1
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Huntzinger E, Sinteff J, Morlet B, Séraphin B. HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon. Nucleic Acids Res 2023; 51:9279-9293. [PMID: 37602378 PMCID: PMC10516660 DOI: 10.1093/nar/gkad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
Proteins containing a RNB domain, originally identified in Escherichia coli RNase II, are widely present throughout the tree of life. Many RNB proteins have 3'-5' exoribonucleolytic activity but some have lost catalytic activity during evolution. Database searches identified a new RNB domain-containing protein in human: HELZ2. Analysis of genomic and expression data combined with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 RNase activity is lost in cells from some cancer patients as a result of somatic mutations. HELZ2 harbors also two RNA helicase domains and several zinc fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3'-5' ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.
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Affiliation(s)
- Eric Huntzinger
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Jordan Sinteff
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
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2
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García-Moreno JF, Lacerda R, da Costa PJ, Pereira M, Gama-Carvalho M, Matos P, Romão L. DIS3L2 knockdown impairs key oncogenic properties of colorectal cancer cells via the mTOR signaling pathway. Cell Mol Life Sci 2023; 80:185. [PMID: 37340282 DOI: 10.1007/s00018-023-04833-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
DIS3L2 degrades different types of RNAs in an exosome-independent manner including mRNAs and several types of non-coding RNAs. DIS3L2-mediated degradation is preceded by the addition of nontemplated uridines at the 3'end of its targets by the terminal uridylyl transferases 4 and 7. Most of the literature that concerns DIS3L2 characterizes its involvement in several RNA degradation pathways, however, there is some evidence that its dysregulated activity may contribute to cancer development. In the present study, we characterize the role of DIS3L2 in human colorectal cancer (CRC). Using the public RNA datasets from The Cancer Genome Atlas (TCGA), we found higher DIS3L2 mRNA levels in CRC tissues versus normal colonic samples as well as worse prognosis in patients with high DIS3L2 expression. In addition, our RNA deep-sequencing data revealed that knockdown (KD) of DIS3L2 induces a strong transcriptomic disturbance in SW480 CRC cells. Moreover, gene ontology (GO) analysis of significant upregulated transcripts displays enrichment in mRNAs encoding proteins involved in cell cycle regulation and cancer-related pathways, which guided us to evaluate which specific hallmarks of cancer are differentially regulated by DIS3L2. To do so, we employed four CRC cell lines (HCT116, SW480, Caco-2 and HT-29) differing in their mutational background and oncogenicity. We demonstrate that depletion of DIS3L2 results in reduced cell viability of highly oncogenic SW480 and HCT116 CRC cells, but had little or no impact in the more differentiated Caco-2 and HT-29 cells. Remarkably, the mTOR signaling pathway, crucial for cell survival and growth, is downregulated after DIS3L2 KD, whereas AZGP1, an mTOR pathway inhibitor, is upregulated. Furthermore, our results indicate that depletion of DIS3L2 disturbs metastasis-associated properties, such as cell migration and invasion, only in highly oncogenic CRC cells. Our work reveals for the first time a role for DIS3L2 in sustaining CRC cell proliferation and provides evidence that this ribonuclease is required to support the viability and invasive behavior of dedifferentiated CRC cells.
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Affiliation(s)
- Juan F García-Moreno
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Rafaela Lacerda
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Paulo J da Costa
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Marcelo Pereira
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Paulo Matos
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
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3
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Nagarajan VK, Stuart CJ, DiBattista AT, Accerbi M, Caplan JL, Green PJ. RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis. THE PLANT CELL 2023; 35:1936-1955. [PMID: 37070465 PMCID: PMC10226599 DOI: 10.1093/plcell/koad085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 05/30/2023]
Abstract
In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5' ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.
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Affiliation(s)
- Vinay K Nagarajan
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Catherine J Stuart
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Anna T DiBattista
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Monica Accerbi
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Jeffrey L Caplan
- Bio-Imaging Center, Delaware Biotechnology Institute, University of
Delaware, Newark, DE 19713-1316, USA
| | - Pamela J Green
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
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4
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Meze K, Axhemi A, Thomas DR, Doymaz A, Joshua-Tor L. A shape-shifting nuclease unravels structured RNA. Nat Struct Mol Biol 2023; 30:339-347. [PMID: 36823385 PMCID: PMC10023572 DOI: 10.1038/s41594-023-00923-x] [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: 11/08/2021] [Accepted: 01/11/2023] [Indexed: 02/25/2023]
Abstract
RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts. Dis3-like 2 (Dis3L2) is a 3'-5' exoribonuclease that plays a critical role in human development. Dis3L2 independently degrades structured substrates, including coding and noncoding 3' uridylated RNAs. While the basis for Dis3L2's substrate recognition has been well characterized, the mechanism of structured RNA degradation by this family of enzymes is unknown. We characterized the discrete steps of the degradation cycle by determining cryogenic electron microscopy structures representing snapshots along the RNA turnover pathway and measuring kinetic parameters for RNA processing. We discovered a dramatic conformational change that is triggered by double-stranded RNA (dsRNA), repositioning two cold shock domains by 70 Å. This movement exposes a trihelix linker region, which acts as a wedge to separate the two RNA strands. Furthermore, we show that the trihelix linker is critical for dsRNA, but not single-stranded RNA, degradation. These findings reveal the conformational plasticity of Dis3L2 and detail a mechanism of structured RNA degradation.
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Affiliation(s)
- Katarina Meze
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, New York, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY, USA
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Armend Axhemi
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, New York, NY, USA
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Dennis R Thomas
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, New York, NY, USA
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Ahmet Doymaz
- School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Leemor Joshua-Tor
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, New York, NY, USA.
- School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY, USA.
- Cold Spring Harbor Laboratory, New York, NY, USA.
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5
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Cesaro G, da Soler HT, Guerra-Slompo E, Haouz A, Legrand P, Zanchin N, Guimaraes B. Trypanosoma brucei RRP44: a versatile enzyme for processing structured and non-structured RNA substrates. Nucleic Acids Res 2022; 51:380-395. [PMID: 36583334 PMCID: PMC9841401 DOI: 10.1093/nar/gkac1199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 11/25/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Rrp44/Dis3 is a conserved eukaryotic ribonuclease that acts on processing and degradation of nearly all types of RNA. It contains an endo- (PIN) and an exonucleolytic (RNB) domain and, its depletion in model organisms supports its essential function for cell viability. In Trypanosoma brucei, depletion of Rrp44 (TbRRP44) blocks maturation of ribosomal RNA, leading to disruption of ribosome synthesis and inhibition of cell proliferation. We have determined the crystal structure of the exoribonucleolytic module of TbRRP44 in an active conformation, revealing novel details of the catalytic mechanism of the RNB domain. For the first time, the position of the second magnesium involved in the two-metal-ion mechanism was determined for a member of the RNase II family. In vitro, TbRRP44 acts preferentially on non-structured uridine-rich RNA substrates. However, we demonstrated for the first time that both TbRRP44 and its homologue from Saccharomyces cerevisiae can also degrade structured substrates without 3'-end overhang, suggesting that Rrp44/Dis3 ribonucleases may be involved in degradation of a wider panel of RNA than has been assumed. Interestingly, deletion of TbRRP44 PIN domain impairs RNA binding to different extents, depending on the type of substrate.
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Affiliation(s)
- Giovanna Cesaro
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
| | | | | | - Ahmed Haouz
- Institut Pasteur, Plate-forme de cristallographie-C2RT, UMR-3528 CNRS, Paris, France
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6
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Bush JA, Meyer SM, Fuerst R, Tong Y, Li Y, Benhamou RI, Aikawa H, Zanon PRA, Gibaut QMR, Angelbello AJ, Gendron TF, Zhang YJ, Petrucelli L, Heick Jensen T, Childs-Disney JL, Disney MD. A blood-brain penetrant RNA-targeted small molecule triggers elimination of r(G 4C 2) exp in c9ALS/FTD via the nuclear RNA exosome. Proc Natl Acad Sci U S A 2022; 119:e2210532119. [PMID: 36409902 PMCID: PMC9860304 DOI: 10.1073/pnas.2210532119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
A hexanucleotide repeat expansion in intron 1 of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia, or c9ALS/FTD. The RNA transcribed from the expansion, r(G4C2)exp, causes various pathologies, including intron retention, aberrant translation that produces toxic dipeptide repeat proteins (DPRs), and sequestration of RNA-binding proteins (RBPs) in RNA foci. Here, we describe a small molecule that potently and selectively interacts with r(G4C2)exp and mitigates disease pathologies in spinal neurons differentiated from c9ALS patient-derived induced pluripotent stem cells (iPSCs) and in two c9ALS/FTD mouse models. These studies reveal a mode of action whereby a small molecule diminishes intron retention caused by the r(G4C2)exp and allows the liberated intron to be eliminated by the nuclear RNA exosome, a multi-subunit degradation complex. Our findings highlight the complexity of mechanisms available to RNA-binding small molecules to alleviate disease pathologies and establishes a pipeline for the design of brain penetrant small molecules targeting RNA with novel modes of action in vivo.
