1
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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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2
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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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3
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Kück U, Schmitt O. The Chloroplast Trans-Splicing RNA-Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii. Cells 2021; 10:cells10020290. [PMID: 33535503 PMCID: PMC7912774 DOI: 10.3390/cells10020290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022] Open
Abstract
In eukaryotes, RNA trans-splicing is a significant RNA modification process for the end-to-end ligation of exons from separately transcribed primary transcripts to generate mature mRNA. So far, three different categories of RNA trans-splicing have been found in organisms within a diverse range. Here, we review trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. We discuss the origin of intronic sequences and the evolutionary relationship between chloroplast ribonucleoprotein complexes and the nuclear spliceosome. Finally, we focus on the ribonucleoprotein supercomplex involved in trans-splicing of chloroplast group II introns from the green alga Chlamydomonas reinhardtii. This complex has been well characterized genetically and biochemically, resulting in a detailed picture of the chloroplast ribonucleoprotein supercomplex. This information contributes substantially to our understanding of the function of RNA-processing machineries and might provide a blueprint for other splicing complexes involved in trans- as well as cis-splicing of organellar intron RNAs.
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4
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Chu H, Perea W, Greenbaum NL. Role of the central junction in folding topology of the protein-free human U2-U6 snRNA complex. RNA (NEW YORK, N.Y.) 2020; 26:836-850. [PMID: 32220895 PMCID: PMC7297123 DOI: 10.1261/rna.073379.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/16/2020] [Indexed: 06/02/2023]
Abstract
U2 and U6 small nuclear (sn)RNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA, but assembly and rearrangement steps prior to catalysis require numerous proteins. Previous studies have shown that the protein-free U2-U6 snRNA complex adopts two conformations in equilibrium, characterized by four and three helices surrounding a central junction. The four-helix conformer is strongly favored in the in vitro protein-free state, but the three-helix conformer predominates in spliceosomes. To analyze the role of the central junction in positioning elements forming the active site, we derived three-dimensional models of the two conformations from distances measured between fluorophores at selected locations in constructs representing the protein-free human U2-U6 snRNA complex by time-resolved fluorescence resonance energy transfer. Data describing four angles in the four-helix conformer suggest tetrahedral geometry; addition of Mg2+ results in shortening of the distances between neighboring helices, indicating compaction of the complex around the junction. In contrast, the three-helix conformer shows a closer approach between helices bearing critical elements, but the addition of Mg2+ widens the distance between them; thus in neither conformer are the critical helices positioned to favor the proposed triplex interaction. The presence of Mg2+ also enhances the fraction of the three-helix conformer, as does incubation with the Prp19-related protein RBM22, which has been implicated in the remodeling of the U2-U6 snRNA complex to render it catalytically active. These data suggest that although the central junction assumes a significant role in orienting helices, spliceosomal proteins and Mg2+ facilitate formation of the catalytically active conformer.
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Affiliation(s)
- Huong Chu
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - William Perea
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10065, USA
| | - Nancy L Greenbaum
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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5
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Borišek J, Magistrato A. All-Atom Simulations Decrypt the Molecular Terms of RNA Catalysis in the Exon-Ligation Step of the Spliceosome. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00390] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Alessandra Magistrato
- CNR-IOM-Democritos national Simulation Center c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
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6
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Zhang L, Vielle A, Espinosa S, Zhao R. RNAs in the spliceosome: Insight from cryoEM structures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1523. [PMID: 30729694 DOI: 10.1002/wrna.1523] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/12/2018] [Accepted: 12/28/2018] [Indexed: 12/28/2022]
Abstract
Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex. The spliceosome undergoes dramatic compositional and conformational changes through the splicing cycle, forming at least 10 distinct complexes. Recent high-resolution cryoEM structures of various spliceosomal complexes revealed unprecedented details of this large molecular machine. This review highlights insight into the structure and function of the spliceosomal RNA components obtained from these new structures, with a focus on the yeast spliceosome. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Anne Vielle
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
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7
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Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs. Genes (Basel) 2018; 9:genes9110531. [PMID: 30400232 PMCID: PMC6266926 DOI: 10.3390/genes9110531] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/26/2018] [Indexed: 12/25/2022] Open
Abstract
Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m⁵C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.
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8
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Shender VO, Arapidi GP, Pavlyukov MS, Shnaider PV, Anufrieva KS, Stepanov GA, Govorun VM. The Role of Intercellular Communication in Cancer Progression. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018040179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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9
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Tagami S, Attwater J, Holliger P. Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function. Nat Chem 2017; 9:325-332. [PMID: 28338682 DOI: 10.1038/nchem.2739] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/20/2017] [Indexed: 11/09/2022]
Abstract
The emergence of functional interactions between nucleic acids and polypeptides was a key transition in the origin of life and remains at the heart of all biology. However, how and why simple non-coded peptides could have become critical for RNA function is unclear. Here, we show that putative ancient peptide segments from the cores of both ribosomal subunits enhance RNA polymerase ribozyme (RPR) function, as do derived homopolymeric peptides comprising lysine or the non-proteinogenic lysine analogues ornithine or, to a lesser extent, diaminobutyric acid, irrespective of chirality or chiral purity. Lysine decapeptides enhance RPR function by promoting holoenzyme assembly through primer-template docking, accelerate RPR evolution, and allow RPR-catalysed RNA synthesis at near physiological (≥1 mM) Mg2+ concentrations, enabling templated RNA synthesis within membranous protocells. Our results outline how compositionally simple, mixed-chirality peptides may have augmented the functional potential of early RNAs and promoted the emergence of the first protocells.
