1
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Kong L, Gong Y, Wang Y, Yuan M, Liu W, Zhou H, Meng X, Guo X, Liu Y, Zhou Y, Zhang T. Multi-omics revealed that DCP1A and SPDL1 determine embryogenesis defects in postovulatory ageing oocytes. Cell Prolif 2025; 58:e13766. [PMID: 39629683 PMCID: PMC11882766 DOI: 10.1111/cpr.13766] [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: 05/15/2024] [Revised: 09/28/2024] [Accepted: 10/14/2024] [Indexed: 03/08/2025] Open
Abstract
Growing evidence indicates that the deterioration of egg quality caused by postovulatory ageing significantly hampers embryonic development. However, the molecular mechanisms by which postovulatory ageing leads to a decline in oocyte quality have not been fully characterized. In this study, we observed an accelerated decay of maternal mRNAs through RNA-seq analyses in postovulatory-aged (PostOA) oocytes. We noted that these downregulated mRNAs should be degraded during the 2-cell stage. Proteomic analyses revealed that the degradation of maternal mRNAs is associated with the accumulation of DCP1A. The injection of exogenous Dcp1a mRNA or siRNA into MII stage oocytes proved that DCP1A could accelerate the degradation of maternal mRNAs. Additionally, we also found that SPDL1 is crucial for maintaining spindle/chromosome structure and chromosome euploidy in PostOA oocytes. Spdl1-mRNA injection remarkably recovered the meiotic defects in PostOA oocytes. Collectively, our findings provide valuable insights into the molecular mechanisms underlying postovulatory ageing.
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Affiliation(s)
- Li Kong
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yutian Gong
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yongyong Wang
- Department of Reproductive Medicine, Qingdao Municipal HospitalUniversity of Health and Rehabilitation SciencesQingdaoChina
| | - Mengjiao Yuan
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Wenxiang Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Heyang Zhou
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Xiangyue Meng
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Xinru Guo
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yongbin Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yang Zhou
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Teng Zhang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life SciencesInner Mongolia UniversityHohhotChina
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2
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Ruiz-Gutierrez N, Dupas J, Auquier E, Barbarin-Bocahu I, Gaudon-Plesse C, Saveanu C, Graille M, Le Hir H. RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex. Nucleic Acids Res 2025; 53:gkaf160. [PMID: 40071934 PMCID: PMC11897886 DOI: 10.1093/nar/gkaf160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 02/06/2025] [Accepted: 02/18/2025] [Indexed: 03/15/2025] Open
Abstract
Upf1 RNA helicase is a pivotal factor in the conserved nonsense-mediated mRNA decay (NMD) process. Upf1 is responsible for coordinating the recognition of premature termination codons (PTCs) in a translation-dependent manner and subsequently triggering mRNA degradation. Multiple factors assist Upf1 during these two consecutive steps. In Saccharomyces cerevisiae, Upf2 and Upf3 associated with Upf1 (Upf1-2/3) contribute to PTC recognition but are absent from the Upf1-decapping complex that includes Nmd4, Ebs1, Dcp1, and Dcp2. Despite their importance for NMD, the organization and dynamics of these Upf1-containing complexes remain unclear. Using recombinant proteins, here we show how distinct domains of Upf1 make direct contacts with Dcp1/Dcp2, Nmd4, and Ebs1. These proteins also bind to each other, forming an extended network of interactions within the Upf1-decapping complex. Dcp2 and Upf2 compete for the same binding site on the N-terminal CH domain of Upf1, which explains the presence of two mutually exclusive Upf1-containing complexes in cells. Our data demonstrate that Nmd4-assisted recruitment of Upf1 promotes anchoring of the decapping enzyme to NMD targets.
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Affiliation(s)
- Nadia Ruiz-Gutierrez
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 46 rue d’Ulm, 75005 Paris, France
| | - Jeanne Dupas
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 46 rue d’Ulm, 75005 Paris, France
| | - Elvire Auquier
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 46 rue d’Ulm, 75005 Paris, France
| | - Irène Barbarin-Bocahu
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Claudine Gaudon-Plesse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM, U1258, Université de Strasbourg, Illkirch, France
| | - Cosmin Saveanu
- Institut Pasteur, Université Paris Cité, Unité de Biologie des ARN des Pathogènes Fongiques, 75015 Paris, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Hervé Le Hir
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 46 rue d’Ulm, 75005 Paris, France
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3
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Chen TW, Liao HW, Noble M, Siao JY, Cheng YH, Chiang WC, Lo YT, Chang CT. Human DCP1 is crucial for mRNA decapping and possesses paralog-specific gene regulating functions. eLife 2024; 13:RP94811. [PMID: 39485278 PMCID: PMC11530239 DOI: 10.7554/elife.94811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2024] Open
Abstract
The mRNA 5'-cap structure removal by the decapping enzyme DCP2 is a critical step in gene regulation. While DCP2 is the catalytic subunit in the decapping complex, its activity is strongly enhanced by multiple factors, particularly DCP1, which is the major activator in yeast. However, the precise role of DCP1 in metazoans has yet to be fully elucidated. Moreover, in humans, the specific biological functions of the two DCP1 paralogs, DCP1a and DCP1b, remain largely unknown. To investigate the role of human DCP1, we generated cell lines that were deficient in DCP1a, DCP1b, or both to evaluate the importance of DCP1 in the decapping machinery. Our results highlight the importance of human DCP1 in decapping process and show that the EVH1 domain of DCP1 enhances the mRNA-binding affinity of DCP2. Transcriptome and metabolome analyses outline the distinct functions of DCP1a and DCP1b in human cells, regulating specific endogenous mRNA targets and biological processes. Overall, our findings provide insights into the molecular mechanism of human DCP1 in mRNA decapping and shed light on the distinct functions of its paralogs.
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Affiliation(s)
- Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2 B), National Yang Ming Chiao Tung UniversityHsinchuTaiwan
| | - Hsiao-Wei Liao
- Department of Pharmacy, National Yang Ming Chiao Tung UniversityTaipei CityTaiwan
| | - Michelle Noble
- Department of Biochemistry, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Jing-Yi Siao
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yu-Hsuan Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Wei-Chung Chiang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yi-Tzu Lo
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental BiologyTübingenGermany
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
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4
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Vukovic I, Barnada SM, Ruffin JW, Karlin J, Lokareddy RK, Cingolani G, McMahon SB. Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b. Life Sci Alliance 2024; 7:e202402938. [PMID: 39256052 PMCID: PMC11387620 DOI: 10.26508/lsa.202402938] [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: 07/11/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024] Open
Abstract
Eukaryotic gene expression is regulated at the transcriptional and post-transcriptional levels, with disruption of regulation contributing significantly to human diseases. The 5' m7G mRNA cap is a central node in post-transcriptional regulation, participating in both mRNA stabilization and translation efficiency. In mammals, DCP1a and DCP1b are paralogous cofactor proteins of the mRNA cap hydrolase DCP2. As lower eukaryotes have a single DCP1 cofactor, the functional advantages gained by this evolutionary divergence remain unclear. We report the first functional dissection of DCP1a and DCP1b, demonstrating that they are non-redundant cofactors of DCP2 with unique roles in decapping complex integrity and specificity. DCP1a is essential for decapping complex assembly and interactions between the decapping complex and mRNA cap-binding proteins. DCP1b is essential for decapping complex interactions with protein degradation and translational machinery. DCP1a and DCP1b impact the turnover of distinct mRNAs. The observation that different ontological groups of mRNA molecules are regulated by DCP1a and DCP1b, along with their non-redundant roles in decapping complex integrity, provides the first evidence that these paralogs have qualitatively distinct functions.
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Affiliation(s)
- Ivana Vukovic
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Samantha M Barnada
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Jon Karlin
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ravi Kumar Lokareddy
- Academic Joint Departments - Biochemistry & Molecular Genetic, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gino Cingolani
- Academic Joint Departments - Biochemistry & Molecular Genetic, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
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5
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Firdous Z, Kalra S, Chattopadhyay R, Bari VK. Current insight into the role of mRNA decay pathways in fungal pathogenesis. Microbiol Res 2024; 283:127671. [PMID: 38479232 DOI: 10.1016/j.micres.2024.127671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Pathogenic fungal species can cause superficial and mucosal infections, to potentially fatal systemic or invasive infections in humans. These infections are more common in immunocompromised or critically ill patients and have a significant morbidity and fatality rate. Fungal pathogens utilize several strategies to adapt the host environment resulting in efficient and comprehensive alterations in their cellular metabolism. Fungal virulence is regulated by several factors and post-transcriptional regulation mechanisms involving mRNA molecules are one of them. Post-transcriptional controls have emerged as critical regulatory mechanisms involved in the pathogenesis of fungal species. The untranslated upstream and downstream regions of the mRNA, as well as RNA-binding proteins, regulate morphogenesis and virulence by controlling mRNA degradation and stability. The limited number of available therapeutic drugs, the emergence of multidrug resistance, and high death rates associated with systemic fungal illnesses pose a serious risk to human health. Therefore, new antifungal treatments that specifically target mRNA pathway components can decrease fungal pathogenicity and when combined increase the effectiveness of currently available antifungal drugs. This review summarizes the mRNA degradation pathways and their role in fungal pathogenesis.
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Affiliation(s)
- Zulikha Firdous
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Sapna Kalra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Rituja Chattopadhyay
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India.
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6
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He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J 2023; 290:5057-5085. [PMID: 36098474 PMCID: PMC10008757 DOI: 10.1111/febs.16626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Decapping is the enzymatic removal of 5' cap structures from mRNAs in eukaryotic cells. Cap structures normally enhance mRNA translation and stability, and their excision commits an mRNA to complete 5'-3' exoribonucleolytic digestion and generally ends the physical and functional cellular presence of the mRNA. Decapping plays a pivotal role in eukaryotic cytoplasmic mRNA turnover and is a critical and highly regulated event in multiple 5'-3' mRNA decay pathways, including general 5'-3' decay, nonsense-mediated mRNA decay (NMD), AU-rich element-mediated mRNA decay, microRNA-mediated gene silencing, and targeted transcript-specific mRNA decay. In the yeast Saccharomyces cerevisiae, mRNA decapping is carried out by a single Dcp1-Dcp2 decapping enzyme in concert with the accessory activities of specific regulators commonly known as decapping activators or enhancers. These regulatory proteins include the general decapping activators Edc1, 2, and 3, Dhh1, Scd6, Pat1, and the Lsm1-7 complex, as well as the NMD-specific factors, Upf1, 2, and 3. Here, we focus on in vivo mRNA decapping regulation in yeast. We summarize recently uncovered molecular mechanisms that control selective targeting of the yeast decapping enzyme and discuss new roles for specific decapping activators in controlling decapping enzyme targeting, assembly of target-specific decapping complexes, and the monitoring of mRNA translation. Further, we discuss the kinetic contribution of mRNA decapping for overall decay of different substrate mRNAs and highlight experimental evidence pointing to the functional coordination and physical coupling between events in mRNA deadenylation, decapping, and 5'-3' exoribonucleolytic decay.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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7
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Krempl C, Lazzaretti D, Sprangers R. A structural biology view on the enzymes involved in eukaryotic mRNA turnover. Biol Chem 2023; 404:1101-1121. [PMID: 37709756 DOI: 10.1515/hsz-2023-0182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
The cellular environment contains numerous ribonucleases that are dedicated to process mRNA transcripts that have been targeted for degradation. Here, we review the three dimensional structures of the ribonuclease complexes (Pan2-Pan3, Ccr4-Not, Xrn1, exosome) and the mRNA decapping enzymes (Dcp2, DcpS) that are involved in mRNA turnover. Structures of major parts of these proteins have been experimentally determined. These enzymes and factors do not act in isolation, but are embedded in interaction networks which regulate enzyme activity and ensure that the appropriate substrates are recruited. The structural details of the higher order complexes that form can, in part, be accurately deduced from known structural data of sub-complexes. Interestingly, many of the ribonuclease and decapping enzymes have been observed in structurally different conformations. Together with experimental data, this highlights that structural changes are often important for enzyme function. We conclude that the known structural data of mRNA decay factors provide important functional insights, but that static structural data needs to be complemented with information regarding protein motions to complete the picture of how transcripts are turned over. In addition, we highlight multiple aspects that influence mRNA turnover rates, but that have not been structurally characterized so far.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Lazzaretti
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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8
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Zhao Q, Pavanello L, Bartlam M, Winkler GS. Structure and function of molecular machines involved in deadenylation-dependent 5'-3' mRNA degradation. Front Genet 2023; 14:1233842. [PMID: 37876592 PMCID: PMC10590902 DOI: 10.3389/fgene.2023.1233842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
In eukaryotic cells, the synthesis, processing, and degradation of mRNA are important processes required for the accurate execution of gene expression programmes. Fully processed cytoplasmic mRNA is characterised by the presence of a 5'cap structure and 3'poly(A) tail. These elements promote translation and prevent non-specific degradation. Degradation via the deadenylation-dependent 5'-3' degradation pathway can be induced by trans-acting factors binding the mRNA, such as RNA-binding proteins recognising sequence elements and the miRNA-induced repression complex. These factors recruit the core mRNA degradation machinery that carries out the following steps: i) shortening of the poly(A) tail by the Ccr4-Not and Pan2-Pan3 poly (A)-specific nucleases (deadenylases); ii) removal of the 5'cap structure by the Dcp1-Dcp2 decapping complex that is recruited by the Lsm1-7-Pat1 complex; and iii) degradation of the mRNA body by the 5'-3' exoribonuclease Xrn1. In this review, the biochemical function of the nucleases and accessory proteins involved in deadenylation-dependent mRNA degradation will be reviewed with a particular focus on structural aspects of the proteins and enzymes involved.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Lorenzo Pavanello
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
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9
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Krempl C, Wurm JP, Beck Erlach M, Kremer W, Sprangers R. Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR. J Mol Biol 2023; 435:167922. [PMID: 37330282 DOI: 10.1016/j.jmb.2022.167922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
Abstract
Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany.
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10
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Krempl C, Sprangers R. Assessing the applicability of 19F labeled tryptophan residues to quantify protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2023; 77:55-67. [PMID: 36639431 PMCID: PMC10149471 DOI: 10.1007/s10858-022-00411-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/20/2022] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited to study the dynamics of biomolecules in solution. Most NMR studies exploit the spins of proton, carbon and nitrogen isotopes, as these atoms are highly abundant in proteins and nucleic acids. As an alternative and complementary approach, fluorine atoms can be introduced into biomolecules at specific sites of interest. These labels can then be used as sensitive probes for biomolecular structure, dynamics or interactions. Here, we address if the replacement of tryptophan with 5-fluorotryptophan residues has an effect on the overall dynamics of proteins and if the introduced fluorine probe is able to accurately report on global exchange processes. For the four different model proteins (KIX, Dcp1, Dcp2 and DcpS) that we examined, we established that 15N CPMG relaxation dispersion or EXSY profiles are not affected by the 5-fluorotryptophan, indicating that this replacement of a proton with a fluorine has no effect on the protein motions. However, we found that the motions that the 5-fluorotryptophan reports on can be significantly faster than the backbone motions. This implies that care needs to be taken when interpreting fluorine relaxation data in terms of global protein motions. In summary, our results underscore the great potential of fluorine NMR methods, but also highlight potential pitfalls that need to be considered.
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Affiliation(s)
- Christina Krempl
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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11
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Maciej VD, Mateva N, Schwarz J, Dittmers T, Mallick M, Urlaub H, Chakrabarti S. Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA. Nucleic Acids Res 2022; 50:10665-10679. [PMID: 36130271 PMCID: PMC9561381 DOI: 10.1093/nar/gkac797] [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: 11/09/2021] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
The RNA-binding protein tristetraprolin (TTP) is a potent activator of mRNA decay, specifically for transcripts bearing AU-rich elements (AREs) in their 3′-untranslated regions. TTP functions as a mediator for mRNA decay by interacting with the decay machinery and recruiting it to the target ARE-mRNA. In this study, we report a weak, but direct interaction between TTP and the human decapping enzyme DCP2, which impacts the stability of ARE transcripts. The TTP–DCP2 interaction is unusual as it involves intrinsically disordered regions (IDRs) of both binding partners. We show that the IDR of DCP2 has a propensity for oligomerization and liquid–liquid phase separation in vitro. Binding of TTP to DCP2 leads to its partitioning into phase-separated droplets formed by DCP2, suggesting that molecular crowding might facilitate the weak interaction between the two proteins and enable assembly of a decapping-competent mRNA–protein complex on TTP-bound transcripts in cells. Our studies underline the role of weak interactions in the cellular interaction network and their contribution towards cellular functionality.
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Affiliation(s)
- Vincent D Maciej
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Nevena Mateva
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Juliane Schwarz
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, D-37077 Goettingen, Germany.,University Medical Center Goettingen, Bioanalytics, Institute for Clinical Chemistry, Robert Koch Strasse 40, D-37075 Goettingen, Germany
| | - Theresa Dittmers
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Megha Mallick
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, D-37077 Goettingen, Germany.,University Medical Center Goettingen, Bioanalytics, Institute for Clinical Chemistry, Robert Koch Strasse 40, D-37075 Goettingen, Germany
| | - Sutapa Chakrabarti
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
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12
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Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 2022; 185:2035-2056.e33. [PMID: 35688132 DOI: 10.1016/j.cell.2022.05.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022]
Abstract
Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. αS associates with multiple decapping proteins in close proximity on the Edc4 scaffold. As αS pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA decay kinetics within PD-relevant pathways are correspondingly disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
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Affiliation(s)
- Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sumaiya Nazeen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Xiou H Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zoe Sheinkopf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shubhangi Sathyakumar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xin Jiang
- Yumanity Therapeutics, Boston, MA 02135, USA
| | - Xianjun Dong
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Genomics and Bioinformatics Hub, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics and Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON M5T 3M7, Canada
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | | | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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13
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He F, Wu C, Jacobson A. Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes. eLife 2022; 11:74410. [PMID: 35604319 PMCID: PMC9170289 DOI: 10.7554/elife.74410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 05/22/2022] [Indexed: 11/13/2022] Open
Abstract
A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5' to 3' decay, but the molecular mechanisms controlling mRNA selectivity by the enzyme remain elusive. Through extensive genetic analyses we reveal that Dcp2 C-terminal domain cis-regulatory elements control decapping enzyme target specificity by orchestrating formation of distinct decapping complexes. Two Upf1-binding motifs direct the decapping enzyme to NMD substrates, a single Edc3-binding motif targets both Edc3 and Dhh1 substrates, and Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Scd6 and Xrn1 also have specific binding sites on Dcp2, allowing them to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, Scd6, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its substrate specificity and enzymatic activation.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Chan Wu
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, United States
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14
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Peters JK, Tibble RW, Warminski M, Jemielity J, Gross JD. Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis. Structure 2022; 30:721-732.e4. [PMID: 35290794 PMCID: PMC9081138 DOI: 10.1016/j.str.2022.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/30/2021] [Accepted: 02/16/2022] [Indexed: 01/06/2023]
Abstract
Poxviruses encode decapping enzymes that remove the protective 5' cap from both host and viral mRNAs to commit transcripts for decay by the cellular exonuclease Xrn1. Decapping by these enzymes is critical for poxvirus pathogenicity by means of simultaneously suppressing host protein synthesis and limiting the accumulation of viral double-stranded RNA (dsRNA), a trigger for antiviral responses. Here we present a high-resolution structural view of the vaccinia virus decapping enzyme D9. This Nudix enzyme contains a domain organization different from other decapping enzymes in which a three-helix bundle is inserted into the catalytic Nudix domain. The 5' mRNA cap is positioned in a bipartite active site at the interface of the two domains. Specificity for the methylated guanosine cap is achieved by stacking between conserved aromatic residues in a manner similar to that observed in canonical cap-binding proteins VP39, eIF4E, and CBP20, and distinct from eukaryotic decapping enzyme Dcp2.
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Affiliation(s)
- Jessica K Peters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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15
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Abstract
The 5'-terminal cap is a fundamental determinant of eukaryotic gene expression which facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation. Enzyme-directed hydrolysis of the cap (decapping) decisively affects mRNA expression and turnover, and is a heavily regulated event. Following the identification of the decapping holoenzyme (Dcp1/2) over two decades ago, numerous studies revealed the complexity of decapping regulation across species and cell types. A conserved set of Dcp1/2-associated proteins, implicated in decapping activation and molecular scaffolding, were identified through genetic and molecular interaction studies, and yet their exact mechanisms of action are only emerging. In this review, we discuss the prevailing models on the roles and assembly of decapping co-factors, with considerations of conservation across species and comparison across physiological contexts. We next discuss the functional convergences of decapping machineries with other RNA-protein complexes in cytoplasmic P bodies and compare current views on their impact on mRNA stability and translation. Lastly, we review the current models of decapping activation and highlight important gaps in our current understanding.
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Affiliation(s)
- Elva Vidya
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Thomas F. Duchaine
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
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16
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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: 0.3] [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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17
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Schiaffini M, Chicois C, Pouclet A, Chartier T, Ubