1
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Malhotra S, Mulvaney T, Cragnolini T, Sidhu H, Joseph A, Beton J, Topf M. RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures. Nucleic Acids Res 2023; 51:9567-9575. [PMID: 37670532 PMCID: PMC10570027 DOI: 10.1093/nar/gkad721] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/10/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for identifying rigid bodies in protein structures exist, however an equivalent for nucleic acid structures is lacking. With the increase in cryo-EM maps containing RNA and progress in RNA structure prediction, there is a need for such tools. We previously developed RIBFIND, a program for clustering protein secondary structures into rigid bodies. In RIBFIND2, this approach is extended to nucleic acid structures. RIBFIND2 can identify biologically relevant rigid bodies in important groups of complex RNA structures, capturing a wide range of dynamics, including large rigid-body movements. The usefulness of RIBFIND2-assigned rigid bodies in cryo-EM model refinement was demonstrated on three examples, with two conformations each: Group II Intron complexed IEP, Internal Ribosome Entry Site and the Processome, using cryo-EM maps at 2.7-5 Å resolution. A hierarchical refinement approach, performed on progressively smaller sets of RIBFIND2 rigid bodies, was clearly shown to have an advantage over classical all-atom refinement. RIBFIND2 is available via a web server with structure visualization and as a standalone tool.
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Affiliation(s)
- Sony Malhotra
- Science and Technology Facilities Council, Scientific Computing, Research Complex at Harwell, Didcot OX11 0FA, UK
| | - Thomas Mulvaney
- Leibniz Institute of Virology, Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg D-22607, Germany
- Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg 20246, Germany
| | - Tristan Cragnolini
- Leibniz Institute of Virology, Hamburg 20251, Germany
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Haneesh Sidhu
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Agnel P Joseph
- Science and Technology Facilities Council, Scientific Computing, Research Complex at Harwell, Didcot OX11 0FA, UK
| | - Joseph G Beton
- Leibniz Institute of Virology, Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg D-22607, Germany
| | - Maya Topf
- Leibniz Institute of Virology, Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg D-22607, Germany
- Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg 20246, Germany
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2
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Jiang W, Long X, Li Z, Hu M, Zhang Y, Lin H, Tang W, Ouyang Y, Jiang L, Chen J, He P, Ouyang X. The Role of Circular RNAs in Ischemic Stroke. Neurochem Res 2023:10.1007/s11064-023-03935-7. [PMID: 37126193 DOI: 10.1007/s11064-023-03935-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023]
Abstract
Ischemic stroke (IS), a devastating condition characterized by intracranial artery stenosis and middle cerebral artery occlusion leading to insufficient oxygen supply to the brain, is a major cause of death and physical disability worldwide. Recent research has demonstrated the critical role of circular RNAs (circRNAs), a class of covalently enclosed noncoding RNAs that are widespread in eukaryotic cells, in regulating various physiological and pathophysiological cellular processes, including cell apoptosis, autophagy, synaptic plasticity, and neuroinflammation. In the past few years, circRNAs have attracted extensive attention in the field of IS research. This review summarizes the current understanding of the mechanisms underlying the involvement of circRNAs in IS development. A better understanding of circRNA-mediated pathogenic mechanisms in IS may pave the way for translating circRNA research into clinical practice, ultimately improving the clinical outcomes of IS patients.
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Affiliation(s)
- Weiwei Jiang
- Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiongquan Long
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, Hunan, China
| | - Zhicheng Li
- Collage of Pharmacy, University of South China, Hengyang, Hunan, China
| | - Mi Hu
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Yangkai Zhang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Huiling Lin
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Wanying Tang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Yuxin Ouyang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Liping Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinzhi Chen
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Pingping He
- The Research Center of Reproduction and Translational Medicine of Hunan Province, Department of Physiology, Medical College, Hunan Normal University, Changsha, 410081, Hunan Province, China
| | - Xinping Ouyang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China.
- The Research Center of Reproduction and Translational Medicine of Hunan Province, Department of Physiology, Medical College, Hunan Normal University, Changsha, 410081, Hunan Province, China.
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3
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Ding P, Liu P, Wu H, Yang P, Tian Y, Zhao Q. Functional properties of circular RNAs and research progress in gastric cancer. Front Oncol 2022; 12:954637. [DOI: 10.3389/fonc.2022.954637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of closed circular non-coding RNAs widely exist in eukaryotes, with high stability and species conservation. A large number of studies have shown that circRNAs are abnormally expressed in various tumor tissues, and are abundant in plasma with long half-life and high specificity, which may be served as potential tumor biomarkers for early diagnosis, treatment and prognosis of malignant tumors. However, the role of circRNAs is still poorly understood in gastric cancer. This article reviews the research progress of circRNAs in gastric cancer in recent years so as to explore the relationship between circRNAs and the occurrence and the development of gastric cancer, and provide new ideas for the diagnosis and treatment of gastric cancer.
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4
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Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM. Structures of a mobile intron retroelement poised to attack its structured DNA target. Science 2022; 378:627-634. [PMID: 36356138 PMCID: PMC10190682 DOI: 10.1126/science.abq2844] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate. We solved cryo-electron microscopy structures of an intact group IIC intron-maturase retroelement that was poised for integration into a DNA stem-loop motif. By visualizing the RNP before and after DNA targeting, we show that it is primed for attack and fits perfectly with its DNA target. This study reveals design principles of a prototypical retroelement and reinforces the hypothesis that group II introns are ancient elements of genetic diversification.
