1
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Elder JJH, Papadopoulos R, Hayne CK, Stanley RE. The making and breaking of tRNAs by ribonucleases. Trends Genet 2024; 40:511-525. [PMID: 38641471 DOI: 10.1016/j.tig.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.
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Affiliation(s)
- Jessica J H Elder
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Ry Papadopoulos
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA; Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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2
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Yim MK, Stuart CJ, Pond MI, van Hoof A, Johnson SJ. Conserved Residues at the Mtr4 C-Terminus Coordinate Helicase Activity and Exosome Interactions. Biochemistry 2024; 63:159-170. [PMID: 38085597 PMCID: PMC10984559 DOI: 10.1021/acs.biochem.3c00401] [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: 01/03/2024]
Abstract
Mtr4 is an essential RNA helicase involved in nuclear RNA processing and degradation and is a member of the Ski2-like helicase family. Ski2-like helicases share a common core architecture that includes two RecA-like domains, a winged helix, and a helical bundle (HB) domain. In Mtr4, a short C-terminal tail immediately follows the HB domain and is positioned at the interface of the RecA-like domains. The tail ends with a SLYΦ sequence motif that is highly conserved in a subset of Ski2-like helicases. Here, we show that this sequence is critical for Mtr4 function. Mutations in the C-terminus result in decreased RNA unwinding activity. Mtr4 is a key activator of the RNA exosome complex, and mutations in the SLYΦ motif produce a slow growth phenotype when combined with a partial exosome defect in S. cerevisiae, suggesting an important role of the C-terminus of Mtr4 and the RNA exosome. We further demonstrate that C-terminal mutations impair RNA degradation activity by the major RNA exosome nuclease Rrp44 in vitro. These data demonstrate a role for the Mtr4 C-terminus in regulating helicase activity and coordinating Mtr4-exosome interactions.
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Affiliation(s)
- Matthew K. Yim
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322, USA
| | - Catherine J. Stuart
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Markell I. Pond
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322, USA
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3
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Krempl C, Lazzaretti D, Sprangers R. A structural biology view on the enzymes involved in eukaryotic mRNA turnover. Biol Chem 2023; 404:1101-1121. [PMID: 37709756 DOI: 10.1515/hsz-2023-0182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
The cellular environment contains numerous ribonucleases that are dedicated to process mRNA transcripts that have been targeted for degradation. Here, we review the three dimensional structures of the ribonuclease complexes (Pan2-Pan3, Ccr4-Not, Xrn1, exosome) and the mRNA decapping enzymes (Dcp2, DcpS) that are involved in mRNA turnover. Structures of major parts of these proteins have been experimentally determined. These enzymes and factors do not act in isolation, but are embedded in interaction networks which regulate enzyme activity and ensure that the appropriate substrates are recruited. The structural details of the higher order complexes that form can, in part, be accurately deduced from known structural data of sub-complexes. Interestingly, many of the ribonuclease and decapping enzymes have been observed in structurally different conformations. Together with experimental data, this highlights that structural changes are often important for enzyme function. We conclude that the known structural data of mRNA decay factors provide important functional insights, but that static structural data needs to be complemented with information regarding protein motions to complete the picture of how transcripts are turned over. In addition, we highlight multiple aspects that influence mRNA turnover rates, but that have not been structurally characterized so far.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Lazzaretti
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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4
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Sterrett MC, Cureton LA, Cohen LN, van Hoof A, Khoshnevis S, Fasken MB, Corbett AH, Ghalei H. Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562946. [PMID: 37904946 PMCID: PMC10614903 DOI: 10.1101/2023.10.18.562946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The RNA exosome is an evolutionarily conserved exoribonuclease complex that consists of a 3-subunit cap, a 6-subunit barrel-shaped core, and a catalytic base subunit. Missense mutations in genes encoding structural subunits of the RNA exosome cause a growing family of diseases with diverse pathologies, collectively termed RNA exosomopathies. The disease symptoms vary and can manifest as neurological defects or developmental disorders. The diversity of the RNA exosomopathy pathologies suggests that the different missense mutations in structural genes result in distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models using budding yeast by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant models rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome, EXOSC2, EXOSC3 and EXOSC5 showed the largest transcriptomic differences. Further analyses revealed shared increased transcripts enriched in translation or ribosomal RNA modification/processing pathways across the three mutant models. Studies of the impact of the mutations on translation revealed shared defects in ribosome biogenesis but distinct impacts on translation. Collectively, our results provide the first comparative analysis of several RNA exosomopathy mutant models and suggest that different RNA exosomopathy mutations result in in vivo consequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.
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Affiliation(s)
- Maria C. Sterrett
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Lauryn A. Cureton
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lauren N. Cohen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Sohail Khoshnevis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Milo B. Fasken
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | | | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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5
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Sterrett MC, Farchi D, Strassler SE, Boise LH, Fasken MB, Corbett AH. In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:jkad049. [PMID: 36861343 PMCID: PMC10411580 DOI: 10.1093/g3journal/jkad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
The RNA exosome is a conserved molecular machine that processes/degrades numerous coding and non-coding RNAs. The 10-subunit complex is composed of three S1/KH cap subunits (human EXOSC2/3/1; yeast Rrp4/40/Csl4), a lower ring of six PH-like subunits (human EXOSC4/7/8/9/5/6; yeast Rrp41/42/43/45/46/Mtr3), and a singular 3'-5' exo/endonuclease DIS3/Rrp44. Recently, several disease-linked missense mutations have been identified in structural cap and core RNA exosome genes. In this study, we characterize a rare multiple myeloma patient missense mutation that was identified in the cap subunit gene EXOSC2. This missense mutation results in a single amino acid substitution, p.Met40Thr, in a highly conserved domain of EXOSC2. Structural studies suggest that this Met40 residue makes direct contact with the essential RNA helicase, MTR4, and may help stabilize the critical interaction between the RNA exosome complex and this cofactor. To assess this interaction in vivo, we utilized the Saccharomyces cerevisiae system and modeled the EXOSC2 patient mutation into the orthologous yeast gene RRP4, generating the variant rrp4-M68T. The rrp4-M68T cells show accumulation of certain RNA exosome target RNAs and show sensitivity to drugs that impact RNA processing. We also identified robust negative genetic interactions between rrp4-M68T and specific mtr4 mutants. A complementary biochemical approach revealed that Rrp4 M68T shows decreased interaction with Mtr4, consistent with these genetic results. This study suggests that the EXOSC2 mutation identified in a multiple myeloma patient impacts the function of the RNA exosome and provides functional insight into a critical interface between the RNA exosome and Mtr4.
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Affiliation(s)
- Maria C Sterrett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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6
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Paira S, Chakraborty A, Das B. The Sequential Recruitments of Rab-GTPase Ypt1p and the NNS Complex onto pre- HAC1 mRNA Promote Its Nuclear Degradation in Baker's Yeast. Mol Cell Biol 2023; 43:371-400. [PMID: 37533322 PMCID: PMC10448977 DOI: 10.1080/10985549.2023.2227016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 08/04/2023] Open
Abstract
Induction of unfolded protein response involves activation of transcription factor Hac1p that is encoded by HAC1 pre-mRNA harboring an intron and a bipartite element (BE), which is subjected to nuclear mRNA decay by the nuclear exosome/Cbc1p-Tif4631p-dependent Exosome Targeting (CTEXT) complex. Using a combination of genetic and biochemical approaches, we demonstrate that a Rab-GTPase Ypt1p controls unfolded protein response signaling dynamics. This regulation relies on the nuclear localization of a small fraction of the cellular Ypt1p pool in the absence of endoplasmic reticulum (ER)-stress causing a strong association of the nuclear Ypt1p with pre-HAC1 mRNA that eventually promotes sequential recruitments of NNS, CTEXT, and the nuclear exosome onto this pre-mRNA. Recruitment of these decay factors onto pre-HAC1 mRNA is accompanied by its rapid nuclear decay that produces a precursor RNA pool lacking functional BE thereby causing its inefficient targeting to Ire1p foci leading to their diminished splicing and translation. ER stress triggers rapid relocalization of the nuclear pool of Ypt1p to the cytoplasm leading to its dissociation from pre-HAC1 mRNA thereby causing decreased recruitment of these decay factors to precursor HAC1 RNA leading to its diminished degradation. Reduced decay results in an increased abundance of pre-HAC1 mRNA with intact functional BE leading to its enhanced recruitment to Ire1p foci.
