1
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Yang WQ, Ge JY, Zhang X, Zhu WY, Lin L, Shi Y, Xu B, Liu RJ. THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration. Nucleic Acids Res 2024; 52:3291-3309. [PMID: 38165050 PMCID: PMC11014329 DOI: 10.1093/nar/gkad1243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
The mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G) on the G72 of U6 snRNA (the catalytic center of the spliceosome) promotes efficient pre-mRNA splicing activity in human cells. This modification was identified to be conserved among vertebrates. Further, THUMPD2 was demonstrated as the methyltransferase responsible for U6 m2G72 by explicitly recognizing the U6-specific sequences and structural elements. The knock-out of THUMPD2 eliminated U6 m2G72 and impaired the pre-mRNA splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mRNAs in human cells. Notably, the aberrantly spliced pre-mRNA population elicited the nonsense-mediated mRNA decay pathway. We further show that THUMPD2 was associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome regulates global pre-mRNA splicing and impacts physiology and disease.
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Affiliation(s)
- Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian-Yang Ge
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaofeng Zhang
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, China
| | - Wen-Yu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lin Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yigong Shi
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310064,Zhejiang Province, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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2
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O'Connell AA, Hanson JA, McCaskill DC, Moore ET, Lewis DC, Grover N. Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop. RNA (NEW YORK, N.Y.) 2019; 25:1779-1792. [PMID: 31548339 PMCID: PMC6859860 DOI: 10.1261/rna.070466.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
U6 RNA contains a 1 × 2-nt internal loop that folds and unfold during spliceosomal assembly and activation. The 1 × 2 loop consists of a C67•A79 base pair that forms an additional hydrogen bond upon protonation, C67•A+79, and uracil (U80) that coordinates the catalytically essential magnesium ions. We designed a series of RNA and DNA constructs with a 1 × 2 loop sequence contained in the ISL, and its modifications, to measure the thermodynamic effects of protonation and magnesium binding using UV-visible thermal denaturation experiments. We show that the wild-type RNA construct gains 0.43 kcal/mol in 1 M KCl upon lowering the pH from 7.5 to 5.5; the presence of magnesium ions increases its stability by 2.17 kcal/mol at pH 7.5 over 1 M KCl. Modifications of the helix closing base pairs from C-G to U•G causes a loss in protonation-dependent stability and a decrease in stability in the presence of magnesium ions, especially in the C68U construct. A79G single-nucleotide bulge loop construct showed the largest gain in stability in the presence of magnesium ions. The DNA wild-type construct shows a smaller effect on stability upon lowering the pH and in the presence of magnesium ions, highlighting differences in RNA and DNA structures. A U6 RNA 1 × 2 loop sequence is rare in the databases examined.
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Affiliation(s)
- Allison A O'Connell
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Jared A Hanson
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Darryl C McCaskill
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Ethan T Moore
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Daniel C Lewis
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Neena Grover
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
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3
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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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4
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An Allosteric Network for Spliceosome Activation Revealed by High-Throughput Suppressor Analysis in Saccharomyces cerevisiae. Genetics 2019; 212:111-124. [PMID: 30898770 DOI: 10.1534/genetics.119.301922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/15/2019] [Indexed: 12/30/2022] Open
Abstract
Selection of suppressor mutations that correct growth defects caused by substitutions in an RNA or protein can reveal functionally important molecular structures and interactions in living cells. This approach is particularly useful for the study of complex biological pathways involving many macromolecules, such as premessenger RNA (pre-mRNA) splicing. When a sufficiently large number of suppressor mutations is obtained and structural information is available, it is possible to generate detailed models of molecular function. However, the laborious and expensive task of identifying suppressor mutations in whole-genome selections limits the utility of this approach. Here I show that a custom targeted sequencing panel can greatly accelerate the identification of suppressor mutations in the Saccharomyces cerevisiae genome. Using a panel that targets 112 genes encoding pre-mRNA splicing factors, I identified 27 unique mutations in six protein-coding genes that each overcome the cold-sensitive block to spliceosome activation caused by a substitution in U4 small nuclear RNA. When mapped to existing structures of spliceosomal complexes, the identified suppressors implicate specific molecular contacts between the proteins Brr2, Prp6, Prp8, Prp31, Sad1, and Snu114 as functionally important in an early step of catalytic activation of the spliceosome. This approach shows great promise for elucidating the allosteric cascade of molecular interactions that direct accurate and efficient pre-mRNA splicing and should be broadly useful for understanding the dynamics of other complex biological assemblies or pathways.