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Affiliation(s)
- Kevin Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Ling Xu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Swapnil C. Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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5
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Kumar A, Satpati P. Structure-based thermodynamics of ion selectivity (Mg 2+versus Ca 2+ and K +versus Na +) in the active site of the eukaryotic lariat group II intron from algae Pylaiella littoralis. Phys Chem Chem Phys 2022; 24:24192-24202. [PMID: 36168989 DOI: 10.1039/d2cp03472g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Group II introns are metalloenzymes that can catalyze self-splicing. Recently, the crystal structures of the eukaryotic group IIB lariat intron from the brown algae Pylaiella littoralis have been reported for two intermediate states (pre-hydrolytic (2s) and post-hydrolytic) along the self-splicing pathway. Three characteristic metal-ion binding sites (M1 and M2 sites for catalytic Mg2+ ions, and K1 site for K+) in the catalytic pocket of the lariat intron have been identified and proposed to be crucial for self-splicing. Using the X-ray structures as a template, we quantitatively estimated the energetics of divalent (Mg2+versus Ca2+) and monovalent (K+versus Na+) ion selectivity and established a direct link between the energetics and structures of this lariat intron (bound to cognate and near-cognate metal ions). Molecular dynamics (MD) free energy simulations showed that the lariat intron was strongly selective between divalent metal ions. The strength of divalent metal-ion selectivity was noticeably high in the post-hydrolytic state (ΔΔG ≈ 20 kcal mol-1) relative to its pre-hydrolytic (2s) state (ΔΔG ≈ 13 kcal mol-1). Quantum chemical calculations ensured that the sign of the estimated divalent metal-ion selectivity was correct. The M1-binding pocket was less solvent-exposed in the case of the post-hydrolytic state relative to the pre-hydrolytic (2s) state, which boosted the metal-ion selectivity of the former. Surprisingly, in contrast to the bacterial linear group II intron, the lariat intron was found to be non-selective between monovalent ions (K+versus Na+). The interaction network in the first coordination shell of Ca2+ in the M1-binding pocket was different relative to Mg2+. Mg2+ substitution by Ca2+ resulted in the substitution of a single M1-RNA interaction by the M1-water interaction. In the pre-hydrolytic (2s) state, Ca2+ substitution completely disrupted the M1⋯5'-exon interaction; thus, the nature of the divalent metal ion is critical for catalysis. The interaction network in the M2 site was independent of the nature of the divalent metal ions (Mg2+ or Ca2+). The monovalent ion was loosely bound in the wet binding pocket (K1 site) of the lariat intron; thus, the substitution of K+ by Na+ could not significantly alter the free energy of the complex. The metal ion selectivity was dependent on the solvent accessibility of the metal-ion-binding-pocket, dry pocket enhanced the selectivity.
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Affiliation(s)
- Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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6
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Matarrese MAG, Loppini A, Nicoletti M, Filippi S, Chiodo L. Assessment of tools for RNA secondary structure prediction and extraction: a final-user perspective. J Biomol Struct Dyn 2022:1-20. [DOI: 10.1080/07391102.2022.2116110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Margherita A. G. Matarrese
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
- Jane and John Justin Neurosciences Center, Cook Children’s Health Care System, TX, USA
- Department of Bioengineering, The University of Texas at Arlington, Arlington, TX, USA
| | - Alessandro Loppini
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
- Center for Life Nano & Neuroscience, Italian Institute of Technology, Rome, Italy
| | - Martina Nicoletti
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
- Center for Life Nano & Neuroscience, Italian Institute of Technology, Rome, Italy
| | - Simonetta Filippi
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
| | - Letizia Chiodo
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
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7
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Costa M. Group II Introns: Flexibility and Repurposing. Front Mol Biosci 2022; 9:916157. [PMID: 35865004 PMCID: PMC9294222 DOI: 10.3389/fmolb.2022.916157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
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8
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Unique and Repeated Stwintrons (Spliceosomal Twin Introns) in the Hypoxylaceae. J Fungi (Basel) 2022; 8:jof8040397. [PMID: 35448628 PMCID: PMC9024468 DOI: 10.3390/jof8040397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 12/04/2022] Open
Abstract
Introns are usually non-coding sequences interrupting open reading frames in pre-mRNAs [D1,2]. Stwintrons are nested spliceosomal introns, where an internal intron splits a second donor sequence into two consecutive splicing reactions leading to mature mRNA. In Hypoxylon sp. CO27-5, 36 highly sequence-similar [D1,2] stwintrons are extant (sister stwintrons). An additional 81 [D1,2] sequence-unrelated stwintrons are described here. Most of them are located at conserved gene positions rooted deep in the Hypoxylaceae. Absence of exonic sequence bias at the exon–stwintron junctions and a very similar phase distribution were noted for both groups. The presence of an underlying sequence symmetry in all 117 stwintrons was striking. This symmetry, more pronounced near the termini of most of the full-length sister stwintrons, may lead to a secondary structure that brings into close proximity the most distal splice sites, the donor of the internal and the acceptor of the external intron. The Hypoxylon stwintrons were overwhelmingly excised by consecutive splicing reactions precisely removing the whole intervening sequence, whereas one excision involving the distal splice sites led to a frameshift. Alternative (mis)splicing took place for both sister and uniquely occurring stwintrons. The extraordinary symmetry of the sister stwintrons thus seems dispensable for the infrequent, direct utilisation of the distal splice sites.