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Affiliation(s)
- Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Anish Chakraborty
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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7
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Schneider C, Bohnsack KE. Caught in the act-Visualizing ribonucleases during eukaryotic ribosome assembly. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1766. [PMID: 36254602 DOI: 10.1002/wrna.1766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 07/20/2023]
Abstract
Ribosomes are essential macromolecular machines responsible for translating the genetic information encoded in mRNAs into proteins. Ribosomes are composed of ribosomal RNAs and proteins (rRNAs and RPs) and the rRNAs fulfill both catalytic and architectural functions. Excision of the mature eukaryotic rRNAs from their precursor transcript is achieved through a complex series of endoribonucleolytic cleavages and exoribonucleolytic processing steps that are precisely coordinated with other aspects of ribosome assembly. Many ribonucleases involved in pre-rRNA processing have been identified and pre-rRNA processing pathways are relatively well defined. However, momentous advances in cryo-electron microscopy have recently enabled structural snapshots of various pre-ribosomal particles from budding yeast (Saccharomyces cerevisiae) and human cells to be captured and, excitingly, these structures not only allow pre-rRNAs to be observed before and after cleavage events, but also enable ribonucleases to be visualized on their target RNAs. These structural views of pre-rRNA processing in action allow a new layer of understanding of rRNA maturation and how it is coordinated with other aspects of ribosome assembly. They illuminate mechanisms of target recognition by the diverse ribonucleases involved and reveal how the cleavage/processing activities of these enzymes are regulated. In this review, we discuss the new insights into pre-rRNA processing gained by structural analyses and the growing understanding of the mechanisms of ribonuclease regulation. This article is categorized under: Translation > Ribosome Biogenesis RNA Processing > rRNA Processing.
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Affiliation(s)
- Claudia Schneider
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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8
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de Amorim JL, Asafu-Adjaye D, Corbett AH. Analysis of RNA Exosome Subunit Transcript Abundance Across Tissues: Implications for Neurological Disease Pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544082. [PMID: 37333323 PMCID: PMC10274776 DOI: 10.1101/2023.06.07.544082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Exosomopathies are a collection of rare diseases caused by mutations in genes that encode structural subunits of a ribonuclease complex termed the RNA exosome. The RNA exosome mediates both RNA processing and degradation of multiple classes of RNA. This complex is evolutionarily conserved and required for fundamental cellular functions, including rRNA processing. Recently, missense mutations in genes encoding structural subunits of the RNA exosome complex have been linked to a variety of distinct neurological diseases, many of them childhood neuronopathies with at least some cerebellar atrophy. Understanding how these missense mutations lead to the disparate clinical presentations that have been reported for this class of diseases necessitates investigation of how these specific changes alter cell-specific RNA exosome function. Although the RNA exosome complex is routinely referred to as ubiquitously expressed, little is known about the tissue- or cell-specific expression of the RNA exosome complex or any individual subunit. Here, we leverage publicly available RNA-sequencing data to analyze RNA exosome subunit transcript levels in healthy human tissues, focusing on those tissues that are impacted in exosomopathy patients described in clinical reports. This analysis provides evidence to support the characterization of the RNA exosome as ubiquitously expressed with transcript levels for the individual subunits that vary in different tissues. However, the cerebellar hemisphere and cerebellum have high levels of nearly all RNA exosome subunit transcripts. These findings could suggest that the cerebellum has a high requirement for RNA exosome function and potentially explain why cerebellar pathology is common in RNA exosomopathies.
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9
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Shan L, Xu G, Yao RW, Luan PF, Huang Y, Zhang PH, Pan YH, Zhang L, Gao X, Li Y, Cao SM, Gao SX, Yang ZH, Li S, Yang LZ, Wang Y, Wong CCL, Yu L, Li J, Yang L, Chen LL. Nucleolar URB1 ensures 3' ETS rRNA removal to prevent exosome surveillance. Nature 2023; 615:526-534. [PMID: 36890225 DOI: 10.1038/s41586-023-05767-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
The nucleolus is the most prominent membraneless condensate in the nucleus. It comprises hundreds of proteins with distinct roles in the rapid transcription of ribosomal RNA (rRNA) and efficient processing within units comprising a fibrillar centre and a dense fibrillar component and ribosome assembly in a granular component1. The precise localization of most nucleolar proteins and whether their specific localization contributes to the radial flux of pre-rRNA processing have remained unknown owing to insufficient resolution in imaging studies2-5. Therefore, how these nucleolar proteins are functionally coordinated with stepwise pre-rRNA processing requires further investigation. Here we screened 200 candidate nucleolar proteins using high-resolution live-cell microscopy and identified 12 proteins that are enriched towards the periphery of the dense fibrillar component (PDFC). Among these proteins, unhealthy ribosome biogenesis 1 (URB1) is a static, nucleolar protein that ensures 3' end pre-rRNA anchoring and folding for U8 small nucleolar RNA recognition and the subsequent removal of the 3' external transcribed spacer (ETS) at the dense fibrillar component-PDFC boundary. URB1 depletion leads to a disrupted PDFC, uncontrolled pre-rRNA movement, altered pre-rRNA conformation and retention of the 3' ETS. These aberrant 3' ETS-attached pre-rRNA intermediates activate exosome-dependent nucleolar surveillance, resulting in decreased 28S rRNA production, head malformations in zebrafish and delayed embryonic development in mice. This study provides insight into functional sub-nucleolar organization and identifies a physiologically essential step in rRNA maturation that requires the static protein URB1 in the phase-separated nucleolus.
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Affiliation(s)
- Lin Shan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pei-Hong Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Pan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Gao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying Li
- Cryo EM facility, Technology Center for Protein Sciences, School of Life Science, Tsinghua University, Beijing, China
| | - Shi-Meng Cao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuai-Xin Gao
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China
| | - Zheng-Hu Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Siqi Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Catharine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
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10
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Ohguchi Y, Ohguchi H. DIS3: The Enigmatic Gene in Multiple Myeloma. Int J Mol Sci 2023; 24:ijms24044079. [PMID: 36835493 PMCID: PMC9958658 DOI: 10.3390/ijms24044079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Recent studies have revealed the genetic aberrations involved in the initiation and progression of various cancers, including multiple myeloma (MM), via next-generation sequencing analysis. Notably, DIS3 mutations have been identified in approximately 10% of patients with MM. Moreover, deletions of the long arm of chromosome 13, that includes DIS3, are present in approximately 40% of patients with MM. Regardless of the high incidence of DIS3 mutations and deletions, their contribution to the pathogenesis of MM has not yet been determined. Herein, we summarize the molecular and physiological functions of DIS3, focusing on hematopoiesis, and discuss the characteristics and potential roles of DIS3 mutations in MM. Recent findings highlight the essential roles of DIS3 in RNA homeostasis and normal hematopoiesis and suggest that the reduced activity of DIS3 may be involved in myelomagenesis by increasing genome instability.
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Affiliation(s)
- Yasuyo Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Hiroto Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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11
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Lee TA, Han H, Polash A, Cho SK, Lee JW, Ra EA, Lee E, Park A, Kang S, Choi JL, Kim JH, Lee JE, Min KW, Yang SW, Hafner M, Lee I, Yoon JH, Lee S, Park B. The nucleolus is the site for inflammatory RNA decay during infection. Nat Commun 2022; 13:5203. [PMID: 36057640 PMCID: PMC9440930 DOI: 10.1038/s41467-022-32856-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/16/2022] [Indexed: 11/12/2022] Open
Abstract
Inflammatory cytokines are key signaling molecules that can promote an immune response, thus their RNA turnover must be tightly controlled during infection. Most studies investigate the RNA decay pathways in the cytosol or nucleoplasm but never focused on the nucleolus. Although this organelle has well-studied roles in ribosome biogenesis and cellular stress sensing, the mechanism of RNA decay within the nucleolus is not completely understood. Here, we report that the nucleolus is an essential site of inflammatory pre-mRNA instability during infection. RNA-sequencing analysis reveals that not only do inflammatory genes have higher intronic read densities compared with non-inflammatory genes, but their pre-mRNAs are highly enriched in nucleoli during infection. Notably, nucleolin (NCL) acts as a guide factor for recruiting cytosine or uracil (C/U)-rich sequence-containing inflammatory pre-mRNAs and the Rrp6-exosome complex to the nucleolus through a physical interaction, thereby enabling targeted RNA delivery to Rrp6-exosomes and subsequent degradation. Consequently, Ncl depletion causes aberrant hyperinflammation, resulting in a severe lethality in response to LPS. Importantly, the dynamics of NCL post-translational modifications determine its functional activity in phases of LPS. This process represents a nucleolus-dependent pathway for maintaining inflammatory gene expression integrity and immunological homeostasis during infection. The nucleolus is the traditional site for ribosomal RNA biogenesis. Here, the authors find that the nucleolus is a site of inflammatory pre-mRNA turnover and elucidated how immune homeostasis can be maintained by controlling inflammatory gene expression.