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Affiliation(s)
- Jessica A. Bush
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Samantha M. Meyer
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Rita Fuerst
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Yuquan Tong
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Raphael I. Benhamou
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Haruo Aikawa
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Patrick R. A. Zanon
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Quentin M. R. Gibaut
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | | | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL32224
| | | | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus CDK-8000, Denmark
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
- Department of Neuroscience, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
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7
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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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8
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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9
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Lange H, Gagliardi D. Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes. THE PLANT CELL 2022; 34:967-988. [PMID: 34954803 PMCID: PMC8894942 DOI: 10.1093/plcell/koab310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 05/08/2023]
Abstract
RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.
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Affiliation(s)
- Heike Lange
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Author for correspondence:
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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10
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Subhramanyam CS, Cao Q, Wang C, Heng ZSL, Zhou Z, Hu Q. piRNAs Interact with Cold-Shock Domain-Containing RNA Binding Proteins and Regulate Neuronal Gene Expression During Differentiation. Mol Neurobiol 2022; 59:1285-1300. [PMID: 34982407 DOI: 10.1007/s12035-021-02678-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022]
Abstract
piRNAs (PIWI-interacting RNAs) are a class of small non-coding RNAs (ncRNAs) abundantly expressed in germline cells and involved in suppressing the transposon activity. Interestingly, recent studies have found piRNA expression in the central nervous system (CNS), yet the underlying biological significance remains largely unknown. In this study, we investigated the expression and function of piRNAs during the retinoic acid (RA)-mediated neuronal differentiation in NT2 cells, a human embryonal carcinoma cell line. We identified a cohort of differentially expressed piRNAs by microarray. Two piRNAs, DQ582359 and DQ596268, were increasingly upregulated during the RA-induced differentiation and involved in regulating the expression of neuronal markers, MAP2 and TUBB3. Furthermore, these piRNAs were found to associate with cold-shock domain (CSD)-containing RNA binding proteins, DIS3, DIS3L2, and YB-1. Markedly, overexpression of these piRNAs further enhanced the protein levels of MAP2 and TUBB3, potentially by downregulating DIS3, DIS3L2, and YB-1. Hence, our study has identified a novel somatic function of piRNAs in regulating neuronal gene expression. The interaction of piRNA with some CSD-containing proteins can be further explored to enhance neuronal differentiation to treat neurodegenerative diseases.
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Affiliation(s)
| | - Qiong Cao
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, 117594, Singapore
| | - Cheng Wang
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, 117594, Singapore
| | - Zealyn Shi-Lin Heng
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, 117594, Singapore
| | - Zhihong Zhou
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593, Singapore
| | - Qidong Hu
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, 117594, Singapore.
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11
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Zhao LW, Zhu YZ, Wu YW, Pi SB, Shen L, Fan HY. Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development. Nucleic Acids Res 2021; 50:458-472. [PMID: 34904664 PMCID: PMC8855302 DOI: 10.1093/nar/gkab1213] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the maternally encoded mRNA decay pathway (M-decay) and the zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. In this study, we identified the zygotically encoded nuclear poly(A) binding protein 1 (PABPN1) as a factor required for maternal mRNA turnover, with a previously undescribed cytoplasmic function. Cytoplasmic PABPN1 docks on 3'-uridylated transcripts, downstream of terminal uridylyl transferases TUT4 and TUT7, and recruits 3'-5' exoribonuclease DIS3L2 to its targets, facilitating maternal mRNA decay. Pabpn1-knockout in mice resulted in preimplantation stage mortality due to early developmental arrest at the morula stage. Maternal mRNAs to be eliminated via the Z-decay pathway failed to be removed from Pabpn1-depleted embryos. Furthermore, PABPN1-mediated Z-decay is essential for major ZGA and regulates the expression of cell fate-determining factors in mouse preimplantation embryos. This study revealed an unforeseen cytoplasmic function of PABPN1 coupled with early embryonic development, characterized the presence of a zygotic destabilizer of maternal mRNA, and elucidated the Z-decay process mechanisms, which potentially contribute to human fertility.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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12
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Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell Mol Life Sci 2021; 78:8049-8071. [PMID: 34748024 DOI: 10.1007/s00018-021-04012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023]
Abstract
Multiple RNA pathways are required to produce functional sperm. Here, we review RNA post-transcriptional regulation during spermatogenesis with particular emphasis on the role of 3' end modifications. From early studies in the 1970s, it became clear that spermiogenesis transcripts could be stored for days only to be translated at advanced stages of spermatid differentiation. The transition between the translationally repressed and active states was observed to correlate with the shortening of the transcripts' poly(A) tail, establishing a link between RNA 3' end metabolism and male germ cell differentiation. Since then, numerous RNA metabolic pathways have been implicated not only in the progression through spermatogenesis, but also in the maintenance of genomic integrity. Recent studies have characterized the elusive 3' biogenesis of Piwi-interacting RNAs (piRNAs), identified a critical role for messenger RNA (mRNA) 3' uridylation in meiotic progression, established the mechanisms that destabilize transcripts with long 3' untranslated regions (3'UTRs) in post-mitotic cells, and defined the physiological relevance of RNA exonucleases and deadenylases in male germ cells. In this review, we discuss RNA processing in the male germline in the light of the most recent findings. A brief recollection of different RNA-processing events will aid future studies exploring post-transcriptional regulation in spermatogenesis.
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Affiliation(s)
- Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA.
| | - Lokesh Kumar
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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13
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Pashler AL, Towler BP, Jones CI, Haime HJ, Burgess T, Newbury SF. Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs. RNA (NEW YORK, N.Y.) 2021; 27:1265-1280. [PMID: 34266995 PMCID: PMC8457002 DOI: 10.1261/rna.078872.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
XRN1 is a highly conserved exoribonuclease which degrades uncapped RNAs in a 5'-3' direction. Degradation of RNAs by XRN1 is important in many cellular and developmental processes and is relevant to human disease. Studies in D. melanogaster demonstrate that XRN1 can target specific RNAs, which have important consequences for developmental pathways. Osteosarcoma is a malignancy of the bone and accounts for 2% of all pediatric cancers worldwide. Five-year survival of patients has remained static since the 1970s and therefore furthering our molecular understanding of this disease is crucial. Previous work has shown a down-regulation of XRN1 in osteosarcoma cells; however, the transcripts regulated by XRN1 which might promote osteosarcoma remain elusive. Here, we confirm reduced levels of XRN1 in osteosarcoma cell lines and patient samples and identify XRN1-sensitive transcripts in human osteosarcoma cells. Using RNA-seq in XRN1-knockdown SAOS-2 cells, we show that 1178 genes are differentially regulated. Using a novel bioinformatic approach, we demonstrate that 134 transcripts show characteristics of direct post-transcriptional regulation by XRN1. Long noncoding RNAs (lncRNAs) are enriched in this group, suggesting that XRN1 normally plays an important role in controlling lncRNA expression in these cells. Among potential lncRNAs targeted by XRN1 is HOTAIR, which is known to be up-regulated in osteosarcoma and contributes to disease progression. We have also identified G-rich and GU motifs in post-transcriptionally regulated transcripts which appear to sensitize them to XRN1 degradation. Our results therefore provide significant insights into the specificity of XRN1 in human cells which are relevant to disease.
