1
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Sebbag-Sznajder N, Brody Y, Hochberg-Laufer H, Shav-Tal Y, Sperling J, Sperling R. Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State. Front Genet 2020; 11:409. [PMID: 32499811 PMCID: PMC7243799 DOI: 10.3389/fgene.2020.00409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Splicing and alternative splicing of pre-mRNA are key sources in the formation of diversity in the human proteome. These processes have a central role in the regulation of the gene expression pathway. Yet, how spliceosomes are assembled on a multi-intronic pre-mRNA is at present not well understood. To study the spliceosomes assembled in vivo on transcripts with variable number of introns, we examined a series of three related transcripts derived from the β-globin gene, where two transcript types contained increasing number of introns, while one had only an exon. Each transcript had multiple MS2 sequence repeats that can be bound by the MS2 coat protein. Using our protocol for isolation of endogenous spliceosomes under native conditions from cell nuclei, we show that all three transcripts are found in supraspliceosomes – 21 MDa dynamic complexes, sedimenting at 200S in glycerol gradients, and composed of four native spliceosomes connected by the transcript. Affinity purification of complexes assembled on the transcript with most introns (termed E6), using the MS2 tag, confirmed the assembly of E6 in supraspliceosomes with components such as Sm proteins and PSF. Furthermore, splicing inhibition by spliceostatin A did not inhibit the assembly of supraspliceosomes on the E6 transcript, yet increased the percentage of E6 pre-mRNA supraspliceosomes. These findings were corroborated in intact cells, using RNA FISH to detect the MS2-tagged E6 mRNA, together with GFP-tagged splicing factors, showing the assembly of splicing factors SRSF2, U1-70K, and PRP8 onto the E6 transcripts under normal conditions and also when splicing was inhibited. This study shows that different transcripts with different number of introns, or lacking an intron, are assembled in supraspliceosomes even when splicing is inhibited. This assembly starts at the site of transcription and can continue during the life of the transcript in the nucleoplasm. This study further confirms the dynamic and universal nature of supraspliceosomes that package RNA polymerase II transcribed pre-mRNAs into complexes composed of four native spliceosomes connected by the transcript, independent of their length, number of introns, or splicing state.
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Affiliation(s)
| | - Yehuda Brody
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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2
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Ma Q, Tatsuno T, Nakamura Y, Izumi S, Tomosugi N, Ishigaki Y. Immuno‐detection of mRNA‐binding protein complex in human cells under transmission electron microscopy. Microsc Res Tech 2019; 82:680-688. [DOI: 10.1002/jemt.23214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Qingfeng Ma
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and Technology Wuhan China
| | - Takanori Tatsuno
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
| | - Yuka Nakamura
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
| | - Shin‐Ichi Izumi
- Department of Cell Biology, Unit of Biomedical SciencesNagasaki University Graduate School of Biomedical Sciences Sakamoto Nagasaki Japan
| | - Naohisa Tomosugi
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
- Medical Care Proteomics Biotechnology Co., Ltd. Uchinada Kahoku Japan
| | - Yasuhito Ishigaki
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
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3
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Karlova MG, Volokh OI, Chertkov OV, Kirpichnikov MP, Studitsky VM, Sokolova OS. Purification and concentration of RNA polymerase on Ni-lipid monolayers. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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4
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Sperling J, Sperling R. Structural studies of the endogenous spliceosome - The supraspliceosome. Methods 2017; 125:70-83. [PMID: 28412289 PMCID: PMC5546952 DOI: 10.1016/j.ymeth.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 12/17/2022] Open
Abstract
Pre-mRNA splicing is executed in mammalian cell nuclei within a huge (21MDa) and highly dynamic molecular machine - the supraspliceosome - that individually package pre-mRNA transcripts of different sizes and number of introns into complexes of a unique structure, indicating their universal nature. Detailed structural analysis of this huge and complex structure requires a stepwise approach using hybrid methods. Structural studies of the supraspliceosome by room temperature electron tomography, cryo-electron tomography, and scanning transmission electron microscope mass measurements revealed that it is composed of four native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA. It also elucidated the arrangement of the native spliceosomes within the intact supraspliceosome. Native spliceosomes and supraspliceosomes contain all five spliceosomal U snRNPs together with other splicing factors, and are active in splicing. The structure of the native spliceosome, at a resolution of 20Å, was determined by cryo-electron microscopy, and a unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in silico studies. The supraspliceosome also harbor components for all pre-mRNA processing activities. Thus the supraspliceosome - the endogenous spliceosome - is a stand-alone complete macromolecular machine capable of performing splicing, alternative splicing, and encompass all nuclear pre-mRNA processing activities that the pre-mRNA has to undergo before it can exit from the nucleus to the cytoplasm to encode for protein. Further high-resolution cryo-electron microscopy studies of the endogenous spliceosome are required to decipher the regulation of alternative splicing, and elucidate the network of processing activities within it.