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9
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Artemyeva-Isman OV, Porter ACG. U5 snRNA Interactions With Exons Ensure Splicing Precision. Front Genet 2021; 12:676971. [PMID: 34276781 PMCID: PMC8283771 DOI: 10.3389/fgene.2021.676971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with the precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron start. Association between these guanines cannot be explained solely by base-pairing with U1 snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon end. Current U5 snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: (1) optimal binding register for human exons and U5-the exon junction positioned at U5Loop1 C39|C38; (2) common mechanism for base-pairing of human U5 snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition-guided by base pair geometry; and (3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Statistical analyses showed increased U5 Watson-Crick pairs with the 5'exon in the absence of +5G at the intron start. In 5'exon positions -3 and -5, this effect is specific to U5 snRNA rather than U1 snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3'exon position +1 coincide with substitutions of the conserved -3C at the intron 3'end. Based on mutation and X-ray evidence, we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3'intron end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3'intron end ensure that the 3'exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6, and U2 snRNAs that stabilize the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA therapeutics and gene repair by reverse splicing.
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Affiliation(s)
- Olga V Artemyeva-Isman
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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11
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Liu N, Dong X, Hu C, Zeng J, Wang J, Wang J, Wang HW, Belfort M. Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing. Nucleic Acids Res 2020; 48:11185-11198. [PMID: 33021674 PMCID: PMC7641739 DOI: 10.1093/nar/gkaa773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/30/2020] [Accepted: 09/30/2020] [Indexed: 11/13/2022] Open
Abstract
Group II introns are the putative progenitors of nuclear spliceosomal introns and use the same two-step splicing pathway. In the cell, the intron RNA forms a ribonucleoprotein (RNP) complex with the intron-encoded protein (IEP), which is essential for splicing. Although structures of spliced group II intron RNAs and RNP complexes have been characterized, structural insights into the splicing process remain enigmatic due to lack of pre-catalytic structural models. Here, we report two cryo-EM structures of endogenously produced group II intron RNPs trapped in their pre-catalytic state. Comparison of the catalytically activated precursor RNP to its previously reported spliced counterpart allowed identification of key structural rearrangements accompanying splicing, including a remodeled active site and engagement of the exons. Importantly, altered RNA-protein interactions were observed upon splicing among the RNP complexes. Furthermore, analysis of the catalytically inert precursor RNP demonstrated the structural impact of the formation of the active site on RNP architecture. Taken together, our results not only fill a gap in understanding the structural basis of IEP-assisted group II intron splicing, but also provide parallels to evolutionarily related spliceosomal splicing.
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Affiliation(s)
- Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolong Dong
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Cuixia Hu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianwei Zeng
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
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12
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Abstract
RNA enzymes or ribozymes catalyze some of the most important reactions in biology and are thought to have played a central role in the origin and evolution of life on earth. Catalytic function in RNA has evolved in crowded cellular environments that are different from dilute solutions in which most in vitro assays are performed. The presence of molecules such as amino acids, polypeptides, alcohols, and sugars in the cell introduces forces that modify the kinetics and thermodynamics of ribozyme-catalyzed reactions. Synthetic molecules are routinely used in in vitro studies to better approximate the properties of biomolecules under in vivo conditions. This review discusses the various forces that operate within simulated crowded solutions in the context of RNA structure, folding, and catalysis. It also explores ideas about how crowding could have been beneficial to the evolution of functional RNAs and the development of primitive cellular systems in a prebiotic milieu.
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Affiliation(s)
- Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
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13
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Dong X, Qu G, Piazza CL, Belfort M. Group II intron as cold sensor for self-preservation and bacterial conjugation. Nucleic Acids Res 2020; 48:6198-6209. [PMID: 32379323 PMCID: PMC7293003 DOI: 10.1093/nar/gkaa313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 01/18/2023] Open
Abstract
Group II introns are self-splicing ribozymes and mobile genetic elements. Splicing is required for both expression of the interrupted host gene and intron retromobility. For the pRS01 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of the intron's host relaxase protein. Relaxase, in turn, initiates horizontal transfer of the conjugative pRS01 plasmid and stimulates retrotransposition of the intron. Little is known about how splicing of bacterial group II introns is influenced by environmental conditions. Here, we show that low temperatures can inhibit Ll.LtrB intron splicing. Whereas autocatalysis is abolished in the cold, splicing is partially restored by the intron-encoded protein (IEP). Structure profiling reveals cold-induced disruptions of key tertiary interactions, suggesting that a kinetic trap prevents the intron RNA from assuming its native state. Interestingly, while reduced levels of transcription and splicing lead to a paucity of excised intron in the cold, levels of relaxase mRNA are maintained, partially due to diminished intron-mediated mRNA targeting, allowing intron spread by conjugal transfer. Taken together, this study demonstrates not only the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for cold-stress adaptation, but also maintenance of horizontal plasmid and intron transfer under cold-shock.