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Affiliation(s)
- Taeyun A Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Heonjong Han
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, South Korea
| | - Ahsan Polash
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Won Lee
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung, South Korea
| | - Eun A Ra
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Eunhye Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Areum Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Junhee L Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Hyun Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji Eun Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea.,Samsung Genome Institute (SGI), Samsung Medical Center, Seoul, South Korea
| | - Kyung-Won Min
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung, South Korea.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.
| | - Sungwook Lee
- Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, South Korea.
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.
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12
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Fujiwara N, Shigemoto M, Hirayama M, Fujita KI, Seno S, Matsuda H, Nagahama M, Masuda S. MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus. Nucleic Acids Res 2022; 50:8779-8806. [PMID: 35902094 PMCID: PMC9410898 DOI: 10.1093/nar/gkac559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/10/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here, we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent substrate decay by the human exosome. Using RNA polymerase II-transcribed poly(A)+ substrate accumulation as an indicator of a perturbed exosome, we found functional redundancy between RRP6 and MPP6 in the decay of these poly(A)+ transcripts. MTR4 binding to the exosome core via MPP6 was essential for MPP6 to exert its redundancy with RRP6. However, at least for the decay of our identified exosome substrates, MTR4 recruitment by MPP6 was not functionally equivalent to recruitment by RRP6. Genome-wide classification of substrates based on their sensitivity to each exosome component revealed that MPP6 deals with a specific range of substrates and highlights the importance of MTR4 for their decay. Considering recent findings of competitive binding to the exosome between auxiliary complexes, our results suggest that the MPP6-incorporated MTR4-exosome complex is one of the multiple alternative complexes rather than the prevailing one.
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Affiliation(s)
- Naoko Fujiwara
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Maki Shigemoto
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Mizuki Hirayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Ken-Ichi Fujita
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan.,Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Seiji Masuda
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan.,Department of Food Science and Nutrition, Faculty of Agriculture Kindai University, Nara, Nara 631-8505, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Nara 631-8505, Japan.,Antiaging center, Kindai University, Higashiosaka, Osaka 577-8502, Japan
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13
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Puno MR, Lima CD. Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. Cell 2022; 185:2132-2147.e26. [PMID: 35688134 PMCID: PMC9210550 DOI: 10.1016/j.cell.2022.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/04/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay.
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Affiliation(s)
- M Rhyan Puno
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.
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14
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Villa T, Porrua O. Pervasive transcription: a controlled risk. FEBS J 2022. [PMID: 35587776 DOI: 10.1111/febs.16530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.
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Affiliation(s)
- Tommaso Villa
- Institut Jacques Monod CNRS, Université de Paris Cité France
| | - Odil Porrua
- Institut Jacques Monod CNRS, Université de Paris Cité France
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15
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Chappleboim A, Joseph-Strauss D, Gershon O, Friedman N. Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. Nucleic Acids Res 2022; 50:5864-5880. [PMID: 35640599 PMCID: PMC9177992 DOI: 10.1093/nar/gkac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 01/02/2023] Open
Abstract
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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16
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Gockert M, Schmid M, Jakobsen L, Jens M, Andersen JS, Jensen TH. Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation. Nucleic Acids Res 2022; 50:1583-1600. [PMID: 35048984 PMCID: PMC8860595 DOI: 10.1093/nar/gkac001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/13/2021] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
Turnover of nucleoplasmic transcripts by the mammalian multi-subunit RNA exosome is mediated by two adaptors: the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely utilized long-term factor depletion strategies, facilitating the appearance of indirect phenotypes. Here, we rapidly deplete NEXT, PAXT and core exosome components, uncovering the direct consequences of their acute losses. Generally, proteome changes are sparse and largely dominated by co-depletion of other exosome and adaptor subunits, reflecting possible subcomplex compositions. While parallel high-resolution 3′ end sequencing of newly synthesized RNA confirms previously established factor specificities, it concomitantly demonstrates an inflation of long-term depletion datasets by secondary effects. Most strikingly, a general intron degradation phenotype, observed in long-term NEXT depletion samples, is undetectable upon short-term depletion, which instead emphasizes NEXT targeting of snoRNA-hosting introns. Further analysis of these introns uncovers an unusual mode of core exosome-independent RNA decay. Our study highlights the accumulation of RNAs as an indirect result of long-term decay factor depletion, which we speculate is, at least partly, due to the exhaustion of alternative RNA decay pathways.
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Affiliation(s)
- Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Marvin Jens
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, 68-271A, Cambridge, MA 02139-4307, USA
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
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17
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Puno MR, Lima CD. Methods to assess helicase and translocation activities of human nuclear RNA exosome and RNA adaptor complexes. Methods Enzymol 2022; 673:453-473. [PMID: 35965016 PMCID: PMC9382703 DOI: 10.1016/bs.mie.2022.03.060] [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] [Indexed: 11/02/2022]
Abstract
The nuclear RNA exosome collaborates with the MTR4 helicase and RNA adaptor complexes to process, surveil, and degrade RNA. Here we outline methods to characterize RNA translocation and strand displacement by exosome-associated helicases and adaptor complexes using fluorescence-based strand displacement assays. The design and preparation of substrates suitable for analysis of helicase and decay activities of reconstituted MTR4–exosome complexes are described. To aid structural and biophysical studies, we present strategies for engineering substrates that can stall helicases during translocation, providing a means to capture snapshots of interactions and molecular steps involved in substrate translocation and delivery to the exosome.
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18
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Moraleva AA, Deryabin AS, Rubtsov YP, Rubtsova MP, Dontsova OA. Eukaryotic Ribosome Biogenesis: The 40S Subunit. Acta Naturae 2022; 14:14-30. [PMID: 35441050 PMCID: PMC9013438 DOI: 10.32607/actanaturae.11540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/02/2022] [Indexed: 11/29/2022] Open
Abstract
The formation of eukaryotic ribosomes is a sequential process of ribosomal
precursors maturation in the nucleolus, nucleoplasm, and cytoplasm. Hundreds of
ribosomal biogenesis factors ensure the accurate processing and formation of
the ribosomal RNAs’ tertiary structure, and they interact with ribosomal
proteins. Most of what we know about the ribosome assembly has been derived
from yeast cell studies, and the mechanisms of ribosome biogenesis in
eukaryotes are considered quite conservative. Although the main stages of
ribosome biogenesis are similar across different groups of eukaryotes, this
process in humans is much more complicated owing to the larger size of the
ribosomes and pre-ribosomes and the emergence of regulatory pathways that
affect their assembly and function. Many of the factors involved in the
biogenesis of human ribosomes have been identified using genome-wide screening
based on RNA interference. This review addresses the key aspects of yeast and
human ribosome biogenesis, using the 40S subunit as an example. The mechanisms
underlying these differences are still not well understood, because, unlike
yeast, there are no effective methods for characterizing pre-ribosomal
complexes in humans. Understanding the mechanisms of human ribosome assembly
would have an incidence on a growing number of genetic diseases
(ribosomopathies) caused by mutations in the genes encoding ribosomal proteins
and ribosome biogenesis factors. In addition, there is evidence that ribosome
assembly is regulated by oncogenic signaling pathways, and that defects in the
ribosome biogenesis are linked to the activation of tumor suppressors.