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Affiliation(s)
- Shunsuke Tagami
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - James Attwater
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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10
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Abstract
Group II introns are self-splicing catalytic RNAs found in bacteria and the organelles of fungi and plants. They are thought to share a common ancestor with the spliceosome, which catalyzes the removal of nuclear introns from pre-mRNAs in eukaryotes. Recent structural and biochemical evidence supports the hypothesis that the spliceosome has a catalytic RNA core homologous to that found in group II introns. The crystal structure of a eukaryotic group IIB intron was recently determined and reveals the architecture of a branched lariat RNA that is also formed by the spliceosome. Here we describe the active site components of this intron and propose a model for RNA splicing involving dynamic base triples in the catalytic triad. Based on this structure, we draw analogies to the U2/U6 snRNA pairing and RNA-protein interactions that form in the active site of the spliceosome.
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Affiliation(s)
- Jessica K Peters
- a Department of Chemistry and Biochemistry ; University of California, San Diego ; La Jolla , CA USA
| | - Navtej Toor
- a Department of Chemistry and Biochemistry ; University of California, San Diego ; La Jolla , CA USA
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11
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Single-molecule fluorescence-based studies on the dynamics, assembly and catalytic mechanism of the spliceosome. Biochem Soc Trans 2015; 42:1211-8. [PMID: 25110027 DOI: 10.1042/bst20140105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pre-mRNA (precursor mRNA) splicing is a key step in cellular gene expression where introns are excised and exons are ligated together to produce mature mRNA. This process is catalysed by the spliceosome, which consists of five snRNPs (small nuclear ribonucleoprotein particles) and numerous protein factors. Assembly of these snRNPs and associated proteins is a highly dynamic process, making it challenging to study the conformational rearrangements and spliceosome assembly kinetics in bulk studies. In the present review, we discuss recent studies utilizing techniques based on single-molecule detection that have helped overcome this challenge. These studies focus on the assembly dynamics and splicing kinetics in real-time, which help understanding of spliceosomal assembly and catalysis.
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12
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Kun Á, Szilágyi A, Könnyű B, Boza G, Zachar I, Szathmáry E. The dynamics of the RNA world: insights and challenges. Ann N Y Acad Sci 2015; 1341:75-95. [PMID: 25735569 DOI: 10.1111/nyas.12700] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The RNA world hypothesis of the origin of life, in which RNA emerged as both enzyme and information carrier, is receiving solid experimental support. The prebiotic synthesis of biomolecules, the catalytic aid offered by mineral surfaces, and the vast enzymatic repertoire of ribozymes are only pieces of the origin of life puzzle; the full picture can only emerge if the pieces fit together by either following from one another or coexisting with each other. Here, we review the theory of the origin, maintenance, and enhancement of the RNA world as an evolving population of dynamical systems. The dynamical view of the origin of life allows us to pinpoint the missing and the not fitting pieces: (1) How can the first self-replicating ribozyme emerge in the absence of template-directed information replication? (2) How can nucleotide replicators avoid competitive exclusion despite utilizing the very same resources (nucleobases)? (3) How can the information catastrophe be avoided? (4) How can enough genes integrate into a cohesive system in order to transition to a cellular stage? (5) How can the way information is stored and metabolic complexity coevolve to pave to road leading out of the RNA world to the present protein-DNA world?
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany; MTA-ELTE-MTMT Ecology Research Group, Budapest, Hungary
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13
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Abstract
We have employed gene-trap insertional mutagenesis to identify candidate genes whose disruption confer phenotypic resistance to lytic infection, in independent studies using 12 distinct viruses and several different cell lines. Analysis of >2,000 virus-resistant clones revealed >1,000 candidate host genes, approximately 20 % of which were disrupted in clones surviving separate infections with 2–6 viruses. Interestingly, there were 83 instances in which the insertional mutagenesis vector disrupted transcripts encoding H/ACA-class and C/D-class small nucleolar RNAs (SNORAs and SNORDs, respectively). Of these, 79 SNORAs and SNORDs reside within introns of 29 genes (predominantly protein-coding), while 4 appear to be independent transcription units. siRNA studies targeting candidate SNORA/Ds provided independent confirmation of their roles in infection when tested against cowpox virus, Dengue Fever virus, influenza A virus, human rhinovirus 16, herpes simplex virus 2, or respiratory syncytial virus. Significantly, eight of the nine SNORA/Ds targeted with siRNAs enhanced cellular resistance to multiple viruses suggesting widespread involvement of SNORA/Ds in virus–host interactions and/or virus-induced cell death.
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14
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Collier SE, Voehler M, Peng D, Ohi R, Gould KL, Reiter NJ, Ohi MD. Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5. Biochemistry 2014; 53:6439-51. [PMID: 25263959 PMCID: PMC4204884 DOI: 10.1021/bi5008639] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The
spliceosome is a dynamic macromolecular machine composed of
five small nuclear ribonucleoparticles (snRNPs), the NineTeen Complex
(NTC), and other proteins that catalyze the removal of introns mature
to form the mature message. The NTC, named after its founding member Saccharomyces cerevisiae Prp19, is a conserved spliceosome
subcomplex composed of at least nine proteins. During spliceosome
assembly, the transition to an active spliceosome correlates with
stable binding of the NTC, although the mechanism of NTC function
is not understood. Schizosaccharomyces pombe Cdc5, a core subunit of the NTC, is an essential protein required
for pre-mRNA splicing. The highly conserved Cdc5 N-terminus contains
two canonical Myb (myeloblastosis) repeats (R1 and R2) and a third
domain (D3) that was previously classified as a Myb-like repeat. Although
the N-terminus of Cdc5 is required for its function, how R1, R2, and
D3 each contribute to functionality is unclear. Using a combination
of yeast genetics, structural approaches, and RNA binding assays,
we show that R1, R2, and D3 are all required for the function of Cdc5
in cells. We also show that the N-terminus of Cdc5 binds RNA in vitro. Structural and functional analyses of Cdc5-D3
show that, while this domain does not adopt a Myb fold, Cdc5-D3 preferentially
binds double-stranded RNA. Our data suggest that the Cdc5 N-terminus
interacts with RNA structures proposed to be near the catalytic core
of the spliceosome.