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Affiliation(s)
- Joseph Sperling
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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5
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Yu G, Li K, Huang P, Jiang X, Jiang W. Antibody-Based Affinity Cryoelectron Microscopy at 2.6-Å Resolution. Structure 2017; 24:1984-1990. [PMID: 27806259 DOI: 10.1016/j.str.2016.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/16/2016] [Accepted: 09/30/2016] [Indexed: 02/02/2023]
Abstract
The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration.
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Affiliation(s)
- Guimei Yu
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Pengwei Huang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Wen Jiang
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.
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6
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Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. BIOPHYSICS REPORTS 2017; 3:17-35. [PMID: 28781998 PMCID: PMC5516000 DOI: 10.1007/s41048-017-0040-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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Vidavsky N, Akiva A, Kaplan-Ashiri I, Rechav K, Addadi L, Weiner S, Schertel A. Cryo-FIB-SEM serial milling and block face imaging: Large volume structural analysis of biological tissues preserved close to their native state. J Struct Biol 2016; 196:487-495. [PMID: 27693309 DOI: 10.1016/j.jsb.2016.09.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/12/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
Abstract
Many important biological questions can be addressed by studying in 3D large volumes of intact, cryo fixed hydrated tissues (⩾10,000μm3) at high resolution (5-20nm). This can be achieved using serial FIB milling and block face surface imaging under cryo conditions. Here we demonstrate the unique potential of the cryo-FIB-SEM approach using two extensively studied model systems; sea urchin embryos and the tail fin of zebrafish larvae. We focus in particular on the environment of mineral deposition sites. The cellular organelles, including mitochondria, Golgi, ER, nuclei and nuclear pores are made visible by the image contrast created by differences in surface potential of different biochemical components. Auto segmentation and/or volume rendering of the image stacks and 3D reconstruction of the skeleton and the cellular environment, provides a detailed view of the relative distribution in space of the tissue/cellular components, and thus of their interactions. Simultaneous acquisition of secondary and back-scattered electron images adds additional information. For example, a serial view of the zebrafish tail reveals the presence of electron dense mineral particles inside mitochondrial networks extending more than 20μm in depth in the block. Large volume imaging using cryo FIB SEM, as demonstrated here, can contribute significantly to the understanding of the structures and functions of diverse biological tissues.
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Affiliation(s)
- Netta Vidavsky
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Anat Akiva
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ifat Kaplan-Ashiri
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lia Addadi
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Steve Weiner
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Andreas Schertel
- Carl Zeiss Microscopy GmbH, Global Applications Support, Oberkochen, Germany
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8
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Sperling R. The nuts and bolts of the endogenous spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27465259 DOI: 10.1002/wrna.1377] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 01/09/2023]
Abstract
The complex life of pre-mRNA from transcription to the production of mRNA that can be exported from the nucleus to the cytoplasm to encode for proteins entails intricate coordination and regulation of a network of processing events. Coordination is required between transcription and splicing and between several processing events including 5' and 3' end processing, splicing, alternative splicing and editing that are major contributors to the diversity of the human proteome, and occur within a huge and dynamic macromolecular machine-the endogenous spliceosome. Detailed mechanistic insight of the splicing reaction was gained from studies of the in vitro spliceosome assembled on a single intron. Because most pre-mRNAs are multiintronic that undergo alternative splicing, the in vivo splicing machine requires additional elements to those of the in vitro machine, to account for all these diverse functions. Information about the endogenous spliceosome is emerging from imaging studies in intact and live cells that support the cotranscriptional commitment to splicing model and provide information about splicing kinetics in vivo. Another source comes from studies of the in vivo assembled spliceosome, isolated from cell nuclei under native conditions-the supraspliceosome-that individually package pre-mRNA transcripts of different sizes and number of introns into complexes of a unique structure, indicating their universal nature. Recent years have portrayed new players affecting alternative splicing and novel connections between splicing, transcription and chromatin. The challenge ahead is to elucidate the structure and function of the endogenous spliceosome and decipher the regulation and coordination of its network of processing activities. WIREs RNA 2017, 8:e1377. doi: 10.1002/wrna.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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9
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Yu G, Li K, Jiang W. Antibody-based affinity cryo-EM grid. Methods 2016; 100:16-24. [PMID: 26804563 DOI: 10.1016/j.ymeth.2016.01.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 12/01/2022] Open
Abstract
The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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10
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Ando D, Korabel N, Huang KC, Gopinathan A. Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics. Biophys J 2015; 109:1574-82. [PMID: 26488648 PMCID: PMC4624159 DOI: 10.1016/j.bpj.2015.08.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/24/2015] [Accepted: 08/24/2015] [Indexed: 10/22/2022] Open
Abstract
Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable timescales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that redirect cargo back to the nucleus caused large variations in network transport. Filament polarity was more important than filament orientation in reducing average transit times, and transport properties were optimized in networks with intermediate motor on and off rates. Our results provide important insights into the functional constraints on intracellular transport under which cells have evolved cytoskeletal structures, and have potential applications for enhancing reactions in biomimetic systems through rational transport network design.