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Affiliation(s)
- Xiaolong Dong
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Guosheng Qu
- College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
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14
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Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. Visualizing group II intron dynamics between the first and second steps of splicing. Nat Commun 2020; 11:2837. [PMID: 32503992 PMCID: PMC7275048 DOI: 10.1038/s41467-020-16741-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/18/2020] [Indexed: 12/21/2022] Open
Abstract
Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy. Group II introns are self-splicing ribozymes. Here, the authors employ enzymatic assay, X-ray crystallography and molecular dynamics simulations to show that protonation of the group II intron catalytic triad plays an important role for the transition from the first to the second step of splicing.
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Affiliation(s)
- Jacopo Manigrasso
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Vito Genna
- Department of Structural and Computational Biology, Institute for Research in Biomedicine (IRB), Parc Científic de Barcelona, C/ Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Pietro Vidossich
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Srinivas Somarowthu
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT, 06511, USA.,Department of Chemistry, Yale University, New Haven, CT, 06511, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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15
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Smathers CM, Robart AR. Transitions between the steps of forward and reverse splicing of group IIC introns. RNA (NEW YORK, N.Y.) 2020; 26:664-673. [PMID: 32127385 PMCID: PMC7161350 DOI: 10.1261/rna.075044.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/27/2020] [Indexed: 06/10/2023]
Abstract
Group II introns are mobile genetic elements that perform both self-splicing and intron mobility reactions. These ribozymes are comprised of a catalytic RNA core that binds to an intron-encoded protein (IEP) to form a ribonucleoprotein (RNP) complex. Splicing proceeds through two competing reactions: hydrolysis or branching. Group IIC intron ribozymes have a minimal RNA architecture, and splice almost exclusively through hydrolysis in ribozyme reactions. Addition of the IEP allows the splicing reaction to form branched lariat RNPs capable of intron mobility. Here we examine ribozyme splicing, IEP-dependent splicing, and mobility reactions of a group IIC intron from the thermophilic bacterium Thermoanerobacter italicus (Ta.it.I1). We show that Ta.it.I1 is highly active for ribozyme activity, forming linear hydrolytic intron products. Addition of purified IEP switches activity to the canonical lariat forming splicing reaction. We demonstrate that the Ta.it.I1 group IIC intron coordinates the progression of the forward splicing reaction through a π-π' interaction between intron domains II and VI. We further show that branched splicing is supported in the absence of the IEP when the π-π' interaction is mutated. We also investigated the regulation of the two steps of reverse splicing during intron mobility into DNA substrates. Using a fluorescent mobility assay that simultaneously visualizes all steps of intron integration into DNA, we show that completion of reverse splicing is tightly coupled to cDNA synthesis regardless of mutation of the π-π' interaction.
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Affiliation(s)
- Claire M Smathers
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 20506, USA
| | - Aaron R Robart
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 20506, USA
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16
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Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. Cell 2020; 178:612-623.e12. [PMID: 31348888 DOI: 10.1016/j.cell.2019.06.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/31/2019] [Accepted: 06/26/2019] [Indexed: 01/08/2023]
Abstract
Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a maturase protein, which promotes splicing through an unknown mechanism. The mechanism of splice site exchange within the RNA active site during catalysis also remains unclear. We determined two cryo-EM structures at 3.6-Å resolution of a group II intron reverse splicing into DNA. These structures reveal that the branch-site domain VI helix swings 90°, enabling substrate exchange during DNA integration. The maturase assists catalysis through a transient RNA-protein contact with domain VI that positions the branch-site adenosine for lariat formation during forward splicing. These findings provide the first direct evidence of the role the maturase plays during group II intron catalysis. The domain VI dynamics closely parallel spliceosomal branch-site helix movement and provide strong evidence for a retroelement origin of the spliceosome.
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17
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Mg 2+ vs Ca 2+ bound active site of group II intron- A MD study. J Mol Graph Model 2020; 97:107546. [PMID: 32018058 DOI: 10.1016/j.jmgm.2020.107546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 11/20/2022]
Abstract
Group II introns are enzymes which undergo self-splicing and remove itself from pre-messenger RNA. X-ray structures of group II intron of Oceanobacillus iheyensis at various stages of the self-splicing pathway (pre-hydrolytic, post-hydrolytic, and ligand-free state) revealed intricate atomic interaction network in the active site of the intron. It has been confirmed that a heteronuclear metal ion cluster consisting of four metal ions (K1, K2 sites with K+ and M1, M2 sites with Mg2+) are crucial for function. Substitution of Mg2+ by Ca2+ results in loss of enzymatic activity. The X-ray structures not only opens up the possibility of modelling Mg2+ and Ca2+ bound active site of group II intron and quantitatively estimate the energetics of Mg2+ vs Ca2+ preference but also explore the relative structural and dynamical differences in response to divalent metal ion substitution. Thus, using X-ray structures as a template we performed molecular dynamics simulations to compare structural and dynamical differences between Mg2+ and Ca2+ bound active site of group II intron at various stages of the splicing pathway (i.e., pre-hydrolytic, post-hydrolytic, and ligand-free state). Quantitative estimation of Mg2+ vs Ca2+ selectivity at the M1, M2 sites confirmed Mg2+ preference at intron active sites relative to Ca2+. Ca2+ is relatively more hydrated in the intron active site relative to Mg2+. The local environment (bound nucleophilic water, interaction with scissile phosphate) around M2 is strikingly different between Mg2+ and Ca2+ bound pre-hydrolytic state. In the post-hydrolytic state, the exon part of the hydrolysis product is involved in direct interaction with the M1, whereas the intron part is highly flexible in our MD trajectories. Solvent exposure of M1, M2 sites are least in the pre-hydrolytic state, highest in the ligand-free state, and intermediate in the post-hydrolytic state.
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18
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Plangger R, Juen MA, Hoernes TP, Nußbaumer F, Kremser J, Strebitzer E, Klingler D, Erharter K, Tollinger M, Erlacher MD, Kreutz C. Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing. Nucleic Acids Res 2019; 47:11430-11440. [PMID: 31665419 PMCID: PMC6868427 DOI: 10.1093/nar/gkz965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 12/29/2022] Open
Abstract
Although group II intron ribozymes are intensively studied the question how structural dynamics affects splicing catalysis has remained elusive. We report for the first time that the group II intron domain 6 exists in a secondary structure equilibrium between a single- and a two-nucleotide bulge conformation, which is directly linked to a switch between sugar puckers of the branch site adenosine. Our study determined a functional sugar pucker equilibrium between the transesterification active C2'-endo conformation of the branch site adenosine in the 1nt bulge and an inactive C3'-endo state in the 2nt bulge fold, allowing the group II intron to switch its activity from the branching to the exon ligation step. Our detailed NMR spectroscopic investigation identified magnesium (II) ions and the branching reaction as regulators of the equilibrium populations. The tuneable secondary structure/sugar pucker equilibrium supports a conformational selection mechanism to up- and downregulate catalytically active and inactive states of the branch site adenosine to orchestrate the multi-step splicing process. The conformational dynamics of group II intron domain 6 is also proposed to be a key aspect for the directionality selection in reversible splicing.
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Affiliation(s)
- Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas Philipp Hoernes
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Elisabeth Strebitzer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - David Klingler
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Matthias David Erlacher
- Institute of Genomics and RNomics, Biocenter, Medical 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
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19
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Meyer M, Walbott H, Oliéric V, Kondo J, Costa M, Masquida B. Conformational adaptation of UNCG loops upon crowding. RNA (NEW YORK, N.Y.) 2019; 25:1522-1531. [PMID: 31427457 PMCID: PMC6795143 DOI: 10.1261/rna.072694.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
If the A-form helix is the major structural motif found in RNA, the loops that cap them constitute the second most important family of motifs. Among those, two are overrepresented, GNRA and UNCG tetraloops. Recent surveys of RNA structures deposited in the PDB show that GNRA and UNCG tetraloops can adopt tertiary folds that are very different from their canonical conformations, characterized by the presence of a U-turn of a Z-turn, respectively. Crystallographic data from both a lariat-capping (LC) ribozyme and a group II intron ribozyme reveal that a given UUCG tetraloop can adopt a distinct fold depending on its structural environment. Specifically, when the crystal packing applies relaxed constraints on the loop, the canonical Z-turn conformation is observed. In contrast, a highly packed environment induces "squashing" of the tetraloop by distorting its sugar-phosphate backbone in a specific way that expels the first and fourth nucleobases out of the loop, and falls in van der Waals distance of the last base pair of the helix, taking the place of the pair formed between the first and fourth residues in Z-turn loops. The biological relevance of our observations is supported by the presence of similarly deformed loops in the highly packed environment of the ribosome and in a complex between a dsRNA and a RNase III. The finding that Z-turn loops change conformation under higher molecular packing suggests that, in addition to their demonstrated role in stabilizing RNA folding, they may contribute to the three-dimensional structure of RNA by mediating tertiary interactions with distal residues.
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Affiliation(s)
| | - Hélène Walbott
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Vincent Oliéric
- Paul Scherrer Institute, Swiss Light Source, 5232 Villigen PSI, Switzerland
| | - Jiro Kondo
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan
| | - Maria Costa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Benoît Masquida
- UMR7156 GMGM Université de Strasbourg - CNRS, 67084 Strasbourg, France
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20
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Dong X, Ranganathan S, Qu G, Piazza CL, Belfort M. Structural accommodations accompanying splicing of a group II intron RNP. Nucleic Acids Res 2019; 46:8542-8556. [PMID: 29790987 PMCID: PMC6144810 DOI: 10.1093/nar/gky416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/03/2018] [Indexed: 01/21/2023] Open
Abstract
Group II introns, the putative progenitors of spliceosomal introns and retrotransposons, are ribozymes that are capable of self-splicing and DNA invasion. In the cell, group II introns form ribonucleoprotein (RNP) complexes with an intron-encoded protein, which is essential to folding, splicing and retromobility of the intron. To understand the structural accommodations underlying splicing, in preparation for retromobility, we probed the endogenously expressed Lactococcus lactis Ll.LtrB group II intron RNP using SHAPE. The results, which are consistent in vivo and in vitro, provide insights into the dynamics of the intron RNP as well as RNA-RNA and RNA-protein interactions. By comparing the excised intron RNP with mutant RNPs in the precursor state, confined SHAPE profile differences were observed, indicative of rearrangements at the active site as well as disengagement at the functional RNA-protein interface in transition between the two states. The exon-binding sequences in the intron RNA, which interact with the 5' exon and the target DNA, show increased flexibility after splicing. In contrast, stability of major tertiary and protein interactions maintains the scaffold of the RNA through the splicing transition, while the active site is realigned in preparation for retromobility.