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Affiliation(s)
- Amy L Pashler
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Benjamin P Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Christopher I Jones
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Hope J Haime
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Tom Burgess
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
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14
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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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15
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Novačić A, Šupljika N, Bekavac N, Žunar B, Stuparević I. Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast. Microbiol Spectr 2021; 9:e0029521. [PMID: 34259554 PMCID: PMC8552689 DOI: 10.1128/spectrum.00295-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/18/2021] [Indexed: 11/20/2022] Open
Abstract
Yeast cell wall stability is important for cell division and survival under stress conditions. The expression of cell-wall-related proteins is regulated by several pathways involving RNA-binding proteins and RNases. The multiprotein RNA exosome complex provides the 3'→5' exoribonuclease activity that is critical for maintaining the stability and integrity of the yeast cell wall under stress conditions such as high temperatures. In this work, we show that the temperature sensitivity of RNA exosome mutants is most pronounced in the W303 genetic background due to the nonfunctional ssd1-d allele. This gene encodes the RNA-binding protein Ssd1, which is involved in the posttranscriptional regulation of cell-wall-related genes. Expression of the functional SSD1-V allele from its native genomic locus or from a centromeric plasmid suppresses the growth defects and aberrant morphology of RNA exosome mutant cells at high temperatures or upon treatment with cell wall stressors. Moreover, combined inactivation of the RNA exosome catalytic subunit Rrp6 and Ssd1 results in a synthetically sick phenotype of cell wall instability, as these proteins may function in parallel pathways (i.e., via different mRNA targets) to maintain cell wall stability. IMPORTANCE Stressful conditions such as high temperatures can compromise cellular integrity and cause bursting. In microorganisms surrounded by a cell wall, such as yeast, the cell wall is the primary shield that protects cells from environmental stress. Therefore, remodeling its structure requires inputs from multiple signaling pathways and regulators. In this work, we identify the interplay of the RNA exosome complex and the RNA-binding protein Ssd1 as an important factor in the yeast cell wall stress response. These proteins operate in independent pathways to support yeast cell wall stability. This work highlights the contribution of RNA-binding proteins in the regulation of yeast cell wall structure, providing new insights into yeast physiology.
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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
| | - Nada Šupljika
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nikša Bekavac
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Bojan Žunar
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - 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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16
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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17
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Ballou ER, Cook AG, Wallace EWJ. Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases. Mol Biol Evol 2021; 38:1837-1846. [PMID: 33313834 PMCID: PMC8097288 DOI: 10.1093/molbev/msaa324] [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] [Indexed: 12/15/2022] Open
Abstract
The RNase II family of 3'-5' exoribonucleases is present in all domains of life, and eukaryotic family members Dis3 and Dis3L2 play essential roles in RNA degradation. Ascomycete yeasts contain both Dis3 and inactive RNase II-like "pseudonucleases." The latter function as RNA-binding proteins that affect cell growth, cytokinesis, and fungal pathogenicity. However, the evolutionary origins of these pseudonucleases are unknown: What sequence of events led to their novel function, and when did these events occur? Here, we show how RNase II pseudonuclease homologs, including Saccharomyces cerevisiae Ssd1, are descended from active Dis3L2 enzymes. During fungal evolution, active site mutations in Dis3L2 homologs have arisen at least four times, in some cases following gene duplication. In contrast, N-terminal cold-shock domains and regulatory features are conserved across diverse dikarya and mucoromycota, suggesting that the nonnuclease function requires these regions. In the basidiomycete pathogenic yeast Cryptococcus neoformans, the single Ssd1/Dis3L2 homolog is required for cytokinesis from polyploid "titan" growth stages. This phenotype of C. neoformans Ssd1/Dis3L2 deletion is consistent with those of inactive fungal pseudonucleases, yet the protein retains an active site sequence signature. We propose that a nuclease-independent function for Dis3L2 arose in an ancestral hyphae-forming fungus. This second function has been conserved across hundreds of millions of years, whereas the RNase activity was lost repeatedly in independent lineages.
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Affiliation(s)
- Elizabeth R Ballou
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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18
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Borbolis F, Syntichaki P. Biological implications of decapping: beyond bulk mRNA decay. FEBS J 2021; 289:1457-1475. [PMID: 33660392 DOI: 10.1111/febs.15798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022]
Abstract
It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
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19
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Tomecki R, Drazkowska K. An integrative approach uncovers transcriptome-wide determinants of mRNA stability regulation in Saccharomyces cerevisiae. FEBS J 2021; 288:3418-3423. [PMID: 33590687 DOI: 10.1111/febs.15742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/29/2021] [Indexed: 11/29/2022]
Abstract
mRNA degradation rate is one of the key stages of gene expression regulation in eukaryotic cells. To date, intertwined processes of post-transcriptional control have been widely investigated, but focused rather on the examination of mechanisms controlling stability of particular protein-coding transcripts. Currently, a wealth of information from structural, biochemical, and high-throughput studies makes it tempting to define general rules governing mRNA stability that could be considered as versatile and valid on a genome-wide scale. Basu et al. analyzed multiple experimental and computational data on Saccharomyces cerevisiae mRNA half-lives as well as on secondary structures and protein-binding sites within transcripts, and collated it with available structures of ribonucleases, that is, enzymes responsible for mRNA degradation. This approach allowed to conclude how particular mRNA features such as lengths of unstructured terminal or internal regions or sequestration into ribonucleoprotein complexes impact half-lives of protein-coding transcripts and to define genome-scale principles of mRNA stability control in yeast.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
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20
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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21
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Dis3L2 regulates cell proliferation and tissue growth through a conserved mechanism. PLoS Genet 2020; 16:e1009297. [PMID: 33370287 PMCID: PMC7793271 DOI: 10.1371/journal.pgen.1009297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 01/08/2021] [Accepted: 12/05/2020] [Indexed: 01/04/2023] Open
Abstract
Dis3L2 is a highly conserved 3’-5’ exoribonuclease which is mutated in the human overgrowth disorders Perlman syndrome and Wilms’ tumour of the kidney. Using Drosophila melanogaster as a model system, we have generated a new dis3L2 null mutant together with wild-type and nuclease-dead genetic lines in Drosophila to demonstrate that the catalytic activity of Dis3L2 is required to control cell proliferation. To understand the cellular pathways regulated by Dis3L2 to control proliferation, we used RNA-seq on dis3L2 mutant wing discs to show that the imaginal disc growth factor Idgf2 is responsible for driving the wing overgrowth. IDGFs are conserved proteins homologous to human chitinase-like proteins such as CHI3L1/YKL-40 which are implicated in tissue regeneration as well as cancers including colon cancer and non-small cell lung cancer. We also demonstrate that loss of DIS3L2 in human kidney HEK-293T cells results in cell proliferation, illustrating the conservation of this important cell proliferation pathway. Using these human cells, we show that loss of DIS3L2 results in an increase in the PI3-Kinase/AKT signalling pathway, which we subsequently show to contribute towards the proliferation phenotype in Drosophila. Our work therefore provides the first mechanistic explanation for DIS3L2-induced overgrowth in humans and flies and identifies an ancient proliferation pathway controlled by Dis3L2 to regulate cell proliferation and tissue growth. Regulation of cell proliferation is not only important during development but also required for repair of damaged tissues and during wound healing. Using human kidney cells as well as the fruit fly Drosophila we have recently discovered that cell proliferation can be regulated by a protein named Dis3L2. Depletion or removal of this protein results in excess proliferation. These results are relevant to human disease as DIS3L2 has been shown to be mutated in an overgrowth syndrome (Perlman syndrome) where affected children have abnormal enlargement of organs (e.g. kidneys) and susceptibility to Wilms’ tumour (a kidney cancer). Dis3L2 is an enzyme known to "chew up" mRNA molecules which instruct the cell to make particular proteins. Using state-of-the-art molecular methods in Drosophila, we have discovered that Dis3L2 targets a small subset of mRNAs, including an mRNA encoding a growth factor named 'imaginal disc growth factor 2' (idgf2). For human kidney cells in culture, we have found that depletion of DIS3L2 results in enhanced proliferation, and that this involves a well-known cellular pathway. Our results mean that we have discovered a new way of controlling cell proliferation, which could, in the future, be used in human therapies.