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Affiliation(s)
- David Ando
- Department of Physics, University of California, Merced, California
| | - Nickolay Korabel
- Department of Physics, University of California, Merced, California; School of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California.
| | - Ajay Gopinathan
- Department of Physics, University of California, Merced, California.
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11
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Shefer K, Sperling J, Sperling R. The Supraspliceosome - A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus. Comput Struct Biotechnol J 2014; 11:113-22. [PMID: 25408845 PMCID: PMC4232567 DOI: 10.1016/j.csbj.2014.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 01/23/2023] Open
Abstract
Pre-mRNA splicing of Pol II transcripts is executed in the mammalian cell nucleus within a huge (21 MDa) and highly dynamic RNP machine — the supraspliceosome. It is composed of four splicing active native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA. Supraspliceosomes harbor protein splicing factors and all the five-spliceosomal U snRNPs. Recent analysis of specific supraspliceosomes at defined splicing stages revealed that they harbor all five spliceosomal U snRNAs at all splicing stages. Supraspliceosomes harbor additional pre-mRNA processing components, such as the 5′-end and 3′-end processing components, and the RNA editing enzymes ADAR1 and ADAR2. The structure of the native spliceosome, at a resolution of 20 Å, was determined by cryo-EM. A unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in-silico studies, localizing the five U snRNPs mostly within its large subunit, and sheltering the active core components deep within the spliceosomal cavity. The supraspliceosome provides a platform for coordinating the numerous processing steps that the pre-mRNA undergoes: 5′ and 3′-end processing activities, RNA editing, constitutive and alternative splicing, and processing of intronic microRNAs. It also harbors a quality control mechanism termed suppression of splicing (SOS) that, under normal growth conditions, suppresses splicing at abundant intronic latent 5′ splice sites in a reading frame-dependent fashion. Notably, changes in these regulatory processing activities are associated with human disease and cancer. These findings emphasize the supraspliceosome as a multi-task master regulator of pre-mRNA processing in the cell nucleus.
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Affiliation(s)
- Kinneret Shefer
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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12
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Supraspliceosomes at defined functional states portray the pre-assembled nature of the pre-mRNA processing machine in the cell nucleus. Int J Mol Sci 2014; 15:11637-64. [PMID: 24983480 PMCID: PMC4139805 DOI: 10.3390/ijms150711637] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/05/2014] [Accepted: 06/18/2014] [Indexed: 02/02/2023] Open
Abstract
When isolated from mammalian cell nuclei, all nuclear pre-mRNAs are packaged in multi-subunit large ribonucleoprotein complexes-supraspliceosomes-composed of four native spliceosomes interconnected by the pre-mRNA. Supraspliceosomes contain all five spliceosomal U snRNPs, together with other splicing factors, and are functional in splicing. Supraspliceosomes studied thus far represent the steady-state population of nuclear pre-mRNAs that were isolated at different stages of the splicing reaction. To analyze specific splicing complexes, here, we affinity purified Pseudomonas aeruginosa phage 7 (PP7)-tagged splicing complexes assembled in vivo on Adenovirus Major Late (AdML) transcripts at specific functional stages, and characterized them using molecular techniques including mass spectrometry. First, we show that these affinity purified splicing complexes assembled on PP7-tagged AdML mRNA or on PP7-tagged AdML pre-mRNA are assembled in supraspliceosomes. Second, similar to the general population of supraspliceosomes, these defined supraspliceosomes populations are assembled with all five U snRNPs at all splicing stages. This study shows that dynamic changes in base-pairing interactions of U snRNA:U snRNA and U snRNA:pre-mRNA that occur in vivo during the splicing reaction do not require changes in U snRNP composition of the supraspliceosome. Furthermore, there is no need to reassemble a native spliceosome for the splicing of each intron, and rearrangements of the interactions will suffice.