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Affiliation(s)
- Xiaolong Dong
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Srivathsan Ranganathan
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Guosheng Qu
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
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21
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Huang W, Huang Y, Xu J, Liao JL. How Does the Spliceosome Catalyze Intron Lariat Formation? Insights from Quantum Mechanics/Molecular Mechanics Free-Energy Simulations. J Phys Chem B 2019; 123:6049-6055. [DOI: 10.1021/acs.jpcb.9b04377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Wenting Huang
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
| | - Yan Huang
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China
| | - Jie-Lou Liao
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
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22
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Eysmont K, Matylla-Kulińska K, Jaskulska A, Magnus M, Konarska MM. Rearrangements within the U6 snRNA Core during the Transition between the Two Catalytic Steps of Splicing. Mol Cell 2019; 75:538-548.e3. [PMID: 31229405 DOI: 10.1016/j.molcel.2019.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 05/12/2019] [Indexed: 12/20/2022]
Abstract
The RNA catalytic core of spliceosomes as visualized by cryoelectron microscopy (cryo-EM) remains unchanged at different stages of splicing. However, we demonstrate that mutations within the core of yeast U6 snRNA modulate conformational changes between the two catalytic steps. We propose that the intramolecular stem-loop (ISL) of U6 exists in two competing states, changing between a default, non-catalytic conformation and a transient, catalytic conformation. Whereas stable interactions in the catalytic triplex promote catalysis and their disruptions favor exit from the catalytic conformation, destabilization of the lower ISL stem promotes catalysis and its stabilization supports exit from the catalytic conformation. Thus, in addition to the catalytic triplex, U6-ISL acts as an important dynamic component of the catalytic center. The relative flexibility of the lower U6-ISL stem is conserved across eukaryotes. Similar features are found in U6atac and domain V of group II introns, arguing for the generality of the proposed mechanism.
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Affiliation(s)
- Katarzyna Eysmont
- Laboratory of RNA Biology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | | | - Agata Jaskulska
- Laboratory of RNA Biology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Magnus
- Laboratory of RNA Biology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Maria M Konarska
- Laboratory of RNA Biology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
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23
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Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
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24
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Molina-Sánchez MD, Toro N. DNA cleavage and reverse splicing of ribonucleoprotein particles reconstituted in vitro with linear RmInt1 RNA. RNA Biol 2019; 16:930-939. [PMID: 30943851 DOI: 10.1080/15476286.2019.1601379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The RmInt1 group II intron is an efficient self-splicing mobile retroelement that catalyzes its own excision as lariat, linear and circular molecules. In vivo, the RmInt1 lariat and the reverse transcriptase (IEP) it encodes form a ribonucleoprotein particle (RNP) that recognizes the DNA target for site-specific full intron insertion via a two-step reverse splicing reaction. RNPs containing linear group II intron RNA are generally thought to be unable to complete the reverse splicing reaction. Here, we show that reconstituted in vitro RNPs containing linear RmInt1 ΔORF RNA can mediate the cleavage of single-stranded DNA substrates in a very precise manner with the attachment of the intron RNA to the 3´exon as the first step of a reverse splicing reaction. Notably, we also observe molecules in which the 5´exon is linked to the RmInt1 RNA, suggesting the completion of the reverse splicing reaction, albeit rather low and inefficiently. That process depends on DNA target recognition and can be successful completed by RmInt1 RNPs with linear RNA displaying 5´ modifications.
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Affiliation(s)
- María Dolores Molina-Sánchez
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
| | - Nicolás Toro
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
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25
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Belfort M, Lambowitz AM. Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032375. [PMID: 30936187 DOI: 10.1101/cshperspect.a032375] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA analysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8-4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processivity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed.
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Affiliation(s)
- Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
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26
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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27
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Chan RT, Peters JK, Robart AR, Wiryaman T, Rajashankar KR, Toor N. Structural basis for the second step of group II intron splicing. Nat Commun 2018; 9:4676. [PMID: 30410046 PMCID: PMC6224600 DOI: 10.1038/s41467-018-06678-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/17/2018] [Indexed: 11/22/2022] Open
Abstract
The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related. Here we report the 3.7 Å crystal structure of a eukaryotic group II intron in the lariat-3' exon form, immediately preceding the second step of splicing, analogous to the spliceosomal P complex. This structure reveals the location of the intact 3' splice site within the catalytic core of the group II intron. The 3'-OH of the 5' exon is positioned in close proximity to the 3' splice site for nucleophilic attack and exon ligation. The active site undergoes conformational rearrangements with the catalytic triplex having different configurations before and after the second step of splicing. We describe a complete model for the second step of group II intron splicing that incorporates a dynamic catalytic triplex being responsible for creating the binding pocket for 3' splice site capture.