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22
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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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23
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Malik D, Kobyłecki K, Krawczyk P, Poznański J, Jakielaszek A, Napiórkowska A, Dziembowski A, Tomecki R, Nowotny M. Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine. Nucleic Acids Res 2020; 48:9387-9405. [PMID: 32785623 PMCID: PMC7498324 DOI: 10.1093/nar/gkaa647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Accepted: 07/27/2020] [Indexed: 11/12/2022] Open
Abstract
Template-independent terminal ribonucleotide transferases (TENTs) catalyze the addition of nucleotide monophosphates to the 3′-end of RNA molecules regulating their fate. TENTs include poly(U) polymerases (PUPs) with a subgroup of 3′ CUCU-tagging enzymes, such as CutA in Aspergillus nidulans. CutA preferentially incorporates cytosines, processively polymerizes only adenosines and does not incorporate or extend guanosines. The basis of this peculiar specificity remains to be established. Here, we describe crystal structures of the catalytic core of CutA in complex with an incoming non-hydrolyzable CTP analog and an RNA with three adenosines, along with biochemical characterization of the enzyme. The binding of GTP or a primer with terminal guanosine is predicted to induce clashes between 2-NH2 of the guanine and protein, which would explain why CutA is unable to use these ligands as substrates. Processive adenosine polymerization likely results from the preferential binding of a primer ending with at least two adenosines. Intriguingly, we found that the affinities of CutA for the CTP and UTP are very similar and the structures did not reveal any apparent elements for specific NTP binding. Thus, the properties of CutA likely result from an interplay between several factors, which may include a conformational dynamic process of NTP recognition.
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Affiliation(s)
- Deepshikha Malik
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Kamil Kobyłecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Aleksandra Jakielaszek
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Agnieszka Napiórkowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
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24
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Roithová A, Feketová Z, Vaňáčová Š, Staněk D. DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs. Nucleic Acids Res 2020; 48:6184-6197. [PMID: 32374871 PMCID: PMC7293007 DOI: 10.1093/nar/gkaa301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) undergo a complex maturation pathway containing multiple steps in the nucleus and in the cytoplasm. snRNP biogenesis is strictly proofread and several quality control checkpoints are placed along the pathway. Here, we analyzed the fate of small nuclear RNAs (snRNAs) that are unable to acquire a ring of Sm proteins. We showed that snRNAs lacking the Sm ring are unstable and accumulate in P-bodies in an LSm1-dependent manner. We further provide evidence that defective snRNAs without the Sm binding site are uridylated at the 3′ end and associate with DIS3L2 3′→5′ exoribonuclease and LSm proteins. Finally, inhibition of 5′→3′ exoribonuclease XRN1 increases association of ΔSm snRNAs with DIS3L2, which indicates competition and compensation between these two degradation enzymes. Together, we provide evidence that defective snRNAs without the Sm ring are uridylated and degraded by alternative pathways involving either DIS3L2 or LSm proteins and XRN1.
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Affiliation(s)
- Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.,Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Zuzana Feketová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A35, 625 00 Brno, Czech Republic
| | - Štěpánka Vaňáčová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A35, 625 00 Brno, Czech Republic
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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25
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Wang Y, Weng C, Chen X, Zhou X, Huang X, Yan Y, Zhu C. CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of rRNA. BMC Biol 2020; 18:115. [PMID: 32887607 PMCID: PMC7472701 DOI: 10.1186/s12915-020-00850-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/17/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Modification of RNAs, particularly at the terminals, is critical for various essential cell processes; for example, uridylation is implicated in tumorigenesis, proliferation, stem cell maintenance, and immune defense against viruses and retrotransposons. Ribosomal RNAs can be regulated by antisense ribosomal siRNAs (risiRNAs), which downregulate pre-rRNAs through the nuclear RNAi pathway in Caenorhabditis elegans. However, the biogenesis and regulation of risiRNAs remain obscure. Previously, we showed that 26S rRNAs are uridylated at the 3'-ends by an unknown terminal polyuridylation polymerase before the rRNAs are degraded by a 3' to 5' exoribonuclease SUSI-1(ceDIS3L2). RESULTS Here, we found that CDE-1, one of the three C.elegans polyuridylation polymerases (PUPs), is specifically involved in suppressing risiRNA production. CDE-1 localizes to perinuclear granules in the germline and uridylates Argonaute-associated 22G-RNAs, 26S, and 5.8S rRNAs at the 3'-ends. Immunoprecipitation followed by mass spectrometry (IP-MS) revealed that CDE-1 interacts with SUSI-1(ceDIS3L2). Consistent with these results, both CDE-1 and SUSI-1(ceDIS3L2) are required for the inheritance of RNAi. CONCLUSIONS This work identified a rRNA surveillance machinery of rRNAs that couples terminal polyuridylation and degradation.
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Affiliation(s)
- Yun Wang
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- School of Bioengineering, Huainan Normal University, Huainan, 232038, Anhui, People's Republic of China.
| | - Chenchun Weng
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xiangyang Chen
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xufei Zhou
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xinya Huang
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Yonghong Yan
- National Institute of Biological Sciences, Beijing, 102206, People's Republic of China
| | - Chengming Zhu
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
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26
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Yang A, Shao TJ, Bofill-De Ros X, Lian C, Villanueva P, Dai L, Gu S. AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2. Nat Commun 2020; 11:2765. [PMID: 32488030 PMCID: PMC7265490 DOI: 10.1038/s41467-020-16533-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) associated with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3' modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligouridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3' end. A set of endogenous miRNAs including miR-7, miR-222 and miR-769 are targeted by this machinery presumably due to target-directed miRNA degradation.
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Affiliation(s)
- Acong Yang
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Chuanjiang Lian
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,State Key Laboratory of Veterinary Biotechnology and Heilongjiang Province Key Laboratory for Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Patricia Villanueva
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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27
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The Perlman syndrome DIS3L2 exoribonuclease safeguards endoplasmic reticulum-targeted mRNA translation and calcium ion homeostasis. Nat Commun 2020; 11:2619. [PMID: 32457326 PMCID: PMC7250864 DOI: 10.1038/s41467-020-16418-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
DIS3L2-mediated decay (DMD) is a surveillance pathway for certain non-coding RNAs (ncRNAs) including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and RMRP. While mutations in DIS3L2 are associated with Perlman syndrome, the biological significance of impaired DMD is obscure and pathological RNAs have not been identified. Here, by ribosome profiling (Ribo-seq) we find specific dysregulation of endoplasmic reticulum (ER)-targeted mRNA translation in DIS3L2-deficient cells. Mechanistically, DMD functions in the quality control of the 7SL ncRNA component of the signal recognition particle (SRP) required for ER-targeted translation. Upon DIS3L2 loss, sustained 3’-end uridylation of aberrant 7SL RNA impacts ER-targeted translation and causes ER calcium leakage. Consequently, elevated intracellular calcium in DIS3L2-deficient cells activates calcium signaling response genes and perturbs ESC differentiation. Thus, DMD is required to safeguard ER-targeted mRNA translation, intracellular calcium homeostasis, and stem cell differentiation. The DIS3L2 exonuclease degrades aberrant 7SL RNAs tagged by an oligouridine 3′-tail. Here the authors analyze DIS3L2 knockout mouse embryonic stem cells and suggest that DIS3L2-mediated quality control of 7SL RNA is important for ER-mediated translation and calcium ion homeostasis.
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28
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Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M. Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation. Mol Cell 2020; 77:1222-1236.e13. [PMID: 32048998 PMCID: PMC7083229 DOI: 10.1016/j.molcel.2020.01.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
RNA decay is crucial for mRNA turnover and surveillance and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized versus redundant roles. Cytoplasmic pathways and links to translation are particularly enigmatic. By directly profiling decay factor targets and normal versus aberrant translation in mouse embryonic stem cells (mESCs), we uncovered extensive decay pathway specialization and crosstalk with translation. XRN1 (5'-3') mediates cytoplasmic bulk mRNA turnover whereas SKIV2L (3'-5') is universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance revealed AVEN and FOCAD as SKIV2L interactors. AVEN prevents ribosome stalls at structured regions, which otherwise require SKIV2L for clearance. This pathway is crucial for histone translation, upstream open reading frame (uORF) regulation, and counteracting ribosome arrest on small ORFs. In summary, we uncovered key targets, components, and functions of mammalian RNA decay pathways and extensive coupling to translation.