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13
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Frankenstein Z, Sperling J, Sperling R, Eisenstein M. A unique spatial arrangement of the snRNPs within the native spliceosome emerges from in silico studies. Structure 2012; 20:1097-106. [PMID: 22578543 DOI: 10.1016/j.str.2012.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/25/2012] [Accepted: 03/26/2012] [Indexed: 02/05/2023]
Abstract
The spliceosome is a mega-Dalton ribonucleoprotein (RNP) assembly that processes primary RNA transcripts, producing functional mRNA. The electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes are available; however, the spatial arrangement of the latter within the native spliceosome is not known. We designed a computational procedure to efficiently fit thousands of conformers into the spliceosome envelope. Despite the low resolution limitations, we obtained only one model that complies with the available biochemical data. Our model localizes the five small nuclear RNPs (snRNPs) mostly within the large subunit of the native spliceosome, requiring only minor conformation changes. The remaining free volume presumably accommodates additional spliceosomal components. The constituents of the active core of the spliceosome are juxtaposed, forming a continuous surface deep within the large spliceosomal cavity, which provides a sheltered environment for the splicing reaction.
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Affiliation(s)
- Ziv Frankenstein
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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14
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Regulation of alternative splicing within the supraspliceosome. J Struct Biol 2011; 177:152-9. [PMID: 22100336 DOI: 10.1016/j.jsb.2011.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/02/2011] [Accepted: 11/05/2011] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a fundamental feature in regulating the eukaryotic transcriptome, as ~95% of multi-exon human Pol II transcripts are subject to this process. Regulated splicing operates through the combinatorial interplay of positive and negative regulatory signals present in the pre-mRNA, which are recognized by trans-acting factors. All these RNA and protein components are assembled in a gigantic, 21 MDa, ribonucleoprotein splicing machine - the supraspliceosome. Because most alternatively spliced mRNA isoforms vary between different cell and tissue types, the ability to perform alternative splicing is expected to be an integral part of the supraspliceosome, which constitutes the splicing machine in vivo. Here we show that both the constitutively and alternatively spliced mRNAs of the endogenous human pol II transcripts: hnRNP A/B, survival of motor neuron (SMN) and ADAR2 are predominantly found in supraspliceosomes. This finding is consistent with our observations that the splicing regulators hnRNP G as well as all phosphorylated SR proteins are predominantly associated with supraspliceosomes. We further show that changes in alternative splicing of hnRNP A/B, affected by up regulation of SRSF5 (SRp40) or by treatment with C6-ceramide, occur within supraspliceosomes. These observations support the proposed role of the supraspliceosome in splicing regulation and alternative splicing.
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15
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Abstract
Structural biology research is increasingly focusing on unraveling structural variations at the micro-, meso-, and macroscale aiming at interpreting dynamic biological processes and pathways. Toward this goal, high-resolution transmission cryoelectron microscopy (cryo-EM) and cryoelectron tomography (cryo-ET) are indispensable, as these provide the ability to determine 3D structures of large, dynamic macromolecular assemblies in their native, fully hydrated state in situ. Underlying such analyses is the implicit assumption that specific structural states yield specific cellular outputs. The dependence on this structure-function paradigm is not unique to studies pertaining a particular pathway or biological process but it sets the foundation for all cell biological analyses of macromolecular assemblies. Yet, the paradigm still awaits formal proof. The field of high-resolution electron microscopy (HREM) is in dire need of establishing approaches and technologies to systematic and quantitative determining structure-function correlates in physiologically relevant environment. Here, using the actin cytoskeletal networks as an example, we will provide snapshots of current advances in defining the structures of these highly dynamic networks in situ. We will further detail some of the major stumbling blocks on the way to quantitatively correlate the dynamic state to network morphology in the same window of time and space.
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16
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Abstract
Lipid monolayers have traditionally been used in electron microscopy (EM) to form two-dimensional (2D) protein arrays for structural studies by electron crystallography. More recently, monolayers containing Nickel-nitrilotriacetic acid (Ni-NTA) lipids have been used to combine the purification and preparation of single-particle EM specimens of His-tagged proteins into a single, convenient step. This monolayer purification technique was further simplified by introducing the Affinity Grid, an EM grid that features a predeposited Ni-NTA lipid-containing monolayer. In this contribution, we provide a detailed description for the use of monolayer purification and Affinity Grids, discuss their advantages and limitations, and present examples to illustrate specific applications of the methods.