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Affiliation(s)
- A. A. Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - Yu. P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. P. Rubtsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
| | - O. A. Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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19
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Li J, Yue L, Li Z, Zhang W, Zhang B, Zhao F, Dong X. aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy. eLife 2021; 10:70464. [PMID: 34964713 PMCID: PMC8716108 DOI: 10.7554/elife.70464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/16/2021] [Indexed: 01/19/2023] Open
Abstract
Recently, aCPSF1 was reported to function as the long-sought global transcription termination factor of archaea; however, the working mechanism remains elusive. This work, through analyzing transcript-3′end-sequencing data of Methanococcus maripaludis, found genome-wide positive correlations of both the terminator uridine(U)-tract and aCPSF1 with hierarchical transcription termination efficacies (TTEs). In vitro assays determined that aCPSF1 specifically binds to the terminator U-tract with U-tract number-related binding affinity, and in vivo assays demonstrated the two elements are indispensable in dictating high TTEs, revealing that aCPSF1 and the terminator U-tract cooperatively determine high TTEs. The N-terminal KH domains equip aCPSF1 with specific-binding capacity to terminator U-tract and the aCPSF1-terminator U-tract cooperation; while the nuclease activity of aCPSF1 was also required for TTEs. aCPSF1 also guarantees the terminations of transcripts with weak intrinsic terminator signals. aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota exhibited similar U-tract cooperation in dictating TTEs. Therefore, aCPSF1 and the intrinsic U-rich terminator could work in a noteworthy two-in-one termination mode in archaea, which may be widely employed by archaeal phyla; using one trans-action factor to recognize U-rich terminator signal and cleave transcript 3′-end, the archaeal aCPSF1-dependent transcription termination may represent a simplified archetypal mode of the eukaryotic RNA polymerase II termination machinery.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhihua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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20
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Petit FG, Jamin SP, Kernanec PY, Becker E, Halet G, Primig M. EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition. Dev Biol 2021; 483:58-65. [PMID: 34965385 DOI: 10.1016/j.ydbio.2021.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 11/03/2022]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 is required for gametogenesis, brain development, erythropoiesis and blood cell enhancer function. The human ortholog is essential for mitosis in cultured cancer cells. Little is known, however, about the role of Exosc10 during embryo development and organogenesis. We generated an Exosc10 knockout model and find that Exosc10-/- mice show an embryonic lethal phenotype. We demonstrate that Exosc10 maternal wild type mRNA is present in mutant oocytes and that the gene is expressed during all stages of early embryogenesis. Furthermore, we observe that EXOSC10 early on localizes to the periphery of nucleolus precursor bodies in blastomeres, which is in keeping with the protein's role in rRNA processing and may indicate a function in the establishment of chromatin domains during initial stages of embryogenesis. Finally, we infer from genotyping data for embryonic days e7.5, e6.5 and e4.5 and embryos cultured in vitro that Exosc10-/- mutants arrest at the eight-cell embryo/morula transition. Our results demonstrate a novel essential role for Exosc10 during early embryogenesis, and they are consistent with earlier work showing that impaired ribosome biogenesis causes a developmental arrest at the morula stage.
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Affiliation(s)
- Fabrice G Petit
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
| | - Soazik P Jamin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Pierre-Yves Kernanec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | | | - Guillaume Halet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
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21
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Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
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Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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22
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Hojka-Osinska A, Chlebowski A, Grochowska J, Owczarek EP, Affek K, Kłosowska-Kosicka K, Szczesny RJ, Dziembowski A. Landscape of functional interactions of human processive ribonucleases revealed by high-throughput siRNA screenings. iScience 2021; 24:103036. [PMID: 34541468 PMCID: PMC8437785 DOI: 10.1016/j.isci.2021.103036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Processive exoribonucleases are executors of RNA decay. In humans, their physical but not functional interactions were thoughtfully investigated. Here we have screened cells deficient in DIS3, XRN2, EXOSC10, DIS3L, and DIS3L2 with a custom siRNA library and determined their genetic interactions (GIs) with diverse pathways of RNA metabolism. We uncovered a complex network of positive interactions that buffer alterations in RNA degradation and reveal reciprocal cooperation with genes involved in transcription, RNA export, and splicing. Further, we evaluated the functional distinctness of nuclear DIS3 and cytoplasmic DIS3L using a library of all known genes associated with RNA metabolism. Our analysis revealed that DIS3 mutation suppresses RNA splicing deficiency, while DIS3L GIs disclose the interplay of cytoplasmic RNA degradation with nuclear RNA processing. Finally, genome-wide DIS3 GI map uncovered relations with genes not directly involved in RNA metabolism, like microtubule organization or regulation of telomerase activity.
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Affiliation(s)
- Anna Hojka-Osinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewelina P. Owczarek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kamila Affek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Roman J. Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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23
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Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H. Structural characterization of NrnC identifies unifying features of dinucleotidases. eLife 2021; 10:70146. [PMID: 34533457 PMCID: PMC8492067 DOI: 10.7554/elife.70146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonuclease, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleases from other exonucleases, the key determinants for dinuclease activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinuclease activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinuclease activity further underlines the important role these analogous proteins play for cell growth.
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Affiliation(s)
- Justin D Lormand
- Department of Molecular Medicine, Cornell University, Ithaca, United States
| | - Soo-Kyoung Kim
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | | | - Bryce A Brownfield
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Jonathan R Goodson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Vincent T Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Holger Sondermann
- Department of Molecular Medicine, Cornell University, Ithaca, United States.,CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Christian-Albrechts-Universität, Kiel, Germany
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24
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Sterrett MC, Enyenihi L, Leung SW, Hess L, Strassler SE, Farchi D, Lee RS, Withers ES, Kremsky I, Baker RE, Basrai MA, van Hoof A, Fasken MB, Corbett AH. A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex. RNA (NEW YORK, N.Y.) 2021; 27:1046-1067. [PMID: 34162742 PMCID: PMC8370739 DOI: 10.1261/rna.078618.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
RNA exosomopathies, a growing family of diseases, are linked to missense mutations in genes encoding structural subunits of the evolutionarily conserved, 10-subunit exoribonuclease complex, the RNA exosome. This complex consists of a three-subunit cap, a six-subunit, barrel-shaped core, and a catalytic base subunit. While a number of mutations in RNA exosome genes cause pontocerebellar hypoplasia, mutations in the cap subunit gene EXOSC2 cause an apparently distinct clinical presentation that has been defined as a novel syndrome SHRF (short stature, hearing loss, retinitis pigmentosa, and distinctive facies). We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by modeling pathogenic EXOSC2 missense mutations (p.Gly30Val and p.Gly198Asp) in the orthologous S. cerevisiae gene RRP4 The resulting rrp4 mutant cells show defects in cell growth and RNA exosome function. Consistent with altered RNA exosome function, we detect significant transcriptomic changes in both coding and noncoding RNAs in rrp4-G226D cells that model EXOSC2 p.Gly198Asp, suggesting defects in nuclear surveillance. Biochemical and genetic analyses suggest that the Rrp4 G226D variant subunit shows impaired interactions with key RNA exosome cofactors that modulate the function of the complex. These results provide the first in vivo evidence that pathogenic missense mutations present in EXOSC2 impair the function of the RNA exosome. This study also sets the stage to compare exosomopathy models to understand how defects in RNA exosome function underlie distinct pathologies.
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Affiliation(s)
- Maria C Sterrett
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Laurie Hess
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Richard S Lee
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Elise S Withers
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Isaac Kremsky
- Loma Linda University School of Medicine, Loma Linda, California 92350, USA
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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25
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Liu Q, Xiao Q, Sun Z, Wang B, Wang L, Wang N, Wang K, Song C, Yang Q. Exosome component 1 cleaves single-stranded DNA and sensitizes human kidney renal clear cell carcinoma cells to poly(ADP-ribose) polymerase inhibitor. eLife 2021; 10:e69454. [PMID: 34159897 PMCID: PMC8260222 DOI: 10.7554/elife.69454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Targeting DNA repair pathway offers an important therapeutic strategy for Homo sapiens (human) cancers. However, the failure of DNA repair inhibitors to markedly benefit patients necessitates the development of new strategies. Here, we show that exosome component 1 (EXOSC1) promotes DNA damages and sensitizes human kidney renal clear cell carcinoma (KIRC) cells to DNA repair inhibitor. Considering that endogenous source of mutation (ESM) constantly assaults genomic DNA and likely sensitizes human cancer cells to the inhibitor, we first analyzed the statistical relationship between the expression of individual genes and the mutations for KIRC. Among the candidates, EXOSC1 most notably promoted DNA damages and subsequent mutations via preferentially cleaving C site(s) in single-stranded DNA. Consistently, EXOSC1 was more significantly correlated with C>A transversions in coding strands than these in template strands in human KIRC. Notably, KIRC patients with high EXOSC1 showed a poor prognosis, and EXOSC1 sensitized human cancer cells to poly(ADP-ribose) polymerase inhibitors. These results show that EXOSC1 acts as an ESM in KIRC, and targeting EXOSC1 might be a potential therapeutic strategy.