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Affiliation(s)
- Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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29
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Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP. The genetic basis of aneuploidy tolerance in wild yeast. eLife 2020; 9:52063. [PMID: 31909711 PMCID: PMC6970514 DOI: 10.7554/elife.52063] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Aneuploidy is highly detrimental during development yet common in cancers and pathogenic fungi – what gives rise to differences in aneuploidy tolerance remains unclear. We previously showed that wild isolates of Saccharomyces cerevisiae tolerate chromosome amplification while laboratory strains used as a model for aneuploid syndromes do not. Here, we mapped the genetic basis to Ssd1, an RNA-binding translational regulator that is functional in wild aneuploids but defective in laboratory strain W303. Loss of SSD1 recapitulates myriad aneuploidy signatures previously taken as eukaryotic responses. We show that aneuploidy tolerance is enabled via a role for Ssd1 in mitochondrial physiology, including binding and regulating nuclear-encoded mitochondrial mRNAs, coupled with a role in mitigating proteostasis stress. Recapitulating ssd1Δ defects with combinatorial drug treatment selectively blocked proliferation of wild-type aneuploids compared to euploids. Our work adds to elegant studies in the sensitized laboratory strain to present a mechanistic understanding of eukaryotic aneuploidy tolerance.
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Affiliation(s)
- James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States
| | - Leah E Escalante
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Katie J Clowers
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - DeElegant Robinson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States
| | - Venera Bouriakov
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Great Lakes Bioenergy Research Center, Madison, United States
| | - Joshua J Coon
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Great Lakes Bioenergy Research Center, Madison, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, Madison, United States
| | - Evgenia Shishkova
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, Madison, United States
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Great Lakes Bioenergy Research Center, Madison, United States
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30
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Viegas SC, Matos RG, Arraiano CM. The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective. Methods Mol Biol 2020; 2062:37-46. [PMID: 31768970 DOI: 10.1007/978-1-4939-9822-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There are striking similarities between the processes of RNA degradation in bacteria and eukaryotes, which rely on the same basic set of enzymatic activities. In particular, enzymes that catalyze 3'→5' RNA decay share evolutionary relationships across the three domains of life. Over the years, a large body of biochemical and structural data has been generated that elucidated the mechanism of action of these enzymes. In this overview, to trace the evolutionary origins of the multisubunit RNA exosome complex, we compare the structural and functional characteristics of the eukaryotic and prokaryotic exoribonucleolytic activities.
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Affiliation(s)
- Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
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31
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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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32
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Experimental supporting data on DIS3L2 over nonsense-mediated mRNA decay targets in human cells. Data Brief 2019; 28:104943. [PMID: 31886366 PMCID: PMC6921154 DOI: 10.1016/j.dib.2019.104943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 11/23/2022] Open
Abstract
In this article, we present supportive data related to the research article “A role for DIS3L2 over natural nonsense-mediated mRNA decay targets in human cells” [1], where interpretation of the data presented here is available. Indeed, here we analyze the impact of the DIS3L2 exoribonuclease over nonsense-mediated mRNA decay (NMD)-targets. Specifically, we present data on: a) the expression of various reporter human β-globin mRNAs, monitored by Northern blot and RT-qPCR, before and after altering DIS3L2 levels in HeLa cells, and b) the gene expression levels of deregulated transcripts generated by re-analyzing publicly available data from UPF1-depleted HeLa cells that were further cross-referenced with a dataset of transcripts upregulated in DIS3L2-depleted cells. These analyses revealed that DIS3L2 regulates the levels of a subset of NMD-targets. These data can be valuable for researchers interested in the NMD mechanism.
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33
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Nagarajan VK, Kukulich PM, von Hagel B, Green PJ. RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4. Nucleic Acids Res 2019; 47:9216-9230. [PMID: 31428786 PMCID: PMC6755094 DOI: 10.1093/nar/gkz712] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5' end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5' ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3' fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.
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Affiliation(s)
- Vinay K Nagarajan
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Patrick M Kukulich
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Bryan von Hagel
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Pamela J Green
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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34
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Liu M, Lu B, Fan Y, He X, Shen S, Jiang C, Zhang Q. TRIBE Uncovers the Role of Dis3 in Shaping the Dynamic Transcriptome in Malaria Parasites. Front Cell Dev Biol 2019; 7:264. [PMID: 31737630 PMCID: PMC6838019 DOI: 10.3389/fcell.2019.00264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023] Open
Abstract
Identification of RNA targets of RNA-binding proteins (RBPs) is essential for complete understanding of their biological functions. However, it is still a challenge to identify the biologically relevant targets of RBPs through in vitro strategies of RIP-seq, HITS-CLIP, or GoldCLIP due to the potentially high background and complicated manipulation. In malaria parasites, RIP-seq and gene disruption are the few tools available currently for identification of RBP targets. Here, we have adopted the TRIBE (Targets of RNA binding proteins identified by editing) system to in vivo identify the RNA targets of PfDis3, a key exoribonuclease subunit of RNA exosome in Plasmodium falciparum. We generated a transgenic parasite line of PfDis3-ADARcd, which catalyzes an adenosine (A)-to-inosine (I) conversion at the potential interacting sites of PfDis3-targeting RNAs. Most of PfDis3 target genes contain one edit site. The majority of the edit sites detected by PfDis3-TRIBE locate in exons and spread across the entire coding regions. The nucleotides adjacent to the edit sites contain ∼75% of A + T. PfDis3-TRIBE target genes are biases toward higher RIP enrichment, suggesting that PfDis3-TRIBE preferentially detects stronger PfDis3 RIP targets. Collectively, PfDis3-TRIBE is a favorable tool to identify in vivo target genes of RBP with high efficiency and reproducibility. Additionally, the PfDis3-targeting genes are involved in stage-related biological processes during the blood-stage development. Thus PfDis3 appears to shape the dynamic transcriptional transcriptome of malaria parasites through post-transcriptional degradation of a variety of unwanted transcripts from both strands in the asexual blood stage.
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Affiliation(s)
- Meng Liu
- Institute of Translational Research, Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Binbin Lu
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanting Fan
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaohui He
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shijun Shen
- Institute of Translational Research, Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cizhong Jiang
- Institute of Translational Research, Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai, China.,The Research Center of Stem Cells and Ageing, Tsingtao Advanced Research Institute, Tongji University, Shanghai, China
| | - Qingfeng Zhang
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
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35
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Chung CZ, Jaramillo JE, Ellis MJ, Bour DYN, Seidl LE, Jo DHS, Turk MA, Mann MR, Bi Y, Haniford DB, Duennwald ML, Heinemann IU. RNA surveillance by uridylation-dependent RNA decay in Schizosaccharomyces pombe. Nucleic Acids Res 2019; 47:3045-3057. [PMID: 30715470 PMCID: PMC6451125 DOI: 10.1093/nar/gkz043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In this study, we investigate the prevalence and impact of uridylation-dependent RNA decay in S. pombe by transcriptionally profiling cid1 and dis3L2 deletion strains. We found that the exonuclease Dis3L2 represents a bottleneck in uridylation-dependent mRNA decay, whereas Cid1 plays a redundant role that can be complemented by other Tutases. Deletion of dis3L2 elicits a cellular stress response, upregulating transcription of genes involved in protein folding and degradation. Misfolded proteins accumulate in both deletion strains, yet only trigger a strong stress response in dis3L2 deficient cells. While a deletion of cid1 increases sensitivity to protein misfolding stress, a dis3L2 deletion showed no increased sensitivity or was even protective. We furthermore show that uridylyl- and adenylyltransferases cooperate to generate a 5'-NxAUUAAAA-3' RNA motif on dak2 mRNA. Our studies elucidate the role of uridylation-dependent RNA decay as part of a global mRNA surveillance, and we found that perturbation of this pathway leads to the accumulation of misfolded proteins and elicits cellular stress responses.
