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Valach M, Benz C, Aguilar LC, Gahura O, Faktorová D, Zíková A, Oeffinger M, Burger G, Gray MW, Lukeš J. Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway. Nucleic Acids Res 2023; 51:6443-6460. [PMID: 37207340 PMCID: PMC10325924 DOI: 10.1093/nar/gkad422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
The mitochondrial ribosome (mitoribosome) has diverged drastically from its evolutionary progenitor, the bacterial ribosome. Structural and compositional diversity is particularly striking in the phylum Euglenozoa, with an extraordinary protein gain in the mitoribosome of kinetoplastid protists. Here we report an even more complex mitoribosome in diplonemids, the sister-group of kinetoplastids. Affinity pulldown of mitoribosomal complexes from Diplonema papillatum, the diplonemid type species, demonstrates that they have a mass of > 5 MDa, contain as many as 130 integral proteins, and exhibit a protein-to-RNA ratio of 11:1. This unusual composition reflects unprecedented structural reduction of ribosomal RNAs, increased size of canonical mitoribosomal proteins, and accretion of three dozen lineage-specific components. In addition, we identified >50 candidate assembly factors, around half of which contribute to early mitoribosome maturation steps. Because little is known about early assembly stages even in model organisms, our investigation of the diplonemid mitoribosome illuminates this process. Together, our results provide a foundation for understanding how runaway evolutionary divergence shapes both biogenesis and function of a complex molecular machine.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada
| | - Corinna Benz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Lisbeth C Aguilar
- Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal (IRCM), Montréal, Quebec, Canada
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Marlene Oeffinger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada
- Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal (IRCM), Montréal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Institute of Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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2
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Bassot A, Chen J, Takahashi-Yamashiro K, Yap MC, Gibhardt CS, Le GNT, Hario S, Nasu Y, Moore J, Gutiérrez T, Mina L, Mast H, Moses A, Bhat R, Ballanyi K, Lemieux H, Sitia R, Zito E, Bogeski I, Campbell RE, Simmen T. The endoplasmic reticulum kinase PERK interacts with the oxidoreductase ERO1 to metabolically adapt mitochondria. Cell Rep 2023; 42:111899. [PMID: 36586409 DOI: 10.1016/j.celrep.2022.111899] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/04/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Endoplasmic reticulum (ER) homeostasis requires molecular regulators that tailor mitochondrial bioenergetics to the needs of protein folding. For instance, calnexin maintains mitochondria metabolism and mitochondria-ER contacts (MERCs) through reactive oxygen species (ROS) from NADPH oxidase 4 (NOX4). However, induction of ER stress requires a quick molecular rewiring of mitochondria to adapt to new energy needs. This machinery is not characterized. We now show that the oxidoreductase ERO1⍺ covalently interacts with protein kinase RNA-like ER kinase (PERK) upon treatment with tunicamycin. The PERK-ERO1⍺ interaction requires the C-terminal active site of ERO1⍺ and cysteine 216 of PERK. Moreover, we show that the PERK-ERO1⍺ complex promotes oxidization of MERC proteins and controls mitochondrial dynamics. Using proteinaceous probes, we determined that these functions improve ER-mitochondria Ca2+ flux to maintain bioenergetics in both organelles, while limiting oxidative stress. Therefore, the PERK-ERO1⍺ complex is a key molecular machinery that allows quick metabolic adaptation to ER stress.
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Affiliation(s)
- Arthur Bassot
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Junsheng Chen
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | | | - Megan C Yap
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Christine Silvia Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Giang N T Le
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Saaya Hario
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yusuke Nasu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jack Moore
- Alberta Proteomics and Mass Spectrometry Facility, University of Alberta, 4096 Katz Research Building, Edmonton AB T6G2E1, Canada
| | - Tomas Gutiérrez
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Lucas Mina
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Heather Mast
- Faculty Saint-Jean, Department of Medicine, Faculty of Medicine and Dentistry, Edmonton, AB T6G2H7, Canada
| | - Audric Moses
- Department of Pediatrics, Edmonton, AB T6G2H7, Canada
| | - Rakesh Bhat
- Precision Biolaboratories, St. Albert, AB T8N 5A7, Canada
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Hélène Lemieux
- Faculty Saint-Jean, Department of Medicine, Faculty of Medicine and Dentistry, Edmonton, AB T6G2H7, Canada
| | - Roberto Sitia
- Division of Genetics and Cell Biology, Università Vita-Salute IRCCS Ospedale San Raffaele, 20132 Milano, Italy
| | - Ester Zito
- Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milano, Italy; Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino PU, Italy
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Thomas Simmen
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada.
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3
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Trahan C, Oeffinger M. Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae. Methods Mol Biol 2022; 2456:185-210. [PMID: 35612743 DOI: 10.1007/978-1-0716-2124-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Protein cross-linking mass spectrometry (XL-MS) has been developed into a powerful and robust tool that is now well implemented and routinely used by an increasing number of laboratories. While bulk cross-linking of complexes provides useful information on whole complexes, it is limiting for the probing of specific protein "neighbourhoods," or vicinity interactomes. For example, it is not unusual to find cross-linked peptide pairs that are disproportionately overrepresented compared to the surface areas of complexes, while very few or no cross-links are identified in other regions. When studying dynamic complexes along their pathways, some vicinity cross-links may be of too low abundance in the pool of heterogenous complexes of interest to be efficiently identified by standard XL-MS. In this chapter, we describe a targeted XL-MS approach from single-step affinity purified (ssAP) complexes that enables the investigation of specific protein "neighbourhoods" within molecular complexes in yeast, using a small cross-linker anchoring tag, the CH-tag. One advantage of this method over a general cross-linking strategy is the possibility to significantly enrich for localized anchored-cross-links within complexes, thus yielding a higher sensitivity to detect highly dynamic or low abundance protein interactions within a specific protein "neighbourhood" occurring along the pathway of a selected bait protein. Moreover, many variations of the method can be employed; the ssAP-tag and the CH-tag can either be fused to the same or different proteins in the complex, or the CH-tag can be fused to multiple protein components in the same cell line to explore dynamic vicinity interactions along a pathway.
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Affiliation(s)
- Christian Trahan
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada.
- Département de biochimie, Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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Eyboulet F, Jeronimo C, Côté J, Robert F. The deubiquitylase Ubp15 couples transcription to mRNA export. eLife 2020; 9:e61264. [PMID: 33226341 PMCID: PMC7682988 DOI: 10.7554/elife.61264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.
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Affiliation(s)
- Fanny Eyboulet
- Institut de recherches cliniques de MontréalMontréalCanada
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - Célia Jeronimo
- Institut de recherches cliniques de MontréalMontréalCanada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - François Robert
- Institut de recherches cliniques de MontréalMontréalCanada
- Département de Médecine, Faculté de Médecine, Université de MontréalMontréalCanada
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5
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Faktorová D, Kaur B, Valach M, Graf L, Benz C, Burger G, Lukeš J. Targeted integration by homologous recombination enables in situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum. Environ Microbiol 2020; 22:3660-3670. [PMID: 32548939 DOI: 10.1111/1462-2920.15130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022]
Abstract
Diplonemids are a group of highly diverse and abundant marine microeukaryotes that belong to the phylum Euglenozoa and form a sister clade to the well-studied, mostly parasitic kinetoplastids. Very little is known about the biology of diplonemids, as few species have been formally described and just one, Diplonema papillatum, has been studied to a decent extent at the molecular level. Following up on our previous results showing stable but random integration of delivered extraneous DNA, we demonstrate here homologous recombination in D. papillatum. Targeting various constructs to the intended position in the nuclear genome was successful when 5' and 3' homologous regions longer than 1 kbp were used, achieving N-terminal tagging with mCherry and gene replacement of α- and β-tubulins. For more convenient genetic manipulation, we designed a modular plasmid, pDP002, which bears a protein-A tag and used it to generate and express a C-terminally tagged mitoribosomal protein. Lastly, we developed an improved transformation protocol for broader applicability across laboratories. Our robust methodology allows the replacement, integration as well as endogenous tagging of D. papillatum genes, thus opening the door to functional studies in this species and establishing a basic toolkit for reverse genetics of diplonemids in general.
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Affiliation(s)
- Drahomíra Faktorová
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
| | - Binnypreet Kaur
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Lena Graf
- Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic.,Present address: Johannes Kepler University, Linz, Austria
| | - Corinna Benz
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Julius Lukeš
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
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6
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Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac MY, Van Nostrand EL, Adivarahan S, Wei KE, Yeo GW, Zenklusen D, Oeffinger M. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism. Nucleic Acids Res 2017; 45:12509-12528. [PMID: 29069457 PMCID: PMC5716212 DOI: 10.1093/nar/gkx963] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, we describe Nol12 as a multifunctional RBP with roles in RNA metabolism and genome maintenance. Nol12 is found in different subcellular compartments-nucleoli, where it associates with ribosomal RNA and is required for efficient separation of large and small subunit precursors at site 2; the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles; as well as GW/P-bodies in the cytoplasm. Loss of Nol12 results in the inability of cells to recover from DNA stress and a rapid p53-independent ATR-Chk1-mediated apoptotic response. Nol12 co-localizes with DNA repair proteins in vivo including Dhx9, as well as with TOPBP1 at sites of replication stalls, suggesting a role for Nol12 in the resolution of DNA stress and maintenance of genome integrity. Identification of a complex Nol12 interactome, which includes NONO, Dhx9, DNA-PK and Stau1, further supports the protein's diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional RBP essential for genome integrity.
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Affiliation(s)
- Daniel D. Scott
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Pierre J. Zindy
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Lisbeth C. Aguilar
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Marc Y. Delubac
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Eric L. Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Srivathsan Adivarahan
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Karen E. Wei
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Molecular Engineering Laboratory, A*STAR, Singapore
| | - Daniel Zenklusen
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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Havugimana PC, Hu P, Emili A. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks. Expert Rev Proteomics 2017; 14:845-855. [PMID: 28918672 DOI: 10.1080/14789450.2017.1374179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OVERVIEW Elucidation of the networks of physical (functional) interactions present in cells and tissues is fundamental for understanding the molecular organization of biological systems, the mechanistic basis of essential and disease-related processes, and for functional annotation of previously uncharacterized proteins (via guilt-by-association or -correlation). After a decade in the field, we felt it timely to document our own experiences in the systematic analysis of protein interaction networks. Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of 'functional proteomics'. These include mass spectrometry-based methods to characterize macromolecular complexes on a global-scale and sophisticated data analysis tools - most notably machine learning - that allow for the generation of high-quality protein association maps. Expert commentary: Here, we recount some key lessons learned, with an emphasis on successful workflows, and challenges, arising from our own and other groups' ongoing efforts to generate, interpret and report proteome-scale interaction networks in increasingly diverse biological contexts.
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Affiliation(s)
- Pierre C Havugimana
- a Donnelly Centre for Cellular and Biomolecular Research , University of Toronto , Toronto , ON , Canada.,b Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada
| | - Pingzhao Hu
- c Department of Biochemistry and Medical Genetics , University of Manitoba , Winnipeg , MB , Canada
| | - Andrew Emili
- a Donnelly Centre for Cellular and Biomolecular Research , University of Toronto , Toronto , ON , Canada.,b Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada
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8
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Reimer KA, Stark MR, Aguilar LC, Stark SR, Burke RD, Moore J, Fahlman RP, Yip CK, Kuroiwa H, Oeffinger M, Rader SD. The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors. RNA (NEW YORK, N.Y.) 2017; 23:952-967. [PMID: 28325844 PMCID: PMC5435867 DOI: 10.1261/rna.058487.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/15/2017] [Indexed: 05/22/2023]
Abstract
Proteins of the Sm and Sm-like (LSm) families, referred to collectively as (L)Sm proteins, are found in all three domains of life and are known to promote a variety of RNA processes such as base-pair formation, unwinding, RNA degradation, and RNA stabilization. In eukaryotes, (L)Sm proteins have been studied, inter alia, for their role in pre-mRNA splicing. In many organisms, the LSm proteins form two distinct complexes, one consisting of LSm1-7 that is involved in mRNA degradation in the cytoplasm, and the other consisting of LSm2-8 that binds spliceosomal U6 snRNA in the nucleus. We recently characterized the splicing proteins from the red alga Cyanidioschyzon merolae and found that it has only seven LSm proteins. The identities of CmLSm2-CmLSm7 were unambiguous, but the seventh protein was similar to LSm1 and LSm8. Here, we use in vitro binding measurements, microscopy, and affinity purification-mass spectrometry to demonstrate a canonical splicing function for the C. merolae LSm complex and experimentally validate our bioinformatic predictions of a reduced spliceosome in this organism. Copurification of Pat1 and its associated mRNA degradation proteins with the LSm proteins, along with evidence of a cytoplasmic fraction of CmLSm complexes, argues that this complex is involved in both splicing and cytoplasmic mRNA degradation. Intriguingly, the Pat1 complex also copurifies with all four snRNAs, suggesting the possibility of a spliceosome-associated pre-mRNA degradation complex in the nucleus.
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Affiliation(s)
- Kirsten A Reimer
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Martha R Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Lisbeth-Carolina Aguilar
- Laboratory of RNP Biochemistry, Institut de Recherches Cliniques de Montréal (IRCM), Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Sierra R Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Jack Moore
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Haruko Kuroiwa
- Kuroiwa Initiative Research Unit, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Marlene Oeffinger
- Laboratory of RNP Biochemistry, Institut de Recherches Cliniques de Montréal (IRCM), Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H2W 1R7, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
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