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17
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Breithaupt H. Seeing is understanding. Improvements in computer software and hardware are revolutionizing three-dimensional imaging in biology. EMBO Rep 2009; 7:467-70. [PMID: 16670676 PMCID: PMC1479552 DOI: 10.1038/sj.embor.7400695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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18
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Hussein WM, Ross BP, Landsberg MJ, Lévy D, Hankamer B, McGeary RP. Synthesis of Nickel-Chelating Fluorinated Lipids for Protein Monolayer Crystallizations. J Org Chem 2009; 74:1473-9. [DOI: 10.1021/jo802651p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Waleed M. Hussein
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Benjamin P. Ross
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Michael J. Landsberg
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Daniel Lévy
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Ben Hankamer
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Ross P. McGeary
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
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19
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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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20
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Monolayer purification: a rapid method for isolating protein complexes for single-particle electron microscopy. Proc Natl Acad Sci U S A 2008; 105:4703-8. [PMID: 18347330 DOI: 10.1073/pnas.0800867105] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Visualizing macromolecular complexes by single-particle electron microscopy (EM) entails stringent biochemical purification, specimen preparation, low-dose imaging, and 3D image reconstruction. Here, we introduce the "monolayer purification" method, which employs nickel-nitrilotriacetic acid (Ni-NTA) functionalized lipids for simultaneously purifying His-tagged complexes directly from cell lysates while producing specimens suitable for single-particle EM. The method was established by using monolayers containing Ni-NTA lipid to specifically adsorb His-tagged transferrin-transferrin receptor (Tf-TfR) complexes from insect and mammalian cell extracts. The specificity and sensitivity of the method could be improved by adding imidazole to the extracts. The monolayer-purified Tf-TfR samples could be vitrified and used to calculate a 3D reconstruction of the complex. Monolayer purification was then used to rapidly isolate ribosomal complexes from bacteria by overexpressing a single His-tagged ribosomal subunit. The resulting monolayer samples allowed calculation of a cryo-EM 3D reconstruction of the Escherichia coli 50S ribosomal subunit.
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21
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Schwartz CL, Sarbash VI, Ataullakhanov FI, McIntosh JR, Nicastro D. Cryo-fluorescence microscopy facilitates correlations between light and cryo-electron microscopy and reduces the rate of photobleaching. J Microsc 2007; 227:98-109. [PMID: 17845705 DOI: 10.1111/j.1365-2818.2007.01794.x] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence light microscopy (LM) has many advantages for the study of cell organization. Specimen preparation is easy and relatively inexpensive, and the use of appropriate tags gives scientists the ability to visualize specific proteins of interest. LM is, however, limited in resolution, so when one is interested in ultrastructure, one must turn to electron microscopy (EM), even though this method presents problems of its own. The biggest difficulty with cellular EM is its limited utility in localizing macromolecules of interest while retaining good structural preservation. We have built a cryo-light microscope stage that allows us to generate LM images of vitreous samples prepared for cryo-EM. Correlative LM and EM allows one to find areas of particular interest by using fluorescent proteins or vital dyes as markers within vitrified samples. Once located, the sample can be placed in the EM for further study at higher resolution. An additional benefit of the cryo-LM stage is that photobleaching is slower at cryogenic temperatures (-140 degrees C) than at room temperature.
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Affiliation(s)
- Cindi L Schwartz
- Boulder Laboratory for 3D Electron Microscopy of Cells, University of Colorado, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO, USA
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22
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Taylor DW, Kelly DF, Cheng A, Taylor KA. On the freezing and identification of lipid monolayer 2-D arrays for cryoelectron microscopy. J Struct Biol 2007; 160:305-12. [PMID: 17561414 PMCID: PMC2268103 DOI: 10.1016/j.jsb.2007.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2005] [Revised: 04/02/2007] [Accepted: 04/04/2007] [Indexed: 11/22/2022]
Abstract
Lipid monolayers provide a convenient vehicle for the crystallization of biological macromolecules for 3-D electron microscopy. Although numerous examples of 3-D images from 2-D protein arrays have been described from negatively stained specimens, only six structures have been done from frozen-hydrated specimens. We describe here a method that makes high quality frozen-hydrated specimens of lipid monolayer arrays for cryoelectron microscopy. The method uses holey carbon films with patterned holes for monolayer recovery, blotting and plunge freezing to produce thin aqueous films which cover >90% of the available grid area. With this method, even specimens with relatively infrequent crystals can be screened using automated data collection techniques. Though developed for microscopic examination of 2-D arrays, the method may have wider application to the preparation of single particle specimens for 3-D image reconstruction.
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Affiliation(s)
- Dianne W Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.