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5
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Didychuk AL, Butcher SE, Brow DA. The life of U6 small nuclear RNA, from cradle to grave. RNA (NEW YORK, N.Y.) 2018; 24:437-460. [PMID: 29367453 PMCID: PMC5855946 DOI: 10.1261/rna.065136.117] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Removal of introns from precursor messenger RNA (pre-mRNA) and some noncoding transcripts is an essential step in eukaryotic gene expression. In the nucleus, this process of RNA splicing is carried out by the spliceosome, a multi-megaDalton macromolecular machine whose core components are conserved from yeast to humans. In addition to many proteins, the spliceosome contains five uridine-rich small nuclear RNAs (snRNAs) that undergo an elaborate series of conformational changes to correctly recognize the splice sites and catalyze intron removal. Decades of biochemical and genetic data, along with recent cryo-EM structures, unequivocally demonstrate that U6 snRNA forms much of the catalytic core of the spliceosome and is highly dynamic, interacting with three snRNAs, the pre-mRNA substrate, and >25 protein partners throughout the splicing cycle. This review summarizes the current state of knowledge on how U6 snRNA is synthesized, modified, incorporated into snRNPs and spliceosomes, recycled, and degraded.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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6
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Martin WJ, Reiter NJ. Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes. Biochemistry 2016; 56:3-13. [PMID: 27935277 DOI: 10.1021/acs.biochem.6b01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Over billions of years of evolution, nature has embraced proteins as the major workhorse molecules of the cell. However, nearly every aspect of metabolism is dependent upon how structured RNAs interact with proteins, ligands, and other nucleic acids. Key processes, including telomere maintenance, RNA processing, and protein synthesis, require large RNAs that assemble into elaborate three-dimensional shapes. These RNAs can (i) act as flexible scaffolds for protein subunits, (ii) participate directly in substrate recognition, and (iii) serve as catalytic components. Here, we juxtapose the near atomic level interactions of three ribonucleoprotein complexes: ribonuclease P (involved in 5' pre-tRNA processing), the spliceosome (responsible for pre-mRNA splicing), and telomerase (an RNA-directed DNA polymerase that extends the ends of chromosomes). The focus of this perspective is profiling the structural and dynamic roles of RNAs at the core of these enzymes, highlighting how large RNAs contribute to molecular recognition and catalysis.
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Affiliation(s)
- William J Martin
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Nicholas J Reiter
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
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7
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Rodgers ML, Didychuk AL, Butcher SE, Brow DA, Hoskins AA. A multi-step model for facilitated unwinding of the yeast U4/U6 RNA duplex. Nucleic Acids Res 2016; 44:10912-10928. [PMID: 27484481 PMCID: PMC5159527 DOI: 10.1093/nar/gkw686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/17/2016] [Accepted: 07/22/2016] [Indexed: 11/15/2022] Open
Abstract
The small nuclear RNA (snRNA) components of the spliceosome undergo many conformational rearrangements during its assembly, catalytic activation and disassembly. The U4 and U6 snRNAs are incorporated into the spliceosome as a base-paired complex within the U4/U6.U5 small nuclear ribonucleoprotein (tri-snRNP). U4 and U6 are then unwound in order for U6 to pair with U2 to form the spliceosome's active site. After splicing, U2/U6 is unwound and U6 annealed to U4 to reassemble the tri-snRNP. U6 rearrangements are crucial for spliceosome formation but are poorly understood. We have used single-molecule Förster resonance energy transfer and unwinding assays to identify interactions that promote U4/U6 unwinding and have studied their impact in yeast. We find that U4/U6 is efficiently unwound using DNA oligonucleotides by coupling unwinding of U4/U6 stem II with strand invasion of stem I. Unwinding is stimulated by the U6 telestem, which transiently forms in the intact U4/U6 RNA complex. Stabilization of the telestem in vivo results in accumulation of U4/U6 di-snRNP and impairs yeast growth. Our data reveal conserved mechanisms for U4/U6 unwinding and indicate telestem dynamics are critical for tri-snRNP assembly and stability.