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Affiliation(s)
- Russell T Chan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jessica K Peters
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron R Robart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Timothy Wiryaman
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kanagalaghatta R Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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Mohr G, Kang SYS, Park SK, Qin Y, Grohman J, Yao J, Stamos JL, Lambowitz AM. A Highly Proliferative Group IIC Intron from Geobacillus stearothermophilus Reveals New Features of Group II Intron Mobility and Splicing. J Mol Biol 2018; 430:2760-2783. [PMID: 29913158 DOI: 10.1016/j.jmb.2018.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/01/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022]
Abstract
The thermostable Geobacillus stearothermophilus GsI-IIC intron is among the few bacterial group II introns found to proliferate to high copy number in its host genome. Here, we developed a bacterial genetic assay for retrohoming and biochemical assays for protein-dependent and self-splicing of GsI-IIC. We found that GsI-IIC, like other group IIC introns, retrohomes into sites having a 5'-exon DNA hairpin, typically from a bacterial transcription terminator, followed by short intron-binding sequences (IBSs) recognized by base pairing of exon-binding sequences (EBSs) in the intron RNA. Intron RNA insertion occurs preferentially but not exclusively into the parental lagging strand at DNA replication forks, using a nascent lagging strand DNA as a primer for reverse transcription. In vivo mobility assays, selections, and mutagenesis indicated that a variety of GC-rich DNA hairpins of 7-19 bp with continuous base pairs or internal elbow regions support efficient intron mobility and identified a critically recognized nucleotide (T-5) between the hairpin and IBS1, a feature not reported previously for group IIC introns. Neither the hairpin nor T-5 is required for intron excision or lariat formation during RNA splicing, but the 5'-exon sequence can affect the efficiency of exon ligation. Structural modeling suggests that the 5'-exon DNA hairpin and T-5 bind to the thumb and DNA-binding domains of GsI-IIC reverse transcriptase. This mode of DNA target site recognition enables the intron to proliferate to high copy number by recognizing numerous transcription terminators and then finding the best match for the EBS/IBS interactions within a short distance downstream.
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Affiliation(s)
- Georg Mohr
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Sean Yoon-Seo Kang
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Seung Kuk Park
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yidan Qin
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jacob Grohman
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Yao
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer L Stamos
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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29
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Toro N, Martínez-Abarca F, Molina-Sánchez MD, García-Rodríguez FM, Nisa-Martínez R. Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution. Front Microbiol 2018; 9:627. [PMID: 29670598 PMCID: PMC5894124 DOI: 10.3389/fmicb.2018.00627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/19/2018] [Indexed: 12/26/2022] Open
Abstract
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti, the nitrogen-fixing endosymbiont of legumes of genus Medicago, harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation.
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Affiliation(s)
- Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - María D Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Fernando M García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Rafael Nisa-Martínez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
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30
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Galej WP, Toor N, Newman AJ, Nagai K. Molecular Mechanism and Evolution of Nuclear Pre-mRNA and Group II Intron Splicing: Insights from Cryo-Electron Microscopy Structures. Chem Rev 2018; 118:4156-4176. [PMID: 29377672 DOI: 10.1021/acs.chemrev.7b00499] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor. Prp8, the largest and most conserved protein in the spliceosome, cradles the active site RNA. Prp8 and group II intron maturase have a similar domain architecture, suggesting that they also share a common evolutionary origin. The interactions between maturase and key group II intron RNA elements, such as the exon-binding loop and domains V and VI, are recapitulated in the interactions between Prp8 and key elements in the spliceosome's catalytic RNA core. Structural comparisons suggest that the extensive RNA scaffold of the group II intron was gradually replaced by proteins as the spliceosome evolved. A plausible model of spliceosome evolution is discussed.
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Affiliation(s)
- Wojciech P Galej
- EMBL Grenoble , 71 Avenue des Martyrs , 38042 Grenoble Cedex 09 , France
| | - Navtej Toor
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , U.K
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31
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Stamos JL, Lentzsch AM, Lambowitz AM. Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications. Mol Cell 2017; 68:926-939.e4. [PMID: 29153391 DOI: 10.1016/j.molcel.2017.10.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/29/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022]
Abstract
Bacterial group II intron reverse transcriptases (RTs) function in both intron mobility and RNA splicing and are evolutionary predecessors of retrotransposon, telomerase, and retroviral RTs as well as the spliceosomal protein Prp8 in eukaryotes. Here we determined a crystal structure of a full-length thermostable group II intron RT in complex with an RNA template-DNA primer duplex and incoming deoxynucleotide triphosphate (dNTP) at 3.0-Å resolution. We find that the binding of template-primer and key aspects of the RT active site are surprisingly different from retroviral RTs but remarkably similar to viral RNA-dependent RNA polymerases. The structure reveals a host of features not seen previously in RTs that may contribute to distinctive biochemical properties of group II intron RTs, and it provides a prototype for many related bacterial and eukaryotic non-LTR retroelement RTs. It also reveals how protein structural features used for reverse transcription evolved to promote the splicing of both group II and spliceosomal introns.