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23
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Cohen-Krausz S, Sperling R, Sperling J. Exploring the architecture of the intact supraspliceosome using electron microscopy. J Mol Biol 2007; 368:319-27. [PMID: 17359996 DOI: 10.1016/j.jmb.2007.01.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 12/19/2006] [Accepted: 01/31/2007] [Indexed: 11/20/2022]
Abstract
Splicing of pre-mRNA takes place on a massive macromolecular machine in the nucleus of eukaryotic cells, the supraspliceosome. This particle is a multicomponent biological complex of RNA and proteins. It is composed of four sub-structures termed native spliceosomes that splice pre-mRNA. The structure of the native spliceosome, determined by cryo-EM at 20 A resolution, showed that it is composed of two distinct subunits. Previously, medium resolution structural analysis of supraspliceosomes by electron tomography was performed, yet little is known of how the native spliceosomes are arranged within the intact particle. To address this question the native spliceosomes were analyzed and reconstructed in the context of the intact particle, using electron microscopy combined with image processing. Good correlation was obtained between the structure of the isolated native spliceosome, solved by cryo-EM, and the native spliceosome within the intact supraspliceosome. An ordered assembly was revealed with different potential roles assigned to the small and large subunits of the native spliceosome. The edges of the small subunits, which are in the center of the supraspliceosome, form a right angle and thus facilitate close contacts between the small subunits generating a 4-fold pattern. The analysis of sub-complex orientation within the particle suggests a possible route within the supraspliceosome for the passage of pre-mRNA, which is known to hold the particle together.
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Affiliation(s)
- Sara Cohen-Krausz
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
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24
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Grünwald D, Spottke B, Buschmann V, Kubitscheck U. Intranuclear binding kinetics and mobility of single native U1 snRNP particles in living cells. Mol Biol Cell 2006; 17:5017-27. [PMID: 16987963 PMCID: PMC1679670 DOI: 10.1091/mbc.e06-06-0559] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are splicing factors, which are diffusely distributed in the nucleoplasm and also concentrated in nuclear speckles. Fluorescently labeled, native U1 snRNPs were microinjected into the cytoplasm of living HeLa cells. After nuclear import single U1 snRNPs could be visualized and tracked at a spatial precision of 30 nm at a frame rate of 200 Hz employing a custom-built microscope with single-molecule sensitivity. The single-particle tracks revealed that most U1 snRNPs were bound to specific intranuclear sites, many of those presumably representing pre-mRNA splicing sites. The dissociation kinetics from these sites showed a multiexponential decay behavior on time scales ranging from milliseconds to seconds, reflecting the involvement of U1 snRNPs in numerous distinct interactions. The average dwell times for U1 snRNPs bound at sites within the nucleoplasm did not differ significantly from those in speckles, indicating that similar processes occur in both compartments. Mobile U1 snRNPs moved with diffusion constants in the range from 0.5 to 8 microm2/s. These values were consistent with uncomplexed U1 snRNPs diffusing at a viscosity of 5 cPoise and U1 snRNPs moving in a largely restricted manner, and U1 snRNPs contained in large supramolecular assemblies such as spliceosomes or supraspliceosomes.
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Affiliation(s)
- David Grünwald
- *Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany; and
| | - Beatrice Spottke
- *Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany; and
| | | | - Ulrich Kubitscheck
- *Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany; and
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25
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Azubel M, Habib N, Sperling R, Sperling J. Native spliceosomes assemble with pre-mRNA to form supraspliceosomes. J Mol Biol 2005; 356:955-66. [PMID: 16386271 DOI: 10.1016/j.jmb.2005.11.078] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 11/28/2005] [Accepted: 11/28/2005] [Indexed: 11/16/2022]
Abstract
Regulation of eukaryotic gene expression is achieved at different levels, which require accurate coordination. Macromolecular assemblies that exist as pre-formed entities can account for such coordination. Processing of pre-mRNA represents one step in this cascade of regulatory events but, moreover, provides explanation for protein versatility. The cellular machine where splicing of pre-mRNA, as well as additional processing events, take place in vivo is termed the supraspliceosome. Here, we show that the supraspliceosome is composed of four active spliceosomes, termed native spliceosomes, connected to each other by the pre-mRNA. Cleavage of pre-mRNA shows that its integrity is essential for the stability of the supraspliceosome. Furthermore, supraspliceosomes can be reconstituted in vitro, from purified native spliceosomes by addition of synthetic pre-mRNAs, providing further support to the supraspliceosome as a preassembled biological complex. The internal setting of the native spliceosomes within the supraspliceosome is most suitable to enable the communication between these structures, which is crucial in order to achieve regulated splicing.