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Affiliation(s)
- Margaret L Rodgers
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Allison L Didychuk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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8
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Tomcho JC, Tillman MR, Znosko BM. Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability. Biochemistry 2015; 54:5290-6. [PMID: 26286708 DOI: 10.1021/acs.biochem.5b00474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.
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Affiliation(s)
- Jeremy C Tomcho
- Department of Chemistry, Saint Louis University , Saint Louis, Missouri 63103, United States
| | - Magdalena R Tillman
- Department of Chemistry, Saint Louis University , Saint Louis, Missouri 63103, United States
| | - Brent M Znosko
- Department of Chemistry, Saint Louis University , Saint Louis, Missouri 63103, United States
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9
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Burke JE, Butcher SE, Brow DA. Spliceosome assembly in the absence of stable U4/U6 RNA pairing. RNA (NEW YORK, N.Y.) 2015; 21:923-34. [PMID: 25762536 PMCID: PMC4408799 DOI: 10.1261/rna.048421.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/10/2015] [Indexed: 05/08/2023]
Abstract
The cycle of spliceosome assembly, intron excision, and spliceosome disassembly involves large-scale structural rearrangements of U6 snRNA that are functionally important. U6 enters the splicing pathway bound to the Prp24 protein, which chaperones annealing of U6 to U4 RNA to form a U4/U6 di-snRNP. During catalytic activation of the assembled spliceosome, U4 snRNP is released and U6 is paired to U2 snRNA. Here we show that point mutations in U4 and U6 that decrease U4/U6 base-pairing in vivo are lethal in combination. However, this synthetic phenotype is rescued by a mutation in U6 that alters a U6-Prp24 contact and stabilizes U2/U6. Remarkably, the resulting viable triple mutant strain lacks detectable U4/U6 base-pairing and U4/U6 di-snRNP. Instead, this strain accumulates free U4 snRNP, protein-free U6 RNA, and a novel complex containing U2/U6 di-snRNP. Further mutational analysis indicates that disruption of the U6-Prp24 interaction rather than stabilization of U2/U6 renders stable U4/U6 di-snRNP assembly nonessential. We propose that an essential function of U4/U6 pairing is to displace Prp24 from U6 RNA, and thus a destabilized U6-Prp24 complex renders stable U4/U6 pairing nonessential.
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MESH Headings
- Base Pairing
- Base Sequence
- Epistasis, Genetic
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Mutation
- Nucleic Acid Conformation
- Protein Multimerization
- RNA Splicing/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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10
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Zhang L, Li X, Hill RC, Qiu Y, Zhang W, Hansen KC, Zhao R. Brr2 plays a role in spliceosomal activation in addition to U4/U6 unwinding. Nucleic Acids Res 2015; 43:3286-97. [PMID: 25670679 PMCID: PMC4381053 DOI: 10.1093/nar/gkv062] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 01/19/2015] [Indexed: 12/22/2022] Open
Abstract
Brr2 is a DExD/H-box RNA helicase that is responsible for U4/U6 unwinding, a critical step in spliceosomal activation. Brr2 is a large protein (∼250 kD) that consists of an N-terminal domain (∼500 residues) with unknown function and two Hel308-like modules that are responsible for RNA unwinding. Here we demonstrate that removal of the entire N-terminal domain is lethal to Saccharomyces cerevisiae and deletion of the N-terminal 120 residues leads to splicing defects and severely impaired growth. This N-terminal truncation does not significantly affect Brr2's helicase activity. Brr2-Δ120 can be successfully assembled into the tri-snRNP (albeit at a lower level than the WT Brr2) and the spliceosomal B complex. However, the truncation significantly impairs spliceosomal activation, leading to a dramatic reduction of U5, U6 snRNAs and accumulation of U1 snRNA in the Bact complex. The N-terminal domain of Brr2 does not seem to be directly involved in regulating U1/5'ss unwinding. Instead, the N-terminal domain seems to be critical for retaining U5 and U6 snRNPs during/after spliceosomal activation through its interaction with snRNAs and possibly other spliceosomal proteins, revealing a new role of Brr2 in spliceosomal activation in addition to U4/U6 unwinding.