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Affiliation(s)
- Jennifer L Stamos
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Alfred M Lentzsch
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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32
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Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K. Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection. Science 2017; 358:1283-1288. [PMID: 29146871 DOI: 10.1126/science.aar3729] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/09/2017] [Indexed: 12/27/2022]
Abstract
Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7-angstrom cryo-electron microscopy structure of the yeast P-complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5' splice site and the branch-point adenosine. After the branching reaction, protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanism of exon ligation.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | | | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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33
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Scheres SH, Nagai K. CryoEM structures of spliceosomal complexes reveal the molecular mechanism of pre-mRNA splicing. Curr Opin Struct Biol 2017; 46:130-139. [PMID: 28888105 DOI: 10.1016/j.sbi.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/26/2017] [Accepted: 08/07/2017] [Indexed: 01/09/2023]
Abstract
The spliceosome is an intricate molecular machine which catalyses the removal of introns from eukaryotic mRNA precursors by two trans-esterification reactions (branching and exon ligation) to produce mature mRNA with uninterrupted protein coding sequences. The structures of the spliceosome in several key states determined by electron cryo-microscopy have greatly advanced our understanding of its molecular mechanism. The catalytic RNA core is formed during the activation of the fully assembled B to Bact complex and remains largely unchanged throughout the splicing cycle. RNA helicases and step specific factors regulate docking and undocking of the substrates (branch site and 3' splice site) to the single RNA-based active site to catalyse the two trans-esterification reactions.
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Affiliation(s)
- Sjors Hw Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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34
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Novikova O, Belfort M. Mobile Group II Introns as Ancestral Eukaryotic Elements. Trends Genet 2017; 33:773-783. [PMID: 28818345 DOI: 10.1016/j.tig.2017.07.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/06/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes. Although there is no doubt that prokaryotic and organellar group II introns are evolutionary related, there are remarkable differences in survival strategies between them. Furthermore, an evolutionary relationship of group II introns to eukaryotic retroelements, including telomeres, and spliceosomes is unmistakable.
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Affiliation(s)
- Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA.
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35
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DasGupta S, Suslov NB, Piccirilli JA. Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme. J Am Chem Soc 2017; 139:9591-9597. [PMID: 28625058 PMCID: PMC5929484 DOI: 10.1021/jacs.7b03655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate helix register into a so-called "shifted" conformation that is critical for substrate binding and activation. We report a 3.3 Å crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme. Comparison to previous NMR structures of isolated, inactive substrates provides a physical description of substrate remodeling, and implicates roles for tertiary interactions in catalytic activation of the cleavage loop. Similarities to the hairpin ribozyme cleavage loop activation suggest general strategies to enhance fidelity in RNA folding and ribozyme cleavage.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- 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
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36
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Zhao C, Pyle AM. Structural Insights into the Mechanism of Group II Intron Splicing. Trends Biochem Sci 2017; 42:470-482. [PMID: 28438387 PMCID: PMC5492998 DOI: 10.1016/j.tibs.2017.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 12/19/2022]
Abstract
While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity. Finally, these ribozymes can now be viewed in their larger, more natural context as components of holoenzymes that include encoded maturase proteins. These studies expand our understanding of group II intron structural diversity and evolution, while setting the stage for rigorous mechanistic analysis of RNA splicing machines.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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37
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Ngu M, Massel K, Bonen L. Group II introns in wheat mitochondria have degenerate structural features and varied splicing pathways. Int J Biochem Cell Biol 2017; 91:156-167. [PMID: 28495309 DOI: 10.1016/j.biocel.2017.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/28/2017] [Accepted: 05/06/2017] [Indexed: 11/29/2022]
Abstract
Mitochondrial introns in flowering plant genes are virtually all classified as members of the group II ribozyme family although certain structural features have degenerated to varying degrees over evolutionary time. We are interested in the impact that unconventional intron architecture might have on splicing biochemistry in vivo and we have focused in particular on intronic domains V and VI, which for self-splicing introns provide a key component of the catalytic core and the bulged branchpoint adenosine, respectively. Notably, the two transesterification steps in classical group II splicing are the same as for nuclear spliceosomal introns and release the intron as a lariat. Using RT-PCR and circularized RT-PCR, we had previously demonstrated that several wheat mitochondrial introns which lack a branchpoint adenosine have atypical splicing pathways, and we have now extended this analysis to the full set of wheat introns, namely six trans-splicing and sixteen cis-splicing ones. A number of introns are excised using non-lariat pathways and interestingly, we find that several introns which do have a conventional domain VI also use pathways that appear to exploit other internal or external nucleophiles, with the lariat form being relatively minor. Somewhat surprisingly, several introns with weakly-structured domain V/VI helices still exhibit classical lariat splicing, suggesting that accessory factors aid in restoring a splicing-competent conformation. Our observations illustrate that the loss of conventional group II features during evolution is correlated with altered splicing biochemistry in an intron-distinctive manner.
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Affiliation(s)
- Matthew Ngu
- Biology Department, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Karen Massel
- Biology Department, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Linda Bonen
- Biology Department, University of Ottawa, Ottawa, K1N 6N5, Canada.
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