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Affiliation(s)
- Maia Azubel
- Deptartment of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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26
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Murphy GE, Jensen GJ. Electron Cryotomography of the E. coli Pyruvate and 2-Oxoglutarate Dehydrogenase Complexes. Structure 2005; 13:1765-73. [PMID: 16338405 DOI: 10.1016/j.str.2005.08.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 07/27/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
The E. coli pyruvate and 2-oxoglutarate dehydrogenases are two closely related, large complexes that exemplify a growing number of multiprotein "machines" whose domains have been studied extensively and modeled in atomic detail, but whose quaternary structures have remained unclear for lack of an effective imaging technology. Here, electron cryotomography was used to show that the E1 and E3 subunits of these complexes are flexibly tethered approximately 11 nm away from the E2 core. This result demonstrates unambiguously that electron cryotomography can reveal the relative positions of features as small as 80 kDa in individual complexes, elucidating quaternary structure and conformational flexibility.
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Affiliation(s)
- Gavin E Murphy
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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27
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Marco S, Boudier T, Messaoudi C, Rigaud JL. Electron tomography of biological samples. BIOCHEMISTRY (MOSCOW) 2005; 69:1219-25. [PMID: 15627375 DOI: 10.1007/s10541-005-0067-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron tomography allows computing three-dimensional (3D) reconstructions of objects from their projections recorded at several angles. Combined with transmission electron microscopy, electron tomography has contributed greatly to the understanding of subcellular structures and organelles. Performed on frozen-hydrated samples, electron tomography has yielded useful information about complex biological structures. Combined with energy filtered transmission electron microscopy (EFTEM) it can be used to analyze the spatial distribution of chemical elements in biological or material sciences samples. In the present review, we present an overview of the requirements, applications, and perspectives of electron tomography in structural biology.
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Affiliation(s)
- S Marco
- Institut Curie, Section Recherche, UMR-CNRS 168 et LRC-CEA 34V 11, 75005 Paris, France.
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28
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Electron tomography of biological samples. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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29
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Wachtel C, Li B, Sperling J, Sperling R. Stop codon-mediated suppression of splicing is a novel nuclear scanning mechanism not affected by elements of protein synthesis and NMD. RNA (NEW YORK, N.Y.) 2004; 10:1740-50. [PMID: 15388876 PMCID: PMC1370662 DOI: 10.1261/rna.7480804] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 07/23/2004] [Indexed: 05/21/2023]
Abstract
The pre-mRNA splicing machine must frequently discriminate between normal and many potential 5'splice sites that match the consensus sequence but remain latent. Suppression of splicing (SOS) at such latent 5'splice sites is required for the maintenance of an open reading frame, and to ensure that only RNAs that encode for functional proteins will be formed. In this study we show that SOS is a novel mechanism distinct from the known RNA surveillance mechanisms. First, SOS is distinct from nonsense-mediated mRNA decay (NMD) because it is not dependent on translation and is not affected by RNAi-mediated down-regulation of hUpf1 and hUpf2--two key components of the NMD pathway. Second, SOS is distinct from nonsense-associated alternative splicing (NAS), because a mutant of hUpf1, which was shown to abrogate NAS, does not activate latent splicing. Elucidating the mechanism of SOS is pertinent to human disease in view of the large number of human genes that harbor latent splice sites.
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Affiliation(s)
- Chaim Wachtel
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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30
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Rafelski SM, Theriot JA. Crawling toward a unified model of cell mobility: spatial and temporal regulation of actin dynamics. Annu Rev Biochem 2004; 73:209-39. [PMID: 15189141 DOI: 10.1146/annurev.biochem.73.011303.073844] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Crawling cells of various morphologies displace themselves in their biological environments by a similar overall mechanism of protrusion through actin assembly at the front coordinated with retraction at the rear. Different cell types organize very distinct protruding structures, yet they do so through conserved biochemical mechanisms to regulate actin polymerization dynamics and vary the mechanical properties of these structures. The moving cell must spatially and temporally regulate the biochemical interactions of its protein components to exert control over higher-order dynamic structures created by these proteins and global cellular responses four or more orders of magnitude larger in scale and longer in time than the individual protein-protein interactions that comprise them. To fulfill its biological role, a cell globally responds with high sensitivity to a local perturbation or signal and coordinates its many intracellular actin-based functional structures with the physical environment it experiences to produce directed movement. This review attempts to codify some unifying principles for cell motility that span organizational scales from single protein polymer filaments to whole crawling cells.