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Affiliation(s)
- Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yan Qiu
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050018, P. R. China
| | - Wenzheng Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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11
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Murray MH, Hard JA, Znosko BM. Improved model to predict the free energy contribution of trinucleotide bulges to RNA duplex stability. Biochemistry 2014; 53:3502-8. [PMID: 24853497 PMCID: PMC4051427 DOI: 10.1021/bi500204e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Trinucleotide
bulges in RNA commonly occur in nature. Yet, little
data exists concerning the thermodynamic parameters of this motif.
Algorithms that predict RNA secondary structure from sequence currently
attribute a constant free energy value of 3.2 kcal/mol to all trinucleotide
bulges, regardless of bulge sequence. To test the accuracy of this
model, RNA duplexes that contain frequent naturally occurring trinucleotide
bulges were optically melted, and their thermodynamic parameters—enthalpy,
entropy, free energy, and melting temperature—were determined.
The thermodynamic data were used to derive a new model to predict
the free energy contribution of trinucleotide bulges to RNA duplex
stability: ΔG°37, trint bulge = ΔG°37, bulge + ΔG°37, AU + ΔG°37, GU. The parameter ΔG°37, bulge is variable depending upon the purine
and pyrimidine composition of the bulge, ΔG°37, AU is a 0.49 kcal/mol penalty for an A-U
closing pair, and ΔG° 37, GU is a −0.56 kcal/mol bonus for a G-U closing pair. With both
closing pair and bulge sequence taken into account, this new model
predicts free energy values within 0.30 kcal/mol of the experimental
value. The new model can be used by algorithms that predict RNA free
energies as well as algorithms that use free energy minimization to
predict RNA secondary structure from sequence.
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Affiliation(s)
- Meghan H Murray
- Department of Chemistry, Saint Louis University , Saint Louis, Missouri 63103, United States
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12
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Montemayor EJ, Curran EC, Liao HH, Andrews KL, Treba CN, Butcher SE, Brow DA. Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution. Nat Struct Mol Biol 2014; 21:544-51. [PMID: 24837192 PMCID: PMC4141773 DOI: 10.1038/nsmb.2832] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/28/2014] [Indexed: 12/11/2022]
Abstract
The spliceosome is a dynamic assembly of five small nuclear ribonucleoproteins
(snRNPs) that removes introns from eukaryotic pre-mRNA. U6 is the most conserved of the
spliceosomal snRNAs and participates directly in catalysis. Here, we report the crystal
structure of the Saccharomyces cerevisiae U6 snRNP core, containing most
of U6 snRNA and all four RRM domains of the Prp24 protein. It reveals a unique interlocked
RNP architecture that sequesters the 5′ splice site-binding bases of U6 snRNA.
RRMs 1, 2 and 4 of Prp24 form an electropositive groove that binds double-stranded RNA and
may nucleate annealing of U4 and U6 snRNAs. Substitutions in Prp24 that suppress a
mutation in U6 localize to direct RNA-protein contacts. Our results provide the most
complete view to date of a multi-RRM protein bound to RNA, and reveal striking
co-evolution of protein and RNA structure.
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Affiliation(s)
- Eric J Montemayor
- 1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2] Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth C Curran
- 1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2]
| | - Hong Hong Liao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kristie L Andrews
- 1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2]
| | - Christine N Treba
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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13
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Li X, Zhang W, Xu T, Ramsey J, Zhang L, Hill R, Hansen KC, Hesselberth JR, Zhao R. Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly. Nucleic Acids Res 2013; 41:3805-18. [PMID: 23393194 PMCID: PMC3616732 DOI: 10.1093/nar/gkt062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Prp8 stands out among hundreds of splicing factors as a protein that is intimately involved in spliceosomal activation and the catalytic reaction. Here, we present the first comprehensive in vivo RNA footprints for Prp8 in budding yeast obtained using CLIP (cross-linking and immunoprecipitation)/CRAC (cross-linking and analyses of cDNAs) and next-generation DNA sequencing. These footprints encompass known direct Prp8-binding sites on U5, U6 snRNA and intron-containing pre-mRNAs identified using site-directed cross-linking with in vitro assembled small nuclear ribonucleoproteins (snRNPs) or spliceosome. Furthermore, our results revealed novel Prp8-binding sites on U1 and U2 snRNAs. We demonstrate that Prp8 directly cross-links with U2, U5 and U6 snRNAs and pre-mRNA in purified activated spliceosomes, placing Prp8 in position to bring the components of the active site together. In addition, disruption of the Prp8 and U1 snRNA interaction reduces tri-snRNP level in the spliceosome, suggesting a previously unknown role of Prp8 in spliceosomal assembly through its interaction with U1 snRNA.
