID: 34110975 PMCID: PMC8632113 DOI: 10.1080/15476286.2021.1930756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/16/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Methylation is a common post-transcriptional modification of tRNAs, particularly in the anticodon loop region. The cytosine 38 (C38) in tRNAs, such as tRNAAsp-GUC, tRNAGly-GCC, tRNAVal-AAC, and tRNAGlu-CUC, can be methylated by human DNMT2/TRDMT1 and some homologs found in bacteria, plants, and animals. However, the substrate properties and recognition mechanism of DNMT2/TRDMT1 remain to be explored. Here, taking into consideration common features of the four known substrate tRNAs, we investigated methylation activities of DNMT2/TRDMT1 on the tRNAGly-GCC truncation and point mutants, and conformational changes of mutants. The results demonstrated that human DNMT2/TRDMT1 preferred substrate tRNAGly-GCC in vitro. L-shaped conformation of classical tRNA could be favourable for DNMT2/TRDMT1 activity. The complete sequence and structure of tRNA were dispensable for DNMT2/TRDMT1 activity, whereas T-arm was indispensable to this activity. G19, U20, and A21 in D-loop were identified as the important bases for DNMT2/TRDMT1 activity, while G53, C56, A58, and C61 in T-loop were found as the critical bases. The conserved CUXXCAC sequence in the anticodon loop was confirmed to be the most critical determinant, and it could stabilize C38-flipping to promote C38 methylation. Based on these tRNA properties, new substrates, tRNAVal-CAC and tRNAGln-CUG, were discovered in vitro. Moreover, a single nucleotide substitute, U32C, could convert non-substrate tRNAAla-AGC into a substrate for DNMT2/TRDMT1. Altogether, our findings imply that DNMT2/TRDMT1 relies on a delicate network involving both the primary sequence and tertiary structure of tRNA for substrate recognition.
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Affiliation(s)
- Huari Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jian Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yunfei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chao Cai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yong Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mian Qin
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hanchuan Dai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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47
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Liu Y, Kotar A, Hodges TL, Abdallah K, Taleb MH, Bitterman BA, Jaime S, Schaubroeck KJ, Mathew E, Morgenstern NW, Lohmeier A, Page JL, Ratanapanichkich M, Arhin G, Johnson BL, Cherepanov S, Moss SC, Zuniga G, Tilson NJ, Yeoh ZC, Johnson BA, Keane SC. NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:479-490. [PMID: 34449019 DOI: 10.1007/s12104-021-10049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the Biological Magnetic Resonance Data Bank (BMRB) to identify sequences that had no (or limited) chemical shift information. Here, we report the chemical shift assignments for 12 RNA hairpins designed specifically to help populate the BMRB.
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Affiliation(s)
- Yaping Liu
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Anita Kotar
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
- Current Address: Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Tracy L Hodges
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Kyrillos Abdallah
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Mallak H Taleb
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Brayden A Bitterman
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Sara Jaime
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Kyle J Schaubroeck
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Ethan Mathew
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Nicholas W Morgenstern
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Anthony Lohmeier
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Jordan L Page
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Matt Ratanapanichkich
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Grace Arhin
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Breanna L Johnson
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Stanislav Cherepanov
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Stephen C Moss
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Gisselle Zuniga
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Nicholas J Tilson
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Zoe C Yeoh
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Sarah C Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA.
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA.
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48
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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'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proc Natl Acad Sci U S A 2021; 118:2112475118. [PMID: 34493679 PMCID: PMC8449379 DOI: 10.1073/pnas.2112475118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
HIV-1 selectively packages two copies of its 5'-capped RNA genome (gRNA) during virus assembly, a process mediated by the nucleocapsid (NC) domain of the viral Gag polyprotein and encapsidation signals located within the dimeric 5' leader of the viral RNA. Although residues within the leader that promote packaging have been identified, the determinants of authentic packaging fidelity and efficiency remain unknown. Here, we show that a previously characterized 159-nt region of the leader that possesses all elements required for RNA dimerization, high-affinity NC binding, and packaging in a noncompetitive RNA packaging assay (ΨCES) is unexpectedly poorly packaged when assayed in competition with the intact 5' leader. ΨCES lacks a 5'-tandem hairpin element that sequesters the 5' cap, suggesting that cap sequestration may be important for packaging. Consistent with this hypothesis, mutations within the intact leader that expose the cap without disrupting RNA structure or NC binding abrogated RNA packaging, and genetic addition of a 5' ribozyme to ΨCES to enable cotranscriptional shedding of the 5' cap promoted ΨCES-mediated RNA packaging to wild-type levels. Additional mutations that either block dimerization or eliminate subsets of NC binding sites substantially attenuated competitive packaging. Our studies indicate that packaging is achieved by a bipartite mechanism that requires both sequestration of the 5' cap and exposure of NC binding sites that reside fully within the ΨCES region of the dimeric leader. We speculate that cap sequestration prevents irreversible capture by the cellular RNA processing and translation machinery, a mechanism likely employed by other viruses that package 5'-capped RNA genomes.
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Olenginski LT, Taiwo KM, LeBlanc RM, Dayie TK. Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies. Molecules 2021; 26:molecules26185581. [PMID: 34577051 PMCID: PMC8466439 DOI: 10.3390/molecules26185581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 01/19/2023] Open
Abstract
RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.
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Affiliation(s)
- Lukasz T. Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
| | - Kehinde M. Taiwo
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
| | - Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
- Vertex Pharmaceuticals, 50 Northern Avenue, Boston, MA 02210, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
- Correspondence: ; Tel.: +1-301-405-3165
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