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Affiliation(s)
- Qiaoling Liu
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Qi Xiao
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Zhen Sun
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Bo Wang
- Department of General Surgery, Second Affiliated Hospital, DaLian Medical UniversityDalianChina
| | - Lina Wang
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Na Wang
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Kai Wang
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Chengli Song
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
| | - Qingkai Yang
- Institute of Cancer Stem Cell, DaLian Medical UniversityDalianChina
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26
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Mehta C, Fraga de Andrade I, Matson DR, Dewey CN, Bresnick EH. RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis. Nucleic Acids Res 2021; 49:9007-9025. [PMID: 34059908 PMCID: PMC8450083 DOI: 10.1093/nar/gkab367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 05/27/2021] [Indexed: 01/03/2023] Open
Abstract
Cellular differentiation requires vast remodeling of transcriptomes, and therefore machinery mediating remodeling controls differentiation. Relative to transcriptional mechanisms governing differentiation, post-transcriptional processes are less well understood. As an important post-transcriptional determinant of transcriptomes, the RNA exosome complex (EC) mediates processing and/or degradation of select RNAs. During erythropoiesis, the erythroid transcription factor GATA1 represses EC subunit genes. Depleting EC structural subunits prior to GATA1-mediated repression is deleterious to erythroid progenitor cells. To assess the importance of the EC catalytic subunits Dis3 and Exosc10 in this dynamic process, we asked if these subunits function non-redundantly to control erythropoiesis. Dis3 or Exosc10 depletion in primary murine hematopoietic progenitor cells reduced erythroid progenitors and their progeny, while sparing myeloid cells. Dis3 loss severely compromised erythroid progenitor and erythroblast survival, rendered erythroblasts hypersensitive to apoptosis-inducing stimuli and induced γ-H2AX, indicative of DNA double-stranded breaks. Dis3 loss-of-function phenotypes were more severe than those caused by Exosc10 depletion. We innovated a genetic rescue system to compare human Dis3 with multiple myeloma-associated Dis3 mutants S447R and R750K, and only wild type Dis3 was competent to rescue progenitors. Thus, Dis3 establishes a disease mutation-sensitive, cell type-specific survival mechanism to enable a differentiation program.
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Affiliation(s)
- Charu Mehta
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Isabela Fraga de Andrade
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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27
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Li J, Liu X, Yin Z, Hu Z, Zhang KQ. An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi. Front Microbiol 2021; 12:638617. [PMID: 33995298 PMCID: PMC8113380 DOI: 10.3389/fmicb.2021.638617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
For decades, more and more long non-coding RNAs (lncRNAs) have been confirmed to play important functions in key biological processes of different organisms. At present, most identified lncRNAs and those with known functional roles are from mammalian systems. However, lncRNAs have also been found in primitive eukaryotic fungi, and they have different functions in fungal development, metabolism, and pathogenicity. In this review, we highlight some recent researches on lncRNAs in the primitive eukaryotic fungi, particularly focusing on the identification of lncRNAs and their regulatory roles in diverse biological processes.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiaoying Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ziyu Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhihong Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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28
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Das M, Zattas D, Zinder JC, Wasmuth EV, Henri J, Lima CD. Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome. Proc Natl Acad Sci U S A 2021; 118:e2024846118. [PMID: 33782132 PMCID: PMC8040639 DOI: 10.1073/pnas.2024846118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quality control requires discrimination between functional and aberrant species to selectively target aberrant substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation followed by helicase-dependent 3' to 5' degradation by the RNA exosome. Using reconstitution biochemistry, we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to protect stable RNA from degradation while selectively targeting and degrading less stable RNA. Substrate discrimination is lost when the distributive exoribonuclease activity of Rrp6 is inactivated, leading to degradation of stable and unstable RNA species. These data support a proofreading mechanism in which deadenylation by Rrp6 competes with Mtr4-dependent degradation to protect stable RNA while selectively targeting and degrading unstable RNA.
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Affiliation(s)
- Mom Das
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Dimitrios Zattas
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - John C Zinder
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elizabeth V Wasmuth
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Julien Henri
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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29
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Yan H, Li Y, Cheng S, Zeng Y. Advances in Analytical Technologies for Extracellular Vesicles. Anal Chem 2021; 93:4739-4774. [PMID: 33635060 DOI: 10.1021/acs.analchem.1c00693] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yutao Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shibo Cheng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
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30
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Gong L, Weng Y, Zhou W, Zhang K, Li W, Jiang J, Zhu J. In vivo CT imaging of gold nanoparticle-labeled exosomes in a myocardial infarction mouse model. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:504. [PMID: 33850901 PMCID: PMC8039714 DOI: 10.21037/atm-21-981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Acute myocardial infarction (MI) is the primary factor leading to cardiovascular diseases, which are the main causes of morbidity and mortality in developed countries. Mesenchymal stem cell (MSC)-derived exosomes have been reported to improve heart function after MI; however, the molecular mechanisms responsible for this are unknown. In vivo imaging can reveal the trafficking process and in vivo biodistribution of exosomes, which may provide an insight into the communication mechanisms and pharmacokinetics of exosomes. Methods Glucose modified gold nanoparticles were used to label MSC-derived exosomes, aimed at minimizing membrane damage and maintaining the integrity of the exosomes. After labeling, the exosomes were visualized by in vivo computed tomography (CT) imaging to determine the biodistribution at 4 and 24 h after injection into a MI mouse model. Results MSC-derived exosomes were successfully labeled by glucose modified gold nanoparticles and CT imaging of these labeled exosomes indicated that MSC-Exo remained in the MI area for up to 24 h after intramyocardial injection. Additionally, few MSC-Exo were observed in some other organs, particularly the liver, spleen, and kidney. Conclusions A gentle method was used for loading GNPs into exosomes, and their successful labeling without causing aggregation was verified. In vivo CT imaging revealed the retention of MSC-Exo in the MI area, indicating their usefulness for improving heart function after infarction.
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Affiliation(s)
- Lianggeng Gong
- Department of Radiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yingying Weng
- Department of Radiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Zhou
- Department of Radiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kunchi Zhang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Wei Li
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Jia Jiang
- Department of Sports Medicine, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jun Zhu
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, China
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31
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Novačić A, Beauvais V, Oskomić M, Štrbac L, Dantec AL, Rahmouni AR, Stuparević I. Yeast RNA exosome activity is necessary for maintaining cell wall stability through proper protein glycosylation. Mol Biol Cell 2021; 32:363-375. [PMID: 33439673 PMCID: PMC8098854 DOI: 10.1091/mbc.e20-08-0544-t] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/25/2020] [Accepted: 01/06/2021] [Indexed: 12/01/2022] Open
Abstract
Nuclear RNA exosome is the main 3'→5' RNA degradation and processing complex in eukaryotic cells and its dysregulation therefore impacts gene expression and viability. In this work we show that RNA exosome activity is necessary for maintaining cell wall stability in yeast Saccharomyces cerevisiae. While the essential RNA exosome catalytic subunit Dis3 provides exoribonuclease catalytic activity, the second catalytic subunit Rrp6 has a noncatalytic role in this process. RNA exosome cofactors Rrp47 and Air1/2 are also involved. RNA exosome mutants undergo osmoremedial cell lysis at high temperature or at physiological temperature upon treatment with cell wall stressors. Finally, we show that a defect in protein glycosylation is a major reason for cell wall instability of RNA exosome mutants. Genes encoding enzymes that act in the early steps of the protein glycosylation pathway are down-regulated at high temperature in cells lacking Rrp6 protein or Dis3 exoribonuclease activity and overexpression of the essential enzyme Psa1, that catalyzes synthesis of the mannosylation precursor, suppresses temperature sensitivity and aberrant morphology of these cells. Furthermore, this defect is connected to a temperature-dependent increase in accumulation of noncoding RNAs transcribed from loci of relevant glycosylation-related genes.