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Affiliation(s)
- Christina Z Chung
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Julia E Jaramillo
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Michael J Ellis
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Daniel Y N Bour
- Department of Pathology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Lauren E Seidl
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - David H S Jo
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Matthew A Turk
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Mitchell R Mann
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Yumin Bi
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - David B Haniford
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Martin L Duennwald
- Department of Pathology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
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36
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da Costa PJ, Menezes J, Saramago M, García-Moreno JF, Santos HA, Gama-Carvalho M, Arraiano CM, Viegas SC, Romão L. A role for DIS3L2 over natural nonsense-mediated mRNA decay targets in human cells. Biochem Biophys Res Commun 2019; 518:664-671. [PMID: 31466720 DOI: 10.1016/j.bbrc.2019.08.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
The nonsense-mediated decay (NMD) pathway selectively degrades mRNAs carrying a premature translation-termination codon but also regulates the abundance of a large number of physiological mRNAs that encode full-length proteins. In human cells, NMD-targeted mRNAs are degraded by endonucleolytic cleavage and exonucleolytic degradation from both 5-' and 3'-ends. This is done by a process not yet completely understood that recruits decapping and 5'-to-3' exonuclease activities, as well as deadenylating and 3'-to-5' exonuclease exosome activities. In yeast, DIS3/Rrp44 protein is the catalytic subunit of the exosome, but in humans, there are three known paralogues of this enzyme: DIS3, DIS3L1, and DIS3L2. However, little is known about their role in NMD. Here, we show that some NMD-targets are DIS3L2 substrates in human cells. In addition, we observed that DIS3L2 acts over full-length transcripts, through a process that also involves UPF1. Moreover, DIS3L2-mediated decay is dependent on the activity of the terminal uridylyl transferases Zcchc6/11 (TUT7/4). Together, our findings establish a role for DIS3L2 and uridylation in NMD.
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Affiliation(s)
- Paulo J da Costa
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, Lisboa, Portugal
| | - Juliane Menezes
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, Lisboa, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Juan F García-Moreno
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, Lisboa, Portugal
| | - Hugo A Santos
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, Lisboa, Portugal
| | - Margarida Gama-Carvalho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, Lisboa, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, Lisboa, Portugal.
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37
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Kroupova A, Ivascu A, Reimão-Pinto MM, Ameres SL, Jinek M. Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Res 2019; 47:1030-1042. [PMID: 30462292 PMCID: PMC6344859 DOI: 10.1093/nar/gky1164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
Non-templated 3′-uridylation of RNAs has emerged as an important mechanism for regulating the processing, stability and biological function of eukaryotic transcripts. In Drosophila, oligouridine tailing by the terminal uridylyl transferase (TUTase) Tailor of numerous RNAs induces their degradation by the exonuclease Dis3L2, which serves functional roles in RNA surveillance and mirtron RNA biogenesis. Tailor preferentially uridylates RNAs terminating in guanosine or uridine nucleotides but the structural basis underpinning its RNA substrate selectivity is unknown. Here, we report crystal structures of Tailor bound to a donor substrate analog or mono- and oligouridylated RNA products. These structures reveal specific amino acid residues involved in donor and acceptor substrate recognition, and complementary biochemical assays confirm the critical role of an active site arginine in conferring selectivity toward 3′-guanosine terminated RNAs. Notably, conservation of these active site features suggests that other eukaryotic TUTases, including mammalian TUT4 and TUT7, might exhibit similar, hitherto unknown, substrate selectivity. Together, these studies provide critical insights into the specificity of 3′-uridylation in eukaryotic post-transcriptional gene regulation.
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Affiliation(s)
- Alena Kroupova
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Anastasia Ivascu
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Madalena M Reimão-Pinto
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
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38
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Chen C, Rodriguez Pino M, Haller PR, Verde F. Conserved NDR/LATS kinase controls RAS GTPase activity to regulate cell growth and chronological lifespan. Mol Biol Cell 2019; 30:2598-2616. [PMID: 31390298 PMCID: PMC6740195 DOI: 10.1091/mbc.e19-03-0172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adaptation to the nutritional environment is critical for all cells. RAS GTPase is a highly conserved GTP-binding protein with crucial functions for cell growth and differentiation in response to environmental conditions. Here, we describe a novel mechanism connecting RAS GTPase to nutrient availability in fission yeast. We report that the conserved NDR/LATS kinase Orb6 responds to nutritional cues and regulates Ras1 GTPase activity. Orb6 increases the protein levels of an Ras1 GTPase activator, the guanine nucleotide exchange factor Efc25, by phosphorylating Sts5, a protein bound to efc25 mRNA. By manipulating the extent of Orb6-mediated Sts5 assembly into RNP granules, we can modulate Efc25 protein levels, Ras1 GTPase activity, and, as a result, cell growth and cell survival. Thus, we conclude that the Orb6-Sts5-Ras1 regulatory axis plays a crucial role in promoting cell adaptation, balancing the opposing demands of promoting cell growth and extending chronological lifespan.
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Affiliation(s)
- Chuan Chen
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Marbelys Rodriguez Pino
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Patrick Roman Haller
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Fulvia Verde
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136
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39
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Hartenian E, Glaunsinger BA. Feedback to the central dogma: cytoplasmic mRNA decay and transcription are interdependent processes. Crit Rev Biochem Mol Biol 2019; 54:385-398. [PMID: 31656086 PMCID: PMC6871655 DOI: 10.1080/10409238.2019.1679083] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/13/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Transcription and RNA decay are key determinants of gene expression; these processes are typically considered as the uncoupled beginning and end of the messenger RNA (mRNA) lifecycle. Here we describe the growing number of studies demonstrating interplay between these spatially disparate processes in eukaryotes. Specifically, cells can maintain mRNA levels by buffering against changes in mRNA stability or transcription, and can also respond to virally induced accelerated decay by reducing RNA polymerase II gene expression. In addition to these global responses, there is also evidence that mRNAs containing a premature stop codon can cause transcriptional upregulation of homologous genes in a targeted fashion. In each of these systems, RNA binding proteins (RBPs), particularly those involved in mRNA degradation, are critical for cytoplasmic to nuclear communication. Although their specific mechanistic contributions are yet to be fully elucidated, differential trafficking of RBPs between subcellular compartments are likely to play a central role in regulating this gene expression feedback pathway.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, Berkeley, CA 94720
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40
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Xing S, Li Z, Ma W, He X, Shen S, Wei H, Li ST, Shu Y, Sun L, Zhong X, Huangfu Y, Su L, Feng J, Zhang X, Gao P, Jia WD, Zhang H. DIS3L2 Promotes Progression of Hepatocellular Carcinoma via hnRNP U-Mediated Alternative Splicing. Cancer Res 2019; 79:4923-4936. [PMID: 31331910 DOI: 10.1158/0008-5472.can-19-0376] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/20/2019] [Accepted: 07/17/2019] [Indexed: 11/16/2022]
Abstract
DIS3-like 3'-5' exoribonuclease 2 (DIS3L2) degrades aberrant RNAs, however, its function in tumorigenesis remains largely unexplored. Here, aberrant DIS3L2 expression promoted human hepatocellular carcinoma (HCC) progression via heterogeneous nuclear ribonucleoproteins (hnRNP) U-mediated alternative splicing. DIS3L2 directly interacted with hnRNP U through its cold-shock domains and promoted inclusion of exon 3b during splicing of pre-Rac1 independent of its exonuclease activity, yielding an oncogenic splicing variant, Rac1b, which is known to stimulate cellular transformation and tumorigenesis. DIS3L2 regulated alternative splicing by recruiting hnRNP U to pre-Rac1. Rac1b was critical for DIS3L2 promotion of liver cancer development both in vitro and in vivo. Importantly, DIS3L2 and Rac1b expression highly correlated with HCC progression and patient survival. Taken together, our findings uncover an oncogenic role of DIS3L2, in which it promotes liver cancer progression through a previously unappreciated mechanism of regulating hnRNP U-mediated alterative splicing. SIGNIFICANCE: These findings establish the role and mechanism of the 3'-5' exoribonuclease DIS3L2 in hepatocellular carcinoma carcinogenesis.