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Affiliation(s)
- Susanne M Rafelski
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
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31
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Azubel M, Wolf SG, Sperling J, Sperling R. Three-Dimensional Structure of the Native Spliceosome by Cryo-Electron Microscopy. Mol Cell 2004; 15:833-9. [PMID: 15350226 DOI: 10.1016/j.molcel.2004.07.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 06/24/2004] [Accepted: 06/29/2004] [Indexed: 11/17/2022]
Abstract
Splicing of pre-mRNA occurs in a multicomponent macromolecular machine--the spliceosome. The spliceosome can be assembled in vitro by a stepwise assembly of a number of snRNPs and additional proteins on exogenously added pre-mRNA. In contrast, splicing in vivo occurs in preformed particles where endogenous pre-mRNAs are packaged with all five spliceosomal U snRNPs (penta-snRNP) together with other splicing factors. Here we present a three-dimensional image reconstruction by cryo-electron microscopy of native spliceosomes, derived from cell nuclei, at a resolution of 20 angstroms. The structure revealed an elongated globular particle made up of two distinct subunits connected to each other leaving a tunnel in between. We show here that the larger subunit is a suitable candidate to accommodate the penta-snRNP, and that the tunnel could accommodate the pre-mRNA component of the spliceosome. The features this structure reveals provide new insight into the global architecture of the native splicing machine.
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Affiliation(s)
- Maia Azubel
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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32
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Miriami E, Motro U, Sperling J, Sperling R. Conservation of an open-reading frame as an element affecting 5' splice site selection. J Struct Biol 2002; 140:116-22. [PMID: 12490159 DOI: 10.1016/s1047-8477(02)00539-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Splice site selection is a key element of pre-mRNA splicing and involves specific recognition of consensus sequences at the 5(') and 3(') splice sites. Evidently, the compliance of a given sequence with the consensus 5(') splice site sequence is not sufficient to define it as a functional 5(') splice site, because not all sequences that conform with the consensus are used for splicing. We have previously hypothesized that the necessity to avoid the inclusion of premature termination codons within mature mRNAs may serve as a criterion that differentiates normal 5(') splice sites from unused (latent) ones. We further provided experimental support to this idea, by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5(') splice site were mutated, and showing that splicing using the latent site is indeed activated by such mutations. Here we evaluate this hypothesis by a computerized survey for latent 5(') splice sites in 446 protein-coding human genes. This data set contains 2311 introns, in which we found 10490 latent 5(') splice sites. The utilization of 10045 (95.8%) of these sites for splicing would have led to the inclusion of an in-frame stop codon within the resultant mRNA. The validity of this finding is confirmed here by statistical analyses. This finding, together with our previous experimental results, invokes a nuclear scanning mechanism, as part of the splicing machine, which identifies in-frame stop codons within the pre-mRNA and prevents splicing that could lead to the formation of a prematurely terminated protein.
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Affiliation(s)
- Elana Miriami
- Department of Genetics, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
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33
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Raitskin O, Angenitzki M, Sperling J, Sperling R. Large nuclear RNP particles--the nuclear pre-mRNA processing machine. J Struct Biol 2002; 140:123-30. [PMID: 12490160 DOI: 10.1016/s1047-8477(02)00541-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Processing of nuclear pre-mRNA is an important step in the regulation of gene expression and involves 5(')- and 3(')-end processing, splicing, and editing. Mammalian nuclear pre-mRNAs are assembled in large ribonucleoprotein (lnRNP) complexes, in which the entire population of nuclear pre-mRNA is individually packaged until it is exported to the cytoplasm. The lnRNP particles are supraspliceosomal complexes. They are composed of four spliceosomal substructures and an additional one, which are interconnected by the pre-mRNA, and have an overall mass of 21MDa. The additional substructure was proposed to harbor additional processing activities, such as editing components that were shown to be associated with the lnRNP particles. Here we show that the cap-binding proteins (CBPs), CBP20 and CBP80, are associated with the lnRNP particles, as well as components of the 3(')-end-processing activity. These results, together with our previous demonstration of the association of splicing factors and A-to-I editing enzymes with lnRNP particles, support the view that the lnRNP particles are the nuclear pre-mRNA processing machine. Such a machine is required to execute the nuclear processing steps of the pre-mRNA in an accurate and regulated manner. The supraspliceosomal pre-mRNA processing machine, in which each substructure represents a functional spliceosome, provides a frame onto which the pre-mRNA is folded. It allows juxtaposition of exons about to be spliced, while introns are looped out of each of the respective spliceosomes. This model can account for regulated alternative splicing, which is a major source of protein versatility in mammals.
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Affiliation(s)
- Oleg Raitskin
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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