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Affiliation(s)
- Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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14
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Rasche N, Dybkov O, Schmitzová J, Akyildiz B, Fabrizio P, Lührmann R. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre. EMBO J 2012; 31:1591-604. [PMID: 22246180 DOI: 10.1038/emboj.2011.502] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 12/15/2011] [Indexed: 11/09/2022] Open
Abstract
RNA-structural elements play key roles in pre-mRNA splicing catalysis; yet, the formation of catalytically competent RNA structures requires the assistance of spliceosomal proteins. We show that the S. cerevisiae Cwc2 protein functions prior to step 1 of splicing, and it is not required for the Prp2-mediated spliceosome remodelling that generates the catalytically active B complex, suggesting that Cwc2 plays a more sophisticated role in the generation of a functional catalytic centre. In active spliceosomes, Cwc2 contacts catalytically important RNA elements, including the U6 internal stem-loop (ISL), and regions of U6 and the pre-mRNA intron near the 5' splice site, placing Cwc2 at/near the spliceosome's catalytic centre. These interactions are evolutionarily conserved, as shown by studies with Cwc2's human counterpart RBM22, indicating that Cwc2/RBM22-RNA contacts are functionally important. We propose that Cwc2 induces an active conformation of the spliceosome's catalytic RNA elements. Thus, the function of RNA-RNA tertiary interactions within group II introns, namely to induce an active conformation of domain V, may be fulfilled by proteins that contact the functionally analogous U6-ISL, within the spliceosome.
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Affiliation(s)
- Nicolas Rasche
- Department of Cellular Biochemistry, Max-Planck-Institute of Biophysical Chemistry, Göttingen, Germany
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15
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Abstract
The spliceosome is a massive complex of 5 RNAs and many proteins that associate to catalyze precursor messenger RNA splicing. The process of splicing involves two phosphoryl transfer reactions that result in intron excision and ligation of the flanking exons. Since it is required for normal protein production in eukaryotic cells, pre-mRNA splicing is an essential step in gene expression. Although high resolution structural views of the spliceosome do not yet exist, a growing body of evidence indicates that the spliceosome is a magnesium-dependent enzyme that utilizes catalytic metal ions to stabilize both transition states during the two phosphoryl transfer steps of splicing. A wealth of data also indicate that the core of the spliceosome is comprised of RNA, and suggest that the spliceosome may be a ribozyme. This chapter presents the evidence for metal ion catalysis by the spliceosome, draws comparisons to similar RNA enzymes, and discusses the future directions for research into the mechanism of pre-mRNA splicing.
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Affiliation(s)
- Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA.
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Delihas N. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids. PLoS One 2009; 4:e7941. [PMID: 19936201 PMCID: PMC2775950 DOI: 10.1371/journal.pone.0007941] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 10/27/2009] [Indexed: 11/19/2022] Open
Abstract
Background Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. Methodology/Principal Findings In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found “free-standing” and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3′ ends of lipoprotein genes (PFam12 and PFam60), however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. Conclusions/Significance Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in an RNA format. The findings show that IS605 stem loop sequences are multifaceted and are selectively conserved during evolution when the transposable element dissipates.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, State University of New York, Stony Brook, New York, United States of America.
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Wahid AM, Coventry VK, Conn GL. The PKR-binding domain of adenovirus VA RNAI exists as a mixture of two functionally non-equivalent structures. Nucleic Acids Res 2009; 37:5830-7. [PMID: 19635730 PMCID: PMC2761268 DOI: 10.1093/nar/gkp595] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
VA RNAI is a non-coding adenoviral transcript that counteracts the host cell anti-viral defenses such as immune responses mediated via PKR. We investigated potential alternate secondary structure conformations within the PKR-binding domain of VA RNAI using site-directed mutagenesis, RNA UV-melting analysis and enzymatic RNA secondary structure probing. The latter data clearly indicated that the wild-type VA RNAI apical stem can adopt two different conformations and that it exists as a mixed population of these two structures. In contrast, in two sequence variants we designed to eliminate one of the possible structures, while leaving the other intact, each formed a unique secondary structure. This clarification of the apical stem pairing also suggests a small alteration to the apical stem–loop secondary structure. The relative ability of the two apical stem conformations to bind PKR and inhibit kinase activity was measured by isothermal titration calorimetry and PKR autophosphorylation inhibition assay. We found that the two sequence variants displayed markedly different activities, with one being a significantly poorer binder and inhibitor of PKR. Whether the presence of the VA RNAI conformation with reduced PKR inhibitory activity is directly beneficial to the virus in the cell for some other function requires further investigation.
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Affiliation(s)
- Ahmed M Wahid
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN
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Venditti V, Clos L, Niccolai N, Butcher SE. Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping. J Mol Biol 2009; 391:894-905. [PMID: 19591840 DOI: 10.1016/j.jmb.2009.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/29/2009] [Accepted: 07/01/2009] [Indexed: 11/28/2022]
Abstract
The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6.5). Lower pH favors formation of a protonated C-A(+) wobble pair and base flipping of the adjacent uracil. Higher pH favors stacking of the uracil and allows an essential metal ion to bind at this position. Here, we define the minimal-energy path for this conformational transition. To do this, we solved the U6 ISL structure at higher pH (8.0) in order to eliminate interference from the low-pH conformer. This structure reveals disruption of the protonated C-A(+) pair and formation of a new C-U pair, which explains the preference for a stacked uracil at higher pH. Next, we used nudged elastic band molecular dynamics simulations to calculate the minimum-energy path between the two conformations. Our results indicate that the C-U pair is dynamic, which allows formation of the more stable C-A(+) pair upon adenine protonation. After formation of the C-A(+) pair, the unpaired uracil follows a minor-groove base-flipping pathway. Molecular dynamics simulations suggest that the extrahelical uracil is stabilized by contacts with the adjacent helix.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, Italy
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19
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Workman H, Flynn PF. Stabilization of RNA oligomers through reverse micelle encapsulation. J Am Chem Soc 2009; 131:3806-7. [PMID: 19292481 DOI: 10.1021/ja8084753] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cellular milieu is rich in diversity of both simple and complex molecules and is also quite crowded. By contrast, typical sample concentrations employed for in vitro investigation of biophysics and structural biology make use of purified macromolecules in simple buffer systems at concentrations that range from micromolar to millimolar. Although this formulation has proven to be compatible with a wide range of biological and structural studies, it is quite different from the relatively crowded conditions typically found within cells. The importance of these crowding effects for proteins has been recognized for some time, but the equivalent analysis is underexplored in nucleic acids. Encapsulation with surfactant-based reverse micelles has emerged as an effective biophysical tool, allowing study of the influence of ionic strength, pH, hydration, and crowding on biologically active macromolecules over a wide range of conditions. We have encapsulated an oligonucleotide model of TAR RNA from HIV and the 5' stem loop oligonucleotide of the U4 snRNA. Observation of imino (1)H resonances is an established method for evaluating the stability of nucleic acid oligonucleotides, implying the presence of stacked, hydrogen bonded base pairs. Inspection of (1)H NMR spectra of the RNA molecules reveals that the intensity of several of the imino resonances increases upon encapsulation. Additional resonances not observed in spectra of the oligonucleotides free in solution support the suggestion that the molecules have gained stability. These results indicate that RNA oligonucleotides may acquire significant stability in the presence of cellular levels of crowding.
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Affiliation(s)
- Hillary Workman
- Department of Chemistry, 315 South 1400 East Room 2020, University of Utah, Salt Lake City, Utah 84112, USA
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Delihas N. Intergenic regions of Borrelia plasmids contain phylogenetically conserved RNA secondary structure motifs. BMC Genomics 2009; 10:101. [PMID: 19267927 PMCID: PMC2674063 DOI: 10.1186/1471-2164-10-101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 03/06/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Borrelia species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences and appear to be in a state of flux, but they may serve as reservoirs for evolutionary change and/or maintain stable motifs such as small RNA genes. RESULTS In an in silico study, intergenic regions of Borrelia plasmids were scanned for phylogenetically conserved stem loop structures that may represent functional units at the RNA level. Five repeat sequences were found that could fold into stable RNA-type stem loop structures, three of which are closely linked to protein genes, one of which is a member of the Borrelia lipoprotein_1 super family genes and another is the complement regulator-acquiring surface protein_1 (CRASP-1) family. Modeled secondary structures of repeat sequences display numerous base-pair compensatory changes in stem regions, including C-G-->A-U transversions when orthologous sequences are compared. Base-pair compensatory changes constitute strong evidence for phylogenetic conservation of secondary structure. CONCLUSION Intergenic regions of Borrelia species carry evolutionarily stable RNA secondary structure motifs. Of major interest is that some motifs are associated with protein genes that show large sequence variability. The cell may conserve these RNA motifs whereas allow a large flux in amino acid sequence, possibly to create new virulence factors but with associated RNA motifs intact.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, Suny, Stony Brook, NY 11794-5222, USA.
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Sperling J, Azubel M, Sperling R. Structure and function of the Pre-mRNA splicing machine. Structure 2009; 16:1605-15. [PMID: 19000813 DOI: 10.1016/j.str.2008.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/22/2008] [Accepted: 08/27/2008] [Indexed: 12/14/2022]
Abstract
Most eukaryotic pre-mRNAs contain non-coding sequences (introns) that must be removed in order to accurately place the coding sequences (exons) in the correct reading frame. This critical regulatory pre-mRNA splicing event is fundamental in development and cancer. It occurs within a mega-Dalton multicomponent machine composed of RNA and proteins, which undergoes dynamic changes in RNA-RNA, RNA-protein, and protein-protein interactions during the splicing reaction. Recent years have seen progress in functional and structural analyses of the splicing machine and its subcomponents, and this review is focused on structural aspects of the pre-mRNA splicing machine and their mechanistic implications on the splicing of multi-intronic pre-mRNAs. It brings together, in a comparative manner, structural information on spliceosomes and their intermediates in the stepwise assembly process in vitro, and on the preformed supraspliceosomes, which are isolated from living cell nuclei, with a view of portraying a consistent picture.
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Affiliation(s)
- Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Chen XS, White WTJ, Collins LJ, Penny D. Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS One 2008; 3:e3106. [PMID: 18769729 PMCID: PMC2518118 DOI: 10.1371/journal.pone.0003106] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 08/11/2008] [Indexed: 11/23/2022] Open
Abstract
RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing mechanisms in eukaryotes. In most eukaryotes splicing is predominantly catalysed by the major spliceosome complex, which consists of five uridine-rich small nuclear RNAs (U-snRNAs) and over 200 proteins in humans. Three major spliceosomal introns have been found experimentally in Giardia; one Giardia U-snRNA (U5) and a number of spliceosomal proteins have also been identified. However, because of the low sequence similarity between the Giardia ncRNAs and those of other eukaryotes, the other U-snRNAs of Giardia had not been found. Using two computational methods, candidates for Giardia U1, U2, U4 and U6 snRNAs were identified in this study and shown by RT-PCR to be expressed. We found that identifying a U2 candidate helped identify U6 and U4 based on interactions between them. Secondary structural modelling of the Giardia U-snRNA candidates revealed typical features of eukaryotic U-snRNAs. We demonstrate a successful approach to combine computational and experimental methods to identify expected ncRNAs in a highly divergent protist genome. Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Allan Wilson Centre for Molecular Ecology and Evolution, IMBS, Massey University, Palmerston North, New Zealand.
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Smith DJ, Query CC, Konarska MM. "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. Mol Cell 2008; 30:657-66. [PMID: 18570869 DOI: 10.1016/j.molcel.2008.04.013] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Indexed: 11/18/2022]
Abstract
The spliceosome is both compositionally and conformationally dynamic. Each transition along the splicing pathway presents an opportunity for progression, pausing, or discard, allowing splice site choice to be regulated throughout both the assembly and catalytic phases of the reaction.
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