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Affiliation(s)
- Scott E Collier
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center , Nashville, Tennessee 37232, United States
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15
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The noncoding RNA revolution-trashing old rules to forge new ones. Cell 2014; 157:77-94. [PMID: 24679528 DOI: 10.1016/j.cell.2014.03.008] [Citation(s) in RCA: 1647] [Impact Index Per Article: 164.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/07/2014] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs (ncRNAs) accomplish a remarkable variety of biological functions. They regulate gene expression at the levels of transcription, RNA processing, and translation. They protect genomes from foreign nucleic acids. They can guide DNA synthesis or genome rearrangement. For ribozymes and riboswitches, the RNA structure itself provides the biological function, but most ncRNAs operate as RNA-protein complexes, including ribosomes, snRNPs, snoRNPs, telomerase, microRNAs, and long ncRNAs. Many, though not all, ncRNAs exploit the power of base pairing to selectively bind and act on other nucleic acids. Here, we describe the pathway of ncRNA research, where every established "rule" seems destined to be overturned.
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16
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Abstract
In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.
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Affiliation(s)
- Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Scott William Roy
- Department of Biology, San Francisco State University, San Francisco, California 94132
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17
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Valadkhan S. The role of snRNAs in spliceosomal catalysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 120:195-228. [PMID: 24156945 DOI: 10.1016/b978-0-12-381286-5.00006-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The spliceosomes, large ribonucleoprotein (RNP) assemblies that remove the intervening sequences from pre-mRNAs, contain a large number of proteins and five small nuclear RNAs (snRNAs). One snRNA, U6, contains highly conserved sequences that are thought to be the functional counterparts of the RNA elements that form the active site of self-splicing group II intron ribozymes. An in vitro-assembled, protein-free complex of U6 with U2, the base-pairing partner in the spliceosomal catalytic core, can catalyze a two-step splicing reaction in the absence of all other spliceosomal factors, suggesting that the two snRNAs may form all or a large share of the spliceosomal active site. On the other hand, several spliceosomal proteins are thought to help in the formation of functionally required RNA-RNA interactions in the catalytic core. Whether they also contribute functional groups to the spliceosomal active site, and thus whether the spliceosomes are RNA or RNP enzymes remain uncertain.
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Affiliation(s)
- Saba Valadkhan
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA
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18
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Abstract
One of the most amazing findings in molecular biology was the discovery that eukaryotic genes are discontinuous, with coding DNA being interrupted by stretches of non-coding sequence. The subsequent realization that the intervening regions are removed from pre-mRNA transcripts via the activity of a common set of small nuclear RNAs (snRNAs), which assemble together with associated proteins into a complex known as the spliceosome, was equally surprising. How do cells coordinate the assembly of this molecular machine? And how does the spliceosome accurately recognize exons and introns to carry out the splicing reaction? Insights into these questions have been gained by studying the life cycle of spliceosomal snRNAs from their transcription, nuclear export and re-import to their dynamic assembly into the spliceosome. This assembly process can also affect the regulation of alternative splicing and has implications for human disease.
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Affiliation(s)
- A Gregory Matera
- Department of Biology, Department of Genetics and Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Zefeng Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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19
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Karunatilaka KS, Rueda D. Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex. RNA (NEW YORK, N.Y.) 2014; 20:16-23. [PMID: 24243115 PMCID: PMC3866641 DOI: 10.1261/rna.041806.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The spliceosome catalyzes precursor-mRNA splicing in all eukaryotes. It consists of over 100 proteins and five small nuclear RNAs (snRNAs), including U2 and U6 snRNAs, which are essential for catalysis. Human and yeast snRNAs share structural similarities despite the fact that human snRNAs contain numerous post-transcriptional modifications. Although functions for these modifications have been proposed, their exact roles are still not well understood. To help elucidate these roles in pre-mRNA splicing, we have used single-molecule fluorescence to characterize the effect of several post-transcriptional modifications in U2 snRNA on the conformation and dynamics of the U2-U6 complex in vitro. Consistent with yeast, the human U2-U6 complex reveals the presence of a magnesium-dependent dynamic equilibrium among three conformations. Interestingly, our data show that modifications in human U2 stem I modulate the dynamic equilibrium of the U2-U6 complex by stabilizing the four-helix structure. However, the small magnitude of this effect suggests that post-transcriptional modifications in human snRNAs may have a primary role in the mediation of specific RNA-protein interactions in vivo.