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Affiliation(s)
- Songge Xing
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China.,Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Zhaoyong Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Wenhao Ma
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Xiaoping He
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Shengqi Shen
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Haoran Wei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Shi-Ting Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Ying Shu
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Linchong Sun
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China.,Guangzhou First People's Hospital, School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, China
| | - Xiuying Zhong
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China.,Guangzhou First People's Hospital, School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, China
| | - Yuhao Huangfu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Lanhong Su
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Junru Feng
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Xiaozhang Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Ping Gao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China.,Guangzhou First People's Hospital, School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, China
| | - Wei-Dong Jia
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China.
| | - Huafeng Zhang
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China. .,Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
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41
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Pirouz M, Munafò M, Ebrahimi AG, Choe J, Gregory RI. Exonuclease requirements for mammalian ribosomal RNA biogenesis and surveillance. Nat Struct Mol Biol 2019; 26:490-500. [PMID: 31160785 PMCID: PMC6554070 DOI: 10.1038/s41594-019-0234-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/25/2019] [Indexed: 12/29/2022]
Abstract
Ribosomal RNA (rRNA) biogenesis is a multistep process requiring several nuclear and cytoplasmic exonucleases. The exact processing steps for mammalian 5.8S rRNA remain obscure. Here, using loss-of-function approaches in mouse embryonic stem cells and deep sequencing of rRNA intermediates, we investigate at nucleotide resolution the requirements of exonucleases known to be involved in 5.8S maturation, and explore the role of the Perlman syndrome-associated 3’-5’ exonuclease Dis3l2 in rRNA processing. We uncover a novel cytoplasmic intermediate that we name ‘7SB’ rRNA that is generated through sequential processing by distinct exosome complexes. 7SB rRNA can be oligoadenylated by an unknown enzyme and/or oligouridylated by TUT4/7 and subsequently processed by Dis3l2 and Eri1. Moreover, exosome depletion triggers Dis3l2-mediated decay (DMD) as a surveillance pathway for rRNAs. Our data identify previously unknown 5.8S rRNA processing steps and provide nucleotide level insight into the exonuclease requirements for mammalian rRNA processing.
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Affiliation(s)
- Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marzia Munafò
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Aref G Ebrahimi
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Junho Choe
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, USA. .,Harvard Initiative for RNA Medicine, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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42
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Abstract
In this Perspective, Bharathavikru and Hastie discuss recent studies published by Hunter et al., investigating the molecular mechanisms by which mutations in the gene encoding the RNA degradation component DIS3L2 lead to Perlman syndrome, and Chen et al., who show that microRNA processing gene mutations in Wilms tumor leads to an increase in the levels of transcription factor PLAG1 that in turn activates IGF2 expression. Overgrowth syndromes such as Perlman syndrome and associated pediatric cancers, including Wilms tumor, arise through genetic and, in certain instances, also epigenetic changes. In the case of the Beckwith-Wiedemann overgrowth syndrome and in Wilms tumor, increased levels of IGF2 have been shown to be causally related to the disease manifestation. In the previous issue of Genes & Development, Hunter and colleagues (pp. 903–908) investigated the molecular mechanisms by which mutations in the gene encoding the RNA degradation component DIS3L2 lead to Perlman syndrome. By analyzing nephron progenitor cells derived from their newly created Dis3l2 mutant mouse lines, the investigators showed that DIS3L2 loss of function leads to up-regulation of IGF2 independently of the let7 microRNA pathway. In a second study in this issue of Genes & Development, Chen and colleagues (pp. 996–1007) show that microRNA processing gene mutations in Wilms tumor lead to an increase in the levels of transcription factor pleomorphic adenoma gene 1 (PLAG1) that in turn activates IGF2 expression. Thus, augmented IGF2 expression seems to be a common downstream factor in both tissue overgrowth and Wilms tumor through several alternative mechanisms.
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Affiliation(s)
- Ruthrothaselvi Bharathavikru
- Medical Research Council, Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Nicholas D Hastie
- Medical Research Council, Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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43
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Morgan M, Kabayama Y, Much C, Ivanova I, Di Giacomo M, Auchynnikava T, Monahan JM, Vitsios DM, Vasiliauskaitė L, Comazzetto S, Rappsilber J, Allshire RC, Porse BT, Enright AJ, O’Carroll D. A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis. Cell Res 2019; 29:221-232. [PMID: 30617251 PMCID: PMC6420129 DOI: 10.1038/s41422-018-0128-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/20/2018] [Indexed: 02/08/2023] Open
Abstract
Several developmental stages of spermatogenesis are transcriptionally quiescent which presents major challenges associated with the regulation of gene expression. Here we identify that the zygotene to pachytene transition is not only associated with the resumption of transcription but also a wave of programmed mRNA degradation that is essential for meiotic progression. We explored whether terminal uridydyl transferase 4- (TUT4-) or TUT7-mediated 3' mRNA uridylation contributes to this wave of mRNA degradation during pachynema. Indeed, both TUT4 and TUT7 are expressed throughout most of spermatogenesis, however, loss of either TUT4 or TUT7 does not have any major impact upon spermatogenesis. Combined TUT4 and TUT7 (TUT4/7) deficiency results in embryonic growth defects, while conditional gene targeting revealed an essential role for TUT4/7 in pachytene progression. Loss of TUT4/7 results in the reduction of miRNA, piRNA and mRNA 3' uridylation. Although this reduction does not greatly alter miRNA or piRNA expression, TUT4/7-mediated uridylation is required for the clearance of many zygotene-expressed transcripts in pachytene cells. We find that TUT4/7-regulated transcripts in pachytene spermatocytes are characterized by having long 3' UTRs with length-adjusted enrichment for AU-rich elements. We also observed these features in TUT4/7-regulated maternal transcripts whose dosage was recently shown to be essential for sculpting a functional maternal transcriptome and meiosis. Therefore, mRNA 3' uridylation is a critical determinant of both male and female germline transcriptomes. In conclusion, we have identified a novel requirement for 3' uridylation-programmed zygotene mRNA clearance in pachytene spermatocytes that is essential for male meiotic progression.
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Affiliation(s)
- Marcos Morgan
- 0000 0004 1936 7988grid.4305.2MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK ,0000 0004 0627 3632grid.418924.2European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015 Monterotondo, Italy ,0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Yuka Kabayama
- 0000 0004 1936 7988grid.4305.2MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK ,0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Christian Much
- 0000 0004 1936 7988grid.4305.2MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK ,0000 0004 0627 3632grid.418924.2European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015 Monterotondo, Italy
| | - Ivayla Ivanova
- 0000 0004 1936 7988grid.4305.2MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
| | - Monica Di Giacomo
- 0000 0004 0627 3632grid.418924.2European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015 Monterotondo, Italy
| | - Tatsiana Auchynnikava
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Jack Michael Monahan
- 0000 0000 9709 7726grid.225360.0European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD UK
| | | | - Lina Vasiliauskaitė
- 0000 0004 1936 7988grid.4305.2MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK ,0000 0004 0627 3632grid.418924.2European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015 Monterotondo, Italy
| | - Stefano Comazzetto
- 0000 0004 0627 3632grid.418924.2European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015 Monterotondo, Italy
| | - Juri Rappsilber
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF UK ,0000 0001 2292 8254grid.6734.6Institute of Biotechnology, Technische Universität Berlin, Berlin, 13355 Germany
| | - Robin Campbell Allshire
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Bo Torben Porse
- 0000 0001 0674 042Xgrid.5254.6Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, 2200 Denmark ,0000 0001 0674 042Xgrid.5254.6The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200 Denmark ,0000 0001 0674 042Xgrid.5254.6Danish Stem Cell Centre (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200 Denmark
| | - Anton James Enright
- 0000 0000 9709 7726grid.225360.0European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD UK
| | - Dónal O’Carroll
- 0000 0004 1936 7988grid.4305.2MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK ,0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF UK
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Pirouz M, Ebrahimi AG, Gregory RI. Unraveling 3'-end RNA uridylation at nucleotide resolution. Methods 2019; 155:10-19. [PMID: 30395968 PMCID: PMC6387850 DOI: 10.1016/j.ymeth.2018.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional modification of RNA, the so-called 'Epitranscriptome', can regulate RNA structure, stability, localization, and function. Numerous modifications have been identified in virtually all classes of RNAs, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), microRNAs (miRNAs), and other noncoding RNAs (ncRNAs). These modifications may occur internally (by base or sugar modifications) and include RNA methylation at different nucleotide positions, or by the addition of various nucleotides at the 3'-end of certain transcripts by a family of terminal nucleotidylyl transferases. Developing methods to specifically and accurately detect and map these modifications is essential for understanding the molecular function(s) of individual RNA modifications and also for identifying and characterizing the proteins that may read, write, or erase them. Here, we focus on the characterization of RNA species targeted by 3' terminal uridylyl transferases (TUTases) (TUT4/7, also known as Zcchc11/6) and a 3'-5' exoribonuclease, Dis3l2, in the recently identified Dis3l2-mediated decay (DMD) pathway - a dedicated quality control pathway for a subset of ncRNAs. We describe the detailed methods used to precisely identify 3'-end modifications at nucleotide level resolution with a particular focus on the U1 and U2 small nuclear RNA (snRNA) components of the Spliceosome. These tools can be applied to investigate any RNA of interest and should facilitate studies aimed at elucidating the functional relevance of 3'-end modifications.