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Affiliation(s)
- Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Valentin Beauvais
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| | - Marina Oskomić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Lucija Štrbac
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Aurélia Le Dantec
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| | - A. Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| | - Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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32
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Stuparević I, Novačić A, Rahmouni AR, Fernandez A, Lamb N, Primig M. Regulation of the conserved 3'-5' exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev Camb Philos Soc 2021; 96:1092-1113. [PMID: 33599082 DOI: 10.1111/brv.12693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 processes and degrades RNA, regulates gene expression and participates in DNA double-strand break repair and control of telomere maintenance via degradation of the telomerase RNA component. EXOSC10/Rrp6 is part of the multimeric nuclear RNA exosome and interacts with numerous proteins. Previous clinical, genetic, biochemical and genomic studies revealed the protein's essential functions in cell division and differentiation, its RNA substrates and its relevance to autoimmune disorders and oncology. However, little is known about the regulatory mechanisms that control the transcription, translation and stability of EXOSC10/Rrp6 during cell growth, development and disease and how these mechanisms evolved from yeast to human. Herein, we provide an overview of the RNA- and protein expression profiles of EXOSC10/Rrp6 during cell division, development and nutritional stress, and we summarize interaction networks and post-translational modifications across species. Additionally, we discuss how known and predicted protein interactions and post-translational modifications influence the stability of EXOSC10/Rrp6. Finally, we explore the idea that different EXOSC10/Rrp6 alleles, which potentially alter cellular protein levels or affect protein function, might influence human development and disease progression. In this review we interpret information from the literature together with genomic data from knowledgebases to inspire future work on the regulation of this essential protein's stability in normal and malignant cells.
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Affiliation(s)
- Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR4301 du CNRS, Orléans, 45071, France
| | - Anne Fernandez
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Ned Lamb
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, 35000, France
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33
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Gao Y, Liu H, Zhang C, Su S, Chen Y, Chen X, Li Y, Shao Z, Zhang Y, Shao Q, Li J, Huang Z, Ma J, Gan J. Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei. Nucleic Acids Res 2021; 49:568-583. [PMID: 33332555 PMCID: PMC7797062 DOI: 10.1093/nar/gkaa1197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Infection with kinetoplastid parasites, including Trypanosoma brucei (T. brucei), Trypanosoma cruzi (T. cruzi) and Leishmania can cause serious disease in humans. Like other kinetoplastid species, mRNAs of these disease-causing parasites must undergo posttranscriptional editing in order to be functional. mRNA editing is directed by gRNAs, a large group of small RNAs. Similar to mRNAs, gRNAs are also precisely regulated. In T. brucei, overexpression of RNase D ribonuclease (TbRND) leads to substantial reduction in the total gRNA population and subsequent inhibition of mRNA editing. However, the mechanisms regulating gRNA binding and cleavage by TbRND are not well defined. Here, we report a thorough structural study of TbRND. Besides Apo- and NMP-bound structures, we also solved one TbRND structure in complexed with single-stranded RNA. In combination with mutagenesis and in vitro cleavage assays, our structures indicated that TbRND follows the conserved two-cation-assisted mechanism in catalysis. TbRND is a unique RND member, as it contains a ZFD domain at its C-terminus. In addition to T. brucei, our studies also advanced our understanding on the potential gRNA degradation pathway in T. cruzi, Leishmania, as well for as other disease-associated parasites expressing ZFD-containing RNDs.
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Affiliation(s)
- Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chong Zhang
- College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiqing Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xi Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yangyang Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jixi Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen Huang
- College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction. Science 2021; 371:science.abe6523. [PMID: 33414189 DOI: 10.1126/science.abe6523] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Polyadenylate [poly(A)] tail addition to the 3' end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A crystal structure of a double ENE from a rice hAT transposon messenger RNA complexed with poly(A)28 at a resolution of 2.89 angstroms reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3'-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA's extreme 3' end.
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Affiliation(s)
- Seyed-Fakhreddin Torabi
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Anand T Vaidya
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.,TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA. .,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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35
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Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
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Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
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36
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Weick EM, Lima CD. RNA helicases are hubs that orchestrate exosome-dependent 3'-5' decay. Curr Opin Struct Biol 2020; 67:86-94. [PMID: 33147539 DOI: 10.1016/j.sbi.2020.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 01/10/2023]
Abstract
The RNA exosome is a conserved complex of proteins that mediates 3'-5' RNA processing and decay. Its functions range from processing of non-coding RNAs such as ribosomal RNAs and decay of aberrant transcripts in the nucleus to cytoplasmic mRNA turnover and quality control. Ski2-like RNA helicases translocate substrates to exosome-associated ribonucleases and interact with the RNA exosome either directly or as part of multi-subunit helicase-containing complexes that identify and target RNA substrates for decay. Recent structures of these helicases with their RNA-binding partners or the RNA exosome have advanced our understanding of a system of modular and mutually exclusive contacts between the exosome and exosome-associated helicase complexes that shape the transcriptome by orchestrating exosome-dependent 3'-5' decay.
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Affiliation(s)
- Eva-Maria Weick
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.
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37
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Hassanpour M, Rezaie J, Nouri M, Panahi Y. The role of extracellular vesicles in COVID-19 virus infection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104422. [PMID: 32544615 PMCID: PMC7293471 DOI: 10.1016/j.meegid.2020.104422] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles releasing from various types of cells contribute to intercellular communication via delivering bio-molecules like nucleic acids, proteins, and lipids to recipient cells. Exosomes are 30-120 nm extracellular vesicles that participate in several pathological conditions. Virus-infected cells release exosomes that are implicated in infection through transferring viral components such as viral-derived miRNAs and proteins. As well, exosomes contain receptors for viruses that make recipient cells susceptible to virus entry. Since December 2019, SARS-CoV-2 (COVID-19) infection has become a worldwide urgent public health concern. There is currently no vaccine or specific antiviral treatment existing for COVID-19 virus infection. Hence, it is critical to find a safe and effective therapeutic tool to patients with severe COVID-19 virus infection. Extracellular vesicles may contribute to spread this virus as they transfer such receptors as CD9 and ACE2, which make recipient cells susceptible to virus docking. Upon entry, COVID-19 virus may be directed into the exosomal pathway, and its component is packaged into exosomes for secretion. Exosome-based strategies for the treatment of COVID-19 virus infection may include following items: inhibition of exosome biogenesis and uptake, exosome-therapy, exosome-based drug delivery system, and exosome-based vaccine. Mesenchymal stem cells can suppress nonproductive inflammation and improve/repair lung cells including endothelial and alveolar cells, which damaged by COVID-19 virus infection. Understanding molecular mechanisms behind extracellular vesicles related COVID-19 virus infection may provide us with an avenue to identify its entry, replication, spreading, and infection to overcome its adverse effects.
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Affiliation(s)
- Mehdi Hassanpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Clinical Biochemistry, Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran,Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Rezaie
- Solid Tumor Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran,Correspondence to: J. Rezaie, Solid Tumor Research Center, Research Institute on Cellular and Molecular Medicine, Urmia University of Medical Sciences, Shafa St, Ershad Blvd., P.O. BoX: 1138, 57147 Urmia, Iran
| | - Mohammad Nouri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Clinical Biochemistry, Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran,Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yunes Panahi
- Pharmacy Department, Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran,Correspondence to: Y. Panahi, Clinical Pharmacy Department, Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran 1435916471, Iran
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38
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Kawabe Y, Mori K, Yamashita T, Gotoh S, Ikeda M. The RNA exosome complex degrades expanded hexanucleotide repeat RNA in C9orf72 FTLD/ALS. EMBO J 2020; 39:e102700. [PMID: 32830871 PMCID: PMC7527818 DOI: 10.15252/embj.2019102700] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Nucleotide repeat expansions in the C9orf72 gene cause frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Transcribed repeat RNA accumulates within RNA foci and is also translated into toxic dipeptide repeat proteins (DPR). The mechanism of repeat RNA accumulation, however, remains unclear. The RNA exosome complex is a multimeric ribonuclease involved in degradation of defective RNA. Here, we uncover the RNA exosome as a major degradation complex for pathogenic C9orf72‐derived repeat RNA. Knockdown of EXOSC10, the catalytic subunit of the complex, enhanced repeat RNA and DPR protein expression levels. RNA degradation assays confirmed that EXOSC10 can degrade both sense and antisense repeats. Furthermore, EXOSC10 reduction increased RNA foci and repeat transcripts in patient‐derived cells. Cells expressing toxic poly‐GR or poly‐PR proteins accumulate a subset of small nucleolar RNA precursors, which are physiological substrates of EXOSC10, as well as excessive repeat RNA, indicating that arginine‐rich DPR proteins impair the intrinsic activity of EXOSC10. Collectively, arginine‐rich DPR‐mediated impairment of EXOSC10 and the RNA exosome complex compromises repeat RNA metabolism and may thus exacerbate C9orf72‐FTLD/ALS pathologies in a vicious cycle.
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Affiliation(s)
- Yuya Kawabe
- Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kohji Mori
- Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tomoko Yamashita
- Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shiho Gotoh
- Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Manabu Ikeda
- Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
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39
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Green ID, Pinello N, Song R, Lee Q, Halstead JM, Kwok CT, Wong ACH, Nair SS, Clark SJ, Roediger B, Schmitz U, Larance M, Hayashi R, Rasko JEJ, Wong JJL. Macrophage development and activation involve coordinated intron retention in key inflammatory regulators. Nucleic Acids Res 2020; 48:6513-6529. [PMID: 32449925 PMCID: PMC7337907 DOI: 10.1093/nar/gkaa435] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/04/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response.
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Affiliation(s)
- Immanuel D Green
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Chau-To Kwok
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst 2010, Australia.,St. Vincent's Clinical School, UNSW, Sydney 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst 2010, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst 2010, Australia.,St. Vincent's Clinical School, UNSW, Sydney 2010, Australia
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Ulf Schmitz
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Mark Larance
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown 2006, New South Wales, Australia
| | - Rippei Hayashi
- The John Curtin School of Medical Research, The Australian National University, ACT 2601, Australia
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
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40
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Wermuth PJ, Jimenez SA. Molecular characteristics and functional differences of anti-PM/Scl autoantibodies and two other distinct and unique supramolecular structures known as "EXOSOMES". Autoimmun Rev 2020; 19:102644. [PMID: 32801042 DOI: 10.1016/j.autrev.2020.102644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
The term "exosome" has been applied to three distinct supramolecular entities, namely the PM/Scl autoantibodies or "RNA exosomes", transforming DNA fragments termed "DNA exosomes", and small size extracellular vesicles knows as "exosomes". Some of the molecular components of the "PM/Scl exosome complex" or "RNA exosome" are recognized by specific autoantibodies present in the serum from some Systemic Sclerosis (SSc), polymyositis (PM) and polymyositis SSc (PM/Scl) overlap syndrome patients. On the other hand, one of the most active focuses of laboratory investigation in the last decade has been the biogenesis and role of extracellular vesicles known as "exosomes". The remarkable ability of these "exosome" vesicles to alter the cellular phenotype following fusion with target cells and the release of their macromolecular cargo has revealed a possible role in the pathogenesis of numerous diseases, including malignant, inflammatory, and autoimmune disorders and may allow them to serve as theranostic agents for personalized and precision medicine. The indiscriminate use of the term "exosome" to refer to these three distinct molecular entities has engendered great confusion in the scientific literature. Here, we review the molecular characteristics and functional differences between the three molecular structures identified as "exosomes". Given the rapidly growing scientific interest in extravesicular exosomes, unless a solution is found the confusion in the literature resulting from the use of the term "exosomes" will markedly increase.
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Affiliation(s)
- Peter J Wermuth
- Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Sergio A Jimenez
- Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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41
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EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells. Sci Rep 2020; 10:9275. [PMID: 32518284 PMCID: PMC7283315 DOI: 10.1038/s41598-020-66455-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/21/2020] [Indexed: 01/16/2023] Open
Abstract
Cancer cells adapt to various stress conditions by optimizing gene expression profiles via transcriptional and translational regulation. However, whether and how EXOSC9, a component of the RNA exosome complex, regulates adaptation to stress conditions and tumorigenicity in cancer cells remain unclear. Here, we examined the effects of EXOSC9 depletion on cancer cell growth under various stress conditions. EXOSC9 depletion attenuated growth and survival under various stress conditions in cancer cells. Interestingly, this also decreased the number of P-bodies, which are messenger ribonucleoprotein particles (mRNPs) required for stress adaptation. Meanwhile, EXOSC2/EXOSC4 depletion also attenuated P-body formation and stress resistance with decreased EXOSC9 protein. EXOSC9-mediated stress resistance and P-body formation were found to depend on the intact RNA-binding motif of this protein. Further, RNA-seq analyses identified 343 EXOSC9-target genes, among which, APOBEC3G contributed to defects in stress resistance and P-body formation in MDA-MB-231 cells. Finally, EXOSC9 also promoted xenografted tumor growth of MDA-MB-231 cells in an intact RNA-binding motif-dependent manner. Database analyses further showed that higher EXOSC9 activity, estimated based on the expression of 343 target genes, was correlated with poorer prognosis in some cancer patients. Thus, drugs targeting activity of the RNA exosome complex or EXOSC9 might be useful for cancer treatment.
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42
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Davidson L, Francis L, Cordiner RA, Eaton JD, Estell C, Macias S, Cáceres JF, West S. Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control. Cell Rep 2020; 26:2779-2791.e5. [PMID: 30840897 PMCID: PMC6403362 DOI: 10.1016/j.celrep.2019.02.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/09/2019] [Accepted: 02/04/2019] [Indexed: 12/26/2022] Open
Abstract
Cell-based studies of human ribonucleases traditionally rely on methods that deplete proteins slowly. We engineered cells in which the 3′→5′ exoribonucleases of the exosome complex, DIS3 and EXOSC10, can be rapidly eliminated to assess their immediate roles in nuclear RNA biology. The loss of DIS3 has the greatest impact, causing the substantial accumulation of thousands of transcripts within 60 min. These transcripts include enhancer RNAs, promoter upstream transcripts (PROMPTs), and products of premature cleavage and polyadenylation (PCPA). These transcripts are unaffected by the rapid loss of EXOSC10, suggesting that they are rarely targeted to it. More direct detection of EXOSC10-bound transcripts revealed its substrates to prominently include short 3′ extended ribosomal and small nucleolar RNAs. Finally, the 5′→3′ exoribonuclease, XRN2, has little activity on exosome substrates, but its elimination uncovers different mechanisms for the early termination of transcription from protein-coding gene promoters. Engineered human cells for rapid inducible degradation of EXOSC10 and DIS3 DIS3 degrades the majority of nuclear exosome substrates Direct targets of EXOSC10 include ribosomal and small nucleolar RNAs XRN2 has little activity on exosome substrates
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Affiliation(s)
- Lee Davidson
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Laura Francis
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Ross A Cordiner
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Joshua D Eaton
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Chris Estell
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Steven West
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK.
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43
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Lingaraju M, Schuller JM, Falk S, Gerlach P, Bonneau F, Basquin J, Benda C, Conti E. To Process or to Decay: A Mechanistic View of the Nuclear RNA Exosome. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:155-163. [PMID: 32493762 DOI: 10.1101/sqb.2019.84.040295] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The RNA exosome was originally discovered in yeast as an RNA-processing complex required for the maturation of 5.8S ribosomal RNA (rRNA), one of the constituents of the large ribosomal subunit. The exosome is now known in eukaryotes as the major 3'-5' RNA degradation machine involved in numerous processing, turnover, and surveillance pathways, both in the nucleus and the cytoplasm. Yet its role in maturing the 5.8S rRNA in the pre-60S ribosomal particle remains probably the most intricate and emblematic among its functions, as it involves all the RNA unwinding, degradation, and trimming activities embedded in this macromolecular complex. Here, we propose a comprehensive mechanistic model, based on current biochemical and structural data, explaining the dual functions of the nuclear exosome-the constructive versus the destructive mode.
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Affiliation(s)
- Mahesh Lingaraju
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Jan M Schuller
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Sebastian Falk
- Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, 1030, Vienna, Austria
| | - Piotr Gerlach
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Fabien Bonneau
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Jérôme Basquin
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Christian Benda
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Elena Conti
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
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44
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Abstract
Malaria remains a major public health and economic burden. The heterochromatin environment controls the silencing of genes associated with the fate of malaria parasites. Previous studies have demonstrated that a group of GC-rich ncRNAs (RUF6) is associated with the mutually exclusive expression of var genes, but the underlying mechanisms remain elusive. Here, through a series of genetic manipulation and genome-wide multiomics analysis, we have identified the plasmodial orthologue of RNA exosome-associated Rrp6 as an upstream regulator of RUF6 expression and revealed that the dysregulation of RUF6 upon Rrp6 knockdown triggered local chromatin alteration, thereby activating most heterochromatic genes via direct interaction of RUF6 and distal gene loci. This finding not only uncovered the in-depth mechanism of RUF6-mediated regulation of heterochromatic genes but also identified Rrp6 as a novel regulator of gene expression in human malaria parasites, which provides a new target for developing intervention strategies against malaria. The heterochromatin environment plays a central role in silencing genes associated with the malaria parasite’s development, survival in the host, and transmission to the mosquito vector. However, the underlying mechanism regulating the dynamic chromatin structure is not understood yet. Here, we have uncovered that Plasmodium falciparum Rrp6, an orthologue of eukaryotic RNA exosome-associated RNase, controls the silencing of heterochromatic genes. PfRrp6 knockdown disrupted the singular expression of the GC-rich ncRNA RUF6 family, a known critical regulator of virulence gene expression, through the stabilization of the nascent transcripts. Mechanistic investigation showed that the accumulation of the multiple RUF6 ncRNAs triggered local chromatin remodeling in situ, which activated their adjacent var genes. Strikingly, chromatin isolation by RNA purification analysis (ChIRP-seq) revealed that a remarkable RUF6 ncRNA had interacted with distal heterochromatin regions directly and stimulated a global derepression effect on heterochromatic genes, including all variant gene families and the sexual commitment-associated regulator ap2-g gene. Collectively, Rrp6 appears to conduct the epigenetic surveillance of heterochromatic gene expression through controlling RUF6 levels, thereby securing antigenic variation and sexual commitment of malaria parasites during the infection of the host.
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Zhang B, Zhao N, Jia L, Che J, He X, Liu K, Bao B. Identification and application of piwi-interacting RNAs from seminal plasma exosomes in Cynoglossus semilaevis. BMC Genomics 2020; 21:302. [PMID: 32293248 PMCID: PMC7158113 DOI: 10.1186/s12864-020-6660-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 03/09/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs) have been linked to epigenetic and post-transcriptional gene silencing of retrotransposons in germ line cells, particularly in spermatogenesis. Exosomes are important mediators of vesicle transport, and the piRNAs in exosomes might play an important role in cell communication and signal pathway regulation. Moreover, exosomic piRNAs are promising biomarkers for disease diagnosis and physiological status indication. We used Cynoglossus semilaevis because of its commercial value and its sexual dimorphism, particularly the sex reversed "pseudomales" who have a female karyotype, produce sperm, and copulate with normal females to produce viable offspring. RESULTS To determine whether piRNAs from fish germ line cells have similar features, seminal plasma exosomes from half-smooth tongue sole, C. semilaevis, were identified, and their small RNAs were sequenced and analysed. We identified six signature piRNAs as biomarkers in exosomes of seminal plasma from males and pseudomale C. semilaevis. Bioinformatic analysis showed that all six signatures were sex-related, and four were DNA methylation-related and transposition-related piRNAs. Their expression profiles were verified using real-time quantitative PCR. The expression of the signature piRNAs was markedly higher in males than in pseudomales. The signature piRNAs could be exploited as male-specific biomarkers in this fish. CONCLUSIONS These signatures provide an effective tool to explore the regulatory mechanism of sex development in C. semilaevis and may provide guidance for future research on the function of piRNAs in the generative mechanism of sex reversed "pseudomales" in C. semilaevis.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.,Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Medicine Biotechnology Co, Ltd, Tianjin, China
| | - Lei Jia
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Jinyuan Che
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoxu He
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Li C, Guo F, Wang X, Liu D, Wu B, Wang F, Chen W. Exosome-based targeted RNA delivery for immune tolerance induction in skin transplantation. J Biomed Mater Res A 2020; 108:1493-1500. [PMID: 32170897 DOI: 10.1002/jbm.a.36919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
Abstract
Exosomes have been widely applied to the delivery of RNA and small molecules currently. However, the low targeting and specificity greatly limited the effect of exosome delivery. Here we designed an exosome that can perform the targeted delivery of two different types of RNA. Based on the mesenchymal stem cells (MSCs) derived exosomes, the RNA delivery system of targeted dendritic cells (DC-Exosome) was constructed, using the layer by layer self-assembly. DC-Exosomes can specifically bind to DCs, while guiding the endocytosis of chimeras and exosome. Then aptamer/siRNA chimera was cut into mTOR siRNA by Dicer, and microRNA was released from exosome under lysosomal digestion. SIGN aptamer performed the rapid induction of immune tolerance, and later mTOR siRNA was formed to inhibit mTOR pathway and suppress immune responses. Exosomes could maintain long time-stability after PEG-PEI polyplexes modification and promote HLA-G expression in DCs continuously. Animal experiments showed that DC-Exosomes could induce immune tolerance at 3, 7, and 14 days after skin transplantation. Compared with the microRNA-Exosome group, the number of CD11c+ DCs in DC-Exosome group decreased, while the proportion of HLA-G+ DCs increased remarkably. In conclusion, we constructed a new exosome-based targeted delivery system which could effectively induce the immune tolerance in transplantation.
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Affiliation(s)
- Chunmin Li
- Department of Vascular Surgery, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Fengjie Guo
- Department of Pathology, The 8th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xueli Wang
- Department of Pathology, The 8th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Dongxu Liu
- Department of Pathology, The 8th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bolun Wu
- Department of Pathology, The 8th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fenghua Wang
- Department of Pathology, The 8th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Wen Chen
- Department of Pathology, The 8th Medical Center of Chinese PLA General Hospital, Beijing, China
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Abstract
We describe procedures to clone, express, and reconstitute an active human nuclear RNA exosome. Individual recombinant subunits are expressed from E. coli and successfully reconstituted into the nuclear complex, which contains the noncatalytic nine-subunit exosome core, the endoribonuclease and exoribonuclease DIS3, the distributive exoribonuclease EXOSC10, the cofactors C1D and MPP6, and the RNA helicase MTR4.
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Affiliation(s)
- Kurt Januszyk
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eva-Maria Weick
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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Abstract
The RNA exosome is a ribonucleolytic multiprotein complex that is conserved and essential in all eukaryotes. Although we tend to speak of "the" exosome complex, it should be more correctly viewed as several different subtypes that share a common core. Subtypes of the exosome complex are present in the cytoplasm, the nucleus and the nucleolus of all eukaryotic cells, and carry out the 3'-5' processing and/or degradation of a wide range of RNA substrates.Because the substrate specificity of the exosome complex is determined by cofactors, the system is highly adaptable, and different organisms have adjusted the machinery to their specific needs. Here, we present an overview of exosome complexes and their cofactors that have been described in different eukaryotes.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany.
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49
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Zinder JC, Lima CD. Reconstitution of S. cerevisiae RNA Exosome Complexes Using Recombinantly Expressed Proteins. Methods Mol Biol 2020; 2062:427-448. [PMID: 31768989 PMCID: PMC8596991 DOI: 10.1007/978-1-4939-9822-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
3' to 5' RNA degradation is primarily catalyzed by the RNA exosome subunits Dis3 and Rrp6 in the nucleus of Saccharomyces cerevisiae. These enzymes form a complex with the nine-subunit noncatalytic core (Exo9) to carry out their functions in vivo. Protein cofactors Rrp47, Mpp6, and the Mtr4 RNA helicase also assist the complex by modulating its activities and/or recruiting it to specific RNAs for processing or degradation. Here we present our preferred strategy for reconstituting RNA exosomes from S. cerevisiae using purified, recombinantly expressed components.
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Affiliation(s)
- John C Zinder
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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Weick EM, Zinder JC, Lima CD. Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts. Methods Mol Biol 2020; 2062:417-425. [PMID: 31768988 PMCID: PMC8565498 DOI: 10.1007/978-1-4939-9822-7_20] [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: 10/18/2023]
Abstract
The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA degradation and processing events. While much of our current understanding of RNA exosome function has been elucidated using genetics and cell biology based studies of protein functions, in particular in S. cerevisiae, many important contributions in the field have been enabled through use of in vitro reconstituted complexes. Here, we present an overview of our approach to purify exosome components from recombinant sources and reconstitute them into functional complexes. Three chapters following this overview provide detailed protocols for reconstituting exosome complexes from S. cerevisiae, S. pombe, and H. sapiens. We additionally provide insight on some of the drawbacks of these methods and highlight several important discoveries that have been achieved using reconstituted complexes.
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Affiliation(s)
- Eva-Maria Weick
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John C Zinder
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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