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Affiliation(s)
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, United Kingdom
- Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, London W12 0NN, United Kingdom
- Corresponding authorE-mail
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20
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Zhao C, Bachu R, Popović M, Devany M, Brenowitz M, Schlatterer JC, Greenbaum NL. Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex. RNA (NEW YORK, N.Y.) 2013; 19:561-73. [PMID: 23426875 PMCID: PMC3677266 DOI: 10.1261/rna.038265.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 05/24/2023]
Abstract
The complex formed between the U2 and U6 small nuclear (sn)RNA molecules of the eukaryotic spliceosome plays a critical role in the catalysis of precursor mRNA splicing. Here, we have used enzymatic structure probing, (19)F NMR, and analytical ultracentrifugation techniques to characterize the fold of a protein-free biophysically tractable paired construct representing the human U2-U6 snRNA complex. Results from enzymatic probing and (19)F NMR for the complex in the absence of Mg(2+) are consistent with formation of a four-helix junction structure as a predominant conformation. However, (19)F NMR data also identify a lesser fraction (up to 14% at 25°C) of a three-helix conformation. Based upon this distribution, the calculated ΔG for inter-conversion to the four-helix structure from the three-helix structure is approximately -4.6 kJ/mol. In the presence of 5 mM Mg(2+), the fraction of the three-helix conformation increased to ∼17% and the Stokes radius, measured by analytical ultracentrifugation, decreased by 2%, suggesting a slight shift to an alternative conformation. NMR measurements demonstrated that addition of an intron fragment to the U2-U6 snRNA complex results in displacement of U6 snRNA from the region of Helix III immediately 5' of the ACAGAGA sequence of U6 snRNA, which may facilitate binding of the segment of the intron adjacent to the 5' splice site to the ACAGAGA sequence. Taken together, these observations indicate conformational heterogeneity in the protein-free human U2-U6 snRNA complex consistent with a model in which the RNA has sufficient conformational flexibility to facilitate inter-conversion between steps of splicing in situ.
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Affiliation(s)
- Caijie Zhao
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Ravichandra Bachu
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Milena Popović
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Matthew Devany
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jörg C. Schlatterer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Nancy L. Greenbaum
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
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21
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Mazières J, Catherinne C, Delfour O, Gouin S, Rouquette I, Delisle MB, Prévot G, Escamilla R, Didier A, Persing DH, Bates M, Michot B. Alternative processing of the U2 small nuclear RNA produces a 19-22nt fragment with relevance for the detection of non-small cell lung cancer in human serum. PLoS One 2013; 8:e60134. [PMID: 23527303 PMCID: PMC3603938 DOI: 10.1371/journal.pone.0060134] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/21/2013] [Indexed: 12/28/2022] Open
Abstract
RNU2 exists in two functional forms (RNU2-1 and RNU2-2) distinguishable by the presence of a unique 4-bases motif. Detailed investigation of datasets obtained from deep sequencing of five human lung primary tumors revealed that both forms express at a high rate a 19-22nt fragment (miR-U2-1 and -2) from its 3' region and contains the 4-bases motif. Deep sequencing of independent pools of serum samples from healthy donors and lung cancer patients revealed that miR-U2-1 and -2 are pervasively processed in lung tissue by means of endonucleolytic cleavages and stably exported to the blood. Then, microarrays hybridization experiments of matched normal/tumor samples revealed a significant over-expression of miR-U2-1 in 14 of 18 lung primary tumors. Subsequently, qRT-PCR of miR-U2-1 using serum from 62 lung cancer patients and 96 various controls demonstrated that its expression levels identify lung cancer patients with 79% sensitivity and 80% specificity. miR-U2-1 expression correlated with the presence or absence of lung cancer in patients with chronic obstructive pulmonary disease (COPD), other diseases of the lung - not cancer, and in healthy controls. These data suggest that RNU2-1 is a new bi-functional ncRNA that produces a 19-22nt fragment which may be useful in detecting lung cancer non-invasively in high risk patients.
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Affiliation(s)
- Julien Mazières
- Service de Pneumologie, Hôpital Larrey, CHU de Toulouse, Université de Toulouse III (Paul Sabatier), Toulouse, France
| | | | | | - Sandrine Gouin
- Service de Pneumologie, Hôpital Larrey, CHU de Toulouse, Université de Toulouse III (Paul Sabatier), Toulouse, France
| | - Isabelle Rouquette
- Service d'anatomie pathologique, Hôpital Rangueil, CHU de Toulouse, Toulouse, France
| | | | - Grégoire Prévot
- Service de Pneumologie, Hôpital Larrey, CHU de Toulouse, Université de Toulouse III (Paul Sabatier), Toulouse, France
| | - Roger Escamilla
- Service de Pneumologie, Hôpital Larrey, CHU de Toulouse, Université de Toulouse III (Paul Sabatier), Toulouse, France
| | - Alain Didier
- Service de Pneumologie, Hôpital Larrey, CHU de Toulouse, Université de Toulouse III (Paul Sabatier), Toulouse, France
| | | | - Mike Bates
- Cepheid USA, Sunnyvale, California, United States of America
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22
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Cech TR. Die RNA aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201205427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Abstract
Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA-RNA and RNA-protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA-RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5' splice site, and U5 and the exonic sequences immediately adjacent to the 5' and 3' splice sites. Thus RNA-RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.
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Affiliation(s)
- Saba Valadkhan
- Center for RNA Molecular Biology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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24
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Abstract
RNA, just another starting material? Nobel Laureate Tom Cech shows that with an education steeped in kinetics, thermodynamics, and molecular structure, and armed with the ability to synthesize molecules, the chemist is ideally suited to investigate RNA.
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Affiliation(s)
- Thomas R Cech
- University of Colorado BioFrontiers Institute, Boulder, CO 80309-0596, USA.