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Affiliation(s)
- Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Aref G Ebrahimi
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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45
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Luan S, Luo J, Liu H, Li Z. Regulation of RNA decay and cellular function by 3'-5' exoribonuclease DIS3L2. RNA Biol 2019; 16:160-165. [PMID: 30638126 DOI: 10.1080/15476286.2018.1564466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DIS3L2, in which mutations have been linked to Perlman syndrome, is an RNA-binding protein with 3'-5' exoribonuclease activity. It contains two CSD domains and one S1 domain, all of which are RNA-binding domains, and one RNB domain that is responsible for the exoribonuclease activity. The 3' polyuridine of RNA substrates can serve as a degradation signal for DIS3L2. Because DIS3L2 is predominantly localized in the cytoplasm, it can recognize, bind, and mediate the degradation of cytoplasmic uridylated RNA, including pre-microRNA, mature microRNA, mRNA, and some other non-coding RNAs. Therefore, DIS3L2 plays an important role in cytoplasmic RNA surveillance and decay. DIS3L2 is involved in multiple biological and physiological processes such as cell division, proliferation, differentiation, and apoptosis. Nonetheless, the function of DIS3L2, especially its association with cancer, remains largely unknown. We summarize here the RNA substrates degraded by DIS3L2 with its exonucleolytic activity, together with the corresponding biological functions it is implicated in. Furthermore, we discuss whether DIS3L2 can function independently of its 3'-5' exoribonuclease activity, as well as its potential tumor-suppressive or oncogenic roles during cancer progression.
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Affiliation(s)
- Siyu Luan
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
| | - Junyun Luo
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
| | - Hui Liu
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
| | - Zhaoyong Li
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
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46
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Huang T, Deng CX. Current Progresses of Exosomes as Cancer Diagnostic and Prognostic Biomarkers. Int J Biol Sci 2019; 15:1-11. [PMID: 30662342 PMCID: PMC6329932 DOI: 10.7150/ijbs.27796] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
Cancer related exosomes are nano-size membrane vesicles that play important roles in tumor microenvironment. Emerging evidence indicates that exosomes can load unique cargoes, including proteins and nucleic acids that reflect the condition of tumor. Therefore, exosomes are being used as diagnostic and prognostic biomarkers for various cancers. In this review, we describe the current progresses of cancer related exosomes, including their biogenesis, molecular contents, biological functions, sources where they are derived from, and methods for their detection. We will also discuss the current exosomal biomarkers and the utilization of them for early diagnosis and prognostics in cancer.
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Affiliation(s)
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
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47
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Saramago M, da Costa PJ, Viegas SC, Arraiano CM. The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:85-98. [PMID: 31342438 DOI: 10.1007/978-3-030-19966-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA degradation is considered a critical posttranscriptional regulatory checkpoint, maintaining the correct functioning of organisms. When a specific RNA transcript is no longer required in the cell, it is signaled for degradation through a number of highly regulated steps. Ribonucleases (or simply RNases) are key enzymes involved in the control of RNA stability. These enzymes can perform the RNA degradation alone or cooperate with other proteins in RNA degradation complexes. Important findings over the last years have shed light into eukaryotic RNA degradation by members of the RNase II/RNB family of enzymes. DIS3 enzyme belongs to this family and represents one of the catalytic subunits of the multiprotein complex exosome. This RNase has a diverse range of functions, mainly within nuclear RNA metabolism. Humans encode two other DIS3-like enzymes: DIS3L (DIS3L1) and DIS3L2. DIS3L1 also acts in association with the exosome but is strictly cytoplasmic. In contrast, DIS3L2 acts independently of the exosome and shows a distinctive preference for uridylated RNAs. These enzymes have been shown to be involved in important cellular processes, such as mitotic control, and associated with human disorders like cancer. This review shows how the impairment of function of each of these enzymes is implicated in human disease.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisboa, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisbon, Lisboa, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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48
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Schmid M, Jensen TH. The Nuclear RNA Exosome and Its Cofactors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:113-132. [PMID: 31811632 DOI: 10.1007/978-3-030-31434-7_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The RNA exosome is a highly conserved ribonuclease endowed with 3'-5' exonuclease and endonuclease activities. The multisubunit complex resides in both the nucleus and the cytoplasm, with varying compositions and activities between the two compartments. While the cytoplasmic exosome functions mostly in mRNA quality control pathways, the nuclear RNA exosome partakes in the 3'-end processing and complete decay of a wide variety of substrates, including virtually all types of noncoding (nc) RNAs. To handle these diverse tasks, the nuclear exosome engages with dedicated cofactors, some of which serve as activators by stimulating decay through oligoA addition and/or RNA helicase activities or, as adaptors, by recruiting RNA substrates through their RNA-binding capacities. Most nuclear exosome cofactors contain the essential RNA helicase Mtr4 (MTR4 in humans). However, apart from Mtr4, nuclear exosome cofactors have undergone significant evolutionary divergence. Here, we summarize biochemical and functional knowledge about the nuclear exosome and exemplify its cofactor variety by discussing the best understood model organisms-the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and human cells.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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Sieburth LE, Vincent JN. Beyond transcription factors: roles of mRNA decay in regulating gene expression in plants. F1000Res 2018; 7. [PMID: 30613385 PMCID: PMC6305221 DOI: 10.12688/f1000research.16203.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Gene expression is typically quantified as RNA abundance, which is influenced by both synthesis (transcription) and decay. Cytoplasmic decay typically initiates by deadenylation, after which decay can occur through any of three cytoplasmic decay pathways. Recent advances reveal several mechanisms by which RNA decay is regulated to control RNA abundance. mRNA can be post-transcriptionally modified, either indirectly through secondary structure or through direct modifications to the transcript itself, sometimes resulting in subsequent changes in mRNA decay rates. mRNA abundances can also be modified by tapping into pathways normally used for RNA quality control. Regulated mRNA decay can also come about through post-translational modification of decapping complex subunits. Likewise, mRNAs can undergo changes in subcellular localization (for example, the deposition of specific mRNAs into processing bodies, or P-bodies, where stabilization and destabilization occur in a transcript- and context-dependent manner). Additionally, specialized functions of mRNA decay pathways were implicated in a genome-wide mRNA decay analysis in Arabidopsis. Advances made using plants are emphasized in this review, but relevant studies from other model systems that highlight RNA decay mechanisms that may also be conserved in plants are discussed.
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Affiliation(s)
- Leslie E Sieburth
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Jessica N Vincent
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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50
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Cerezo E, Plisson-Chastang C, Henras AK, Lebaron S, Gleizes PE, O'Donohue MF, Romeo Y, Henry Y. Maturation of pre-40S particles in yeast and humans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1516. [PMID: 30406965 DOI: 10.1002/wrna.1516] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/02/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022]
Abstract
The synthesis of ribosomal subunits in eukaryotes requires the interplay of numerous maturation and assembly factors (AFs) that intervene in the insertion of ribosomal proteins within pre-ribosomal particles, the ribosomal subunit precursors, as well as in pre-ribosomal RNA (rRNA) processing and folding. Here, we review the intricate nuclear and cytoplasmic maturation steps of pre-40S particles, the precursors to the small ribosomal subunits, in both yeast and human cells, with particular emphasis on the timing and mechanisms of AF association with and dissociation from pre-40S particles and the roles of these AFs in the maturation process. We highlight the particularly complex pre-rRNA processing pathway in human cells, compared to yeast, to generate the mature 18S rRNA. We discuss the information gained from the recently published cryo-electron microscopy atomic models of yeast and human pre-40S particles, as well as the checkpoint/quality control systems that seem to operate to probe functional sites within yeast cytoplasmic pre-40S particles. This article is categorized under: RNA Processing > rRNA Processing Translation > Ribosome Biogenesis.
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Affiliation(s)
- Emilie Cerezo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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