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25
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Turunen JJ, Niemelä EH, Verma B, Frilander MJ. The significant other: splicing by the minor spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:61-76. [PMID: 23074130 PMCID: PMC3584512 DOI: 10.1002/wrna.1141] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The removal of non-coding sequences, introns, from the mRNA precursors is an essential step in eukaryotic gene expression. U12-type introns are a minor subgroup of introns, distinct from the major or U2-type introns. U12-type introns are present in most eukaryotes but only account for less than 0.5% of all introns in any given genome. They are processed by a specific U12-dependent spliceosome, which is similar to, but distinct from, the major spliceosome. U12-type introns are spliced somewhat less efficiently than the major introns, and it is believed that this limits the expression of the genes containing such introns. Recent findings on the role of U12-dependent splicing in development and human disease have shown that it can also affect multiple cellular processes not directly related to the functions of the host genes of U12-type introns. At the same time, advances in understanding the regulation and phylogenetic distribution of the minor spliceosome are starting to shed light on how the U12-type introns and the minor spliceosome may have evolved. © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Janne J Turunen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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26
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Schmitzová J, Pena V. Emerging views about the molecular structure of the spliceosomal catalytic center. RNA Biol 2012; 9:1311-8. [PMID: 23064115 DOI: 10.4161/rna.22359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pre-mRNA splicing occurs in two chemical steps that are catalyzed by a large, dynamic RNA-protein complex called the spliceosome. Initially assembled in a catalytically inactive form, the spliceosome undergoes massive compositional and conformational remodeling, through which disparate RNA elements are re-configured and juxtaposed into a functional catalytic center. The intricate construction of the catalytic center requires the assistance of spliceosomal proteins. Recent structure-function analyses have demonstrated that the yeast-splicing factor Cwc2 is a main player that contacts and shapes the catalytic center of the spliceosome into a functional conformation. With this advance, corroborated by the atomic structure of the evolutionarily related group IIC introns, our understanding of the organization and formation of the spliceosomal catalytic center has progressed to a new level.
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Affiliation(s)
- Jana Schmitzová
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical, Macromolecular Crystallography Group, Göttingen, Germany
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27
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Liberman JA, Guo M, Jenkins JL, Krucinska J, Chen Y, Carey PR, Wedekind JE. A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis. J Am Chem Soc 2012; 134:16933-6. [PMID: 22989273 DOI: 10.1021/ja3070528] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pK(a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pK(a) value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pK(a) values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pK(a) > 0.8 log unit relative to the precatalytic state. The agreement of the microscopic and macroscopic pK(a) values and the accompanying structural analysis supports a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.
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Affiliation(s)
- Joseph A Liberman
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA
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28
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Abstract
There are two RNA worlds. The first is the primordial RNA world, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today's biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection. This second RNA world is not at all hypothetical, and although we do not have all the answers about how it works, we have the tools to continue our interrogation of this world and refine our understanding. The fun comes when we try to use our secure knowledge of the modern RNA world to infer what the primordial RNA world might have looked like.
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Affiliation(s)
- Thomas R Cech
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309-0215, USA.
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29
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van der Feltz C, Anthony K, Brilot A, Pomeranz Krummel DA. Architecture of the Spliceosome. Biochemistry 2012; 51:3321-33. [DOI: 10.1021/bi201215r] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Clarisse van der Feltz
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts
02454, United States
| | - Kelsey Anthony
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts
02454, United States
| | - Axel Brilot
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts
02454, United States
| | - Daniel A. Pomeranz Krummel
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts
02454, United States
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30
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Burke JE, Sashital DG, Zuo X, Wang YX, Butcher SE. Structure of the yeast U2/U6 snRNA complex. RNA (NEW YORK, N.Y.) 2012; 18:673-83. [PMID: 22328579 PMCID: PMC3312555 DOI: 10.1261/rna.031138.111] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The U2/U6 snRNA complex is a conserved and essential component of the active spliceosome that interacts with the pre-mRNA substrate and essential protein splicing factors to promote splicing catalysis. Here we have elucidated the solution structure of a 111-nucleotide U2/U6 complex using an approach that integrates SAXS, NMR, and molecular modeling. The U2/U6 structure contains a three-helix junction that forms an extended "Y" shape. The U6 internal stem-loop (ISL) forms a continuous stack with U2/U6 Helices Ib, Ia, and III. The coaxial stacking of Helix Ib on the U6 ISL is a configuration that is similar to the Domain V structure in group II introns. Interestingly, essential features of the complex--including the U80 metal binding site, AGC triad, and pre-mRNA recognition sites--localize to one face of the molecule. This observation suggests that the U2/U6 structure is well-suited for orienting substrate and cofactors during splicing catalysis.
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Affiliation(s)
- Jordan E. Burke
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Dipali G. Sashital
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Xiaobing Zuo
- Advanced Photon Source, Argonne National Laboratory, Chicago, Illinois 60437, USA
| | - Yun-Xing Wang
- National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
- Corresponding author.E-mail .
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31
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Roca X, Karginov FV. RNA biology in a test tube--an overview of in vitro systems/assays. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:509-27. [PMID: 22447682 DOI: 10.1002/wrna.1115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In vitro systems have provided a wealth of information in the field of RNA biology, as they constitute a superior and sometimes the unique approach to address many important questions. Such cell-free methods can be sorted by the degree of complexity of the preparation of enzymatic and/or regulatory activity. Progress in the study of pre-mRNA processing has largely relied on traditional in vitro methods, as these reactions have been recapitulated in cell-free systems. The pre-mRNA capping, editing, and cleavage/polyadenylation reactions have even been reconstituted using purified components, and the enzymes responsible for catalysis have been characterized by such techniques. In vitro splicing using nuclear or cytoplasmic extracts has yielded clues on spliceosome assembly, kinetics, and mechanisms of splicing and has been essential to elucidate the function of splicing factors. Coupled systems have been important to functionally connect distinct processes, like transcription and splicing. Extract preparation has also been adapted to cells from a variety of tissues and species, revealing general versus species-specific mechanisms. Cell-free assays have also been applied to newly discovered pathways such as those involving small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs). The first two pathways have been well characterized largely by in vitro methods, which need to be developed for piRNAs. Finally, new techniques, such as single-molecule studies, are continuously being established, providing new and important insights into the field. Thus, in vitro approaches have been, are, and will continue being at the forefront of RNA research.
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Affiliation(s)
- Xavier Roca
- Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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32
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Piccirilli JA, Koldobskaya Y. Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment. Philos Trans R Soc Lond B Biol Sci 2012; 366:2918-28. [PMID: 21930583 DOI: 10.1098/rstb.2011.0144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
All models of the RNA world era invoke the presence of ribozymes that can catalyse RNA polymerization. The class I ligase ribozyme selected in vitro 15 years ago from a pool of random RNA sequences catalyses formation of a 3',5'-phosphodiester linkage analogous to a single step of RNA polymerization. Recently, the three-dimensional structure of the ligase was solved in complex with U1A RNA-binding protein and independently in complex with an antibody fragment. The RNA adopts a tripod arrangement and appears to use a two-metal ion mechanism similar to protein polymerases. Here, we discuss structural implications for engineering a true polymerase ribozyme and describe the use of the antibody framework both as a portable chaperone for crystallization of other RNAs and as a platform for exploring steps in evolution from the RNA world to the RNA-protein world.
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Affiliation(s)
- Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W406, Chicago, IL 60637, USA.
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33
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Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW. How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 2012; 63:528-37. [PMID: 21698757 DOI: 10.1002/iub.489] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Complex cellular machines and processes are commonly believed to be products of selection, and it is typically understood to be the job of evolutionary biologists to show how selective advantage can account for each step in their origin and subsequent growth in complexity. Here, we describe how complex machines might instead evolve in the absence of positive selection through a process of "presuppression," first termed constructive neutral evolution (CNE) more than a decade ago. If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely. Thus, CNE is a unidirectional evolutionary ratchet leading to complexity, if complexity is equated with the number of components or steps necessary to carry out a cellular process. CNE can explain "functions" that seem to make little sense in terms of cellular economy, like RNA editing or splicing, but it may also contribute to the complexity of machines with clear benefit to the cell, like the ribosome, and to organismal complexity overall. We suggest that CNE-based evolutionary scenarios are in these and other cases less forced than the selectionist or adaptationist narratives that are generally told.
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Affiliation(s)
- Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, České Budĕjovice (Budweis), Czech Republic
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34
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Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C. RNAcentral: A vision for an international database of RNA sequences. RNA (NEW YORK, N.Y.) 2011; 17:1941-6. [PMID: 21940779 PMCID: PMC3198587 DOI: 10.1261/rna.2750811] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.
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Affiliation(s)
- Alex Bateman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
- Corresponding author.E-mail .
| | - Shipra Agrawal
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore 560 100, India
- BioCOS Life Sciences Private Limited, Bangalore 560 100, India
| | - Ewan Birney
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Elspeth A. Bruford
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Umultowska 89, 61-614 Poznan, Poland
| | - Guy Cochrane
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - James R. Cole
- Microbial Ecology Center, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Marcel E. Dinger
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Anton J. Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Paul P. Gardner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Daniel Gautheret
- Institut de Génétique et Microbiologie–UMR CNRS 8621, Université Paris-Sud–Bâtiment 400, 91405 Orsay Cedex, France
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, United Kingdom
| | - Jen Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Ian H. Holmes
- Department of Bioengineering, University of California, Berkeley, California 94720-1762, USA
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, 30050, Taiwan
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Paul Kersey
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Ana Kozomara
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, United Kingdom
| | - Todd M. Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Manja Marz
- RNA Bioinformatics Group, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany
| | - Simon Moxon
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Tore Samuelsson
- Department of Medical Biochemistry, University of Goteborg, Medicinareg. 9A, S-405 30 Goteborg, Sweden
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04009 Leipzig, Germany
| | - Albert J. Vilella
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Kelly P. Williams
- Sandia National Laboratories, MS 9291, Livermore, California 94551-0969, USA
| | - Mathew W. Wright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Christian Zwieb
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3901, USA
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35
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Lambowitz AM, Zimmerly S. Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol 2011; 3:a003616. [PMID: 20463000 DOI: 10.1101/cshperspect.a003616] [Citation(s) in RCA: 306] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Group II introns are mobile ribozymes that self-splice from precursor RNAs to yield excised intron lariat RNAs, which then invade new genomic DNA sites by reverse splicing. The introns encode a reverse transcriptase that stabilizes the catalytically active RNA structure for forward and reverse splicing, and afterwards converts the integrated intron RNA back into DNA. The characteristics of group II introns suggest that they or their close relatives were evolutionary ancestors of spliceosomal introns, the spliceosome, and retrotransposons in eukaryotes. Further, their ribozyme-based DNA integration mechanism enabled the development of group II introns into gene targeting vectors ("targetrons"), which have the unique feature of readily programmable DNA target specificity.
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Affiliation(s)
- Alan M Lambowitz
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.
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36
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Abstract
Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton ribonucleoprotein (RNP) complex comprised of five snRNPs and numerous proteins. Intricate RNA-RNA and RNP networks, which serve to align the reactive groups of the pre-mRNA for catalysis, are formed and repeatedly rearranged during spliceosome assembly and catalysis. Both the conformation and composition of the spliceosome are highly dynamic, affording the splicing machinery its accuracy and flexibility, and these remarkable dynamics are largely conserved between yeast and metazoans. Because of its dynamic and complex nature, obtaining structural information about the spliceosome represents a major challenge. Electron microscopy has revealed the general morphology of several spliceosomal complexes and their snRNP subunits, and also the spatial arrangement of some of their components. X-ray and NMR studies have provided high resolution structure information about spliceosomal proteins alone or complexed with one or more binding partners. The extensive interplay of RNA and proteins in aligning the pre-mRNA's reactive groups, and the presence of both RNA and protein at the core of the splicing machinery, suggest that the spliceosome is an RNP enzyme. However, elucidation of the precise nature of the spliceosome's active site, awaits the generation of a high-resolution structure of its RNP core.
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Affiliation(s)
- Cindy L Will
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany
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37
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Jaladat Y, Zhang B, Mohammadi A, Valadkhan S. Splicing of an intervening sequence by protein-free human snRNAs. RNA Biol 2011; 8:372-7. [PMID: 21445000 DOI: 10.4161/rna.8.3.15386] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Significant structural and mechanistic similarities between the spliceosomal snRNAs and catalytically critical domains of self-splicing group II introns have led to the hypothesis that the spliceosomes and group II introns may be evolutionarily related. We have previously shown that in vitro-transcribed, protein-free U6 and U2 snRNAs can catalyze a two-step splicing reaction in trans on two short RNA oligonucleotides that is identical to the splicing reactions performed by many self-splicing group II introns. Here we show that the same two snRNAs can perform splicing in cis by removal of an intervening sequence from a model substrate. These results prove that the protein-free snRNAs are competent to perform splicing on pre-mRNAs and further strengthen the possibility of an evolutionary relationship to group II introns.
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Affiliation(s)
- Yasaman Jaladat
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, USA
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38
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Buske FA, Mattick JS, Bailey TL. Potential in vivo roles of nucleic acid triple-helices. RNA Biol 2011; 8:427-39. [PMID: 21525785 DOI: 10.4161/rna.8.3.14999] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The ability of double-stranded DNA to form a triple-helical structure by hydrogen bonding with a third strand is well established, but the biological functions of these structures remain largely unknown. There is considerable albeit circumstantial evidence for the existence of nucleic triplexes in vivo and their potential participation in a variety of biological processes including chromatin organization, DNA repair, transcriptional regulation, and RNA processing has been investigated in a number of studies to date. There is also a range of possible mechanisms to regulate triplex formation through differential expression of triplex-forming RNAs, alteration of chromatin accessibility, sequence unwinding and nucleotide modifications. With the advent of next generation sequencing technology combined with targeted approaches to isolate triplexes, it is now possible to survey triplex formation with respect to their genomic context, abundance and dynamical changes during differentiation and development, which may open up new vistas in understanding genome biology and gene regulation.
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Affiliation(s)
- Fabian A Buske
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
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39
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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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Valadkhan S, Jaladat Y. The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine. Proteomics 2010; 10:4128-41. [PMID: 21080498 DOI: 10.1002/pmic.201000354] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Almost all primary transcripts in higher eukaryotes undergo several splicing events and alternative splicing is a major factor in generating proteomic diversity. Thus, the spliceosome, the ribonucleoprotein assembly that performs splicing, is a highly critical cellular machine and as expected, a very complex one. Indeed, the spliceosome is one of the largest, if not the largest, molecular machine in the cell with over 150 different components in human. A large fraction of the spliceosomal proteome is organized into small nuclear ribonucleoprotein particles by associating with one of the small nuclear RNAs, and the function of many spliceosomal proteins revolve around their association or interaction with the spliceosomal RNAs or the substrate pre-messenger RNAs. In addition to the complex web of protein-RNA interactions, an equally complex network of protein-protein interactions exists in the spliceosome, which includes a number of large, conserved proteins with critical functions in the spliceosomal catalytic core. These include the largest conserved nuclear protein, Prp8, which plays a critical role in spliceosomal function in a hitherto unknown manner. Taken together, the large spliceosomal proteome and its dynamic nature has made it a highly challenging system to study, and at the same time, provides an exciting example of the evolution of a proteome around a backbone of primordial RNAs likely dating from the RNA World.
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Affiliation(s)
- Saba Valadkhan
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44113, USA.
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41
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Lee C, Jaladat Y, Mohammadi A, Sharifi A, Geisler S, Valadkhan S. Metal binding and substrate positioning by evolutionarily invariant U6 sequences in catalytically active protein-free snRNAs. RNA (NEW YORK, N.Y.) 2010; 16:2226-38. [PMID: 20826700 PMCID: PMC2957061 DOI: 10.1261/rna.2170910] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Accepted: 07/31/2010] [Indexed: 05/20/2023]
Abstract
We have previously shown that a base-paired complex formed by two of the spliceosomal RNA components, U6 and U2 small nuclear RNAs (snRNAs), can catalyze a two-step splicing reaction that depended on an evolutionarily invariant region in U6, the ACAGAGA box. Here we further analyze this RNA-catalyzed reaction and show that while the 5' and 3' splice site substrates are juxtaposed and positioned near the ACAGAGA sequence in U6, the role of the snRNAs in the reaction is beyond mere juxtaposition of the substrates and likely involves the formation of a sophisticated active site. Interestingly, the snRNA-catalyzed reaction is metal dependent, as is the case with other known splicing RNA enzymes, and terbium(III) cleavage reactions indicate metal binding by the U6/U2 complex within the evolutionarily conserved regions of U6. The above results, combined with the structural similarities between U6 and catalytically critical domains in group II self-splicing introns, suggest that the base-paired complex of U6 and U2 snRNAs is a vestigial ribozyme and a likely descendant of a group II-like self-splicing intron.
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Affiliation(s)
- Caroline Lee
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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42
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Koodathingal P, Novak T, Piccirilli JA, Staley JP. The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing. Mol Cell 2010; 39:385-95. [PMID: 20705241 DOI: 10.1016/j.molcel.2010.07.014] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 03/31/2010] [Accepted: 06/03/2010] [Indexed: 12/24/2022]
Abstract
To investigate the mechanisms underlying accurate pre-mRNA splicing, we developed an in vitro assay sensitive to proofreading of 5' splice site cleavage. We inactivated spliceosomes by disrupting a metal-ligand interaction at the catalytic center and discovered that, when the DEAH box ATPase Prp16 was disabled, these spliceosomes catalyzed 5' splice site cleavage but at a reduced rate. Although Prp16 does not promote splicing of a genuine substrate until after 5' splice site cleavage, we found that Prp16 can associate with spliceosomes before 5' splice site cleavage, consistent with a role for Prp16 in proofreading 5' splice site cleavage. We established that Prp16-mediated rejection is reversible, necessitating a downstream discard pathway that we found requires the DEAH box ATPase Prp43, a spliceosome disassembly factor. These data indicate that spliceosomes distinguish slow substrates and that the mechanisms for establishing the fidelity of 5' splice site cleavage and exon ligation share a common ATP-dependent framework.
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Affiliation(s)
- Prakash Koodathingal
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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43
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Pyle AM. The tertiary structure of group II introns: implications for biological function and evolution. Crit Rev Biochem Mol Biol 2010; 45:215-32. [PMID: 20446804 DOI: 10.3109/10409231003796523] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Group II introns are some of the largest ribozymes in nature, and they are a major source of information about RNA assembly and tertiary structural organization. These introns are of biological significance because they are self-splicing mobile elements that have migrated into diverse genomes and played a major role in the genomic organization and metabolism of most life forms. The tertiary structure of group II introns has been the subject of many phylogenetic, genetic, biochemical and biophysical investigations, all of which are consistent with the recent crystal structure of an intact group IIC intron from the alkaliphilic eubacterium Oceanobacillus iheyensis. The crystal structure reveals that catalytic intron domain V is enfolded within the other intronic domains through an elaborate network of diverse tertiary interactions. Within the folded core, DV adopts an activated conformation that readily binds catalytic metal ions and positions them in a manner appropriate for reaction with nucleic acid targets. The tertiary structure of the group II intron reveals new information on motifs for RNA architectural organization, mechanisms of group II intron catalysis, and the evolutionary relationships among RNA processing systems. Guided by the structure and the wealth of previous genetic and biochemical work, it is now possible to deduce the probable location of DVI and the site of additional domains that contribute to the function of the highly derived group IIB and IIA introns.
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Affiliation(s)
- Anna Marie Pyle
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute and Yale University, New Haven, CT, USA.
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Zhao C, Bellur DL, Lu S, Zhao F, Grassi MA, Bowne SJ, Sullivan LS, Daiger SP, Chen LJ, Pang CP, Zhao K, Staley JP, Larsson C. Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs. Am J Hum Genet 2009; 85:617-27. [PMID: 19878916 DOI: 10.1016/j.ajhg.2009.09.020] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/19/2009] [Accepted: 09/30/2009] [Indexed: 01/20/2023] Open
Abstract
Mutations in genes associated with the U4/U6-U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome are implicated in autosomal-dominant retinitis pigmentosa (adRP), a group of progressive retinal degenerative disorders leading to visual impairment, loss of visual field, and even blindness. We recently assigned a locus (RP33) for adRP to 2cen-q12.1, a region that harbors the SNRNP200 gene encoding hBrr2, another U4/U6-U5 snRNP component that is required for unwinding of U4/U6 snRNAs during spliceosome activation and for disassembly of the spliceosome. Here, we report the identification of a missense mutation, c.3260C>T (p.S1087L), in exon 25 of the SNRNP200 gene in an RP33-linked family. The c.3260C>T substitution showed complete cosegregation with the retinitis pigmentosa (RP) phenotype over four generations, but was absent in a panel of 400 controls. The p.S1087L mutation and p.R1090L, another adRP-associated allele, reside in the "ratchet" helix of the first of two Sec63 domains implicated in the directionality and processivity of nucleic acid unwinding. Indeed, marked defects in U4/U6 unwinding, but not U4/U6-U5 snRNP assembly, were observed in budding yeast for the analogous mutations (N1104L and R1107L) of the corresponding Brr2p residues. The linkage of hBrr2 to adRP suggests that the mechanism of pathogenesis for splicing-factor-related RP may fundamentally derive from a defect in hBrr2-dependent RNA unwinding and a consequent defect in spliceosome activation.
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Single-molecule analysis of protein-free U2-U6 snRNAs. Nat Struct Mol Biol 2009; 16:1154-9. [PMID: 19881500 PMCID: PMC2784090 DOI: 10.1038/nsmb.1672] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 08/17/2009] [Indexed: 02/06/2023]
Abstract
Spliceosomes catalyze the maturation of precursor mRNAs from yeast to humans. Their catalytic core comprises three small nuclear RNAs (U2, U5 and U6) involved in substrate positioning and catalysis. It has been postulated, but never shown experimentally, that the U2/U6 complex adopts at least two conformations that reflect different activation states. We have used single-molecule fluorescence to probe the structural dynamics of a protein-free RNA complex modeling U2/U6 from yeast and mutants of highly conserved regions. Our data show the presence of at least three distinct conformations in equilibrium. The minimal folding pathway consists of a two-step process with an obligatory intermediate. The first step is strongly magnesium dependent and we provide evidence suggesting the second corresponds to the formation of the genetically conserved helix IB. Site-specific mutations in the highly conserved AGC triad and the U80 base in U6 suggest that the observed conformational dynamics correlate with residues that play an important role in splicing.
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46
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An Overview of the Introns-First Theory. J Mol Evol 2009; 69:527-40. [DOI: 10.1007/s00239-009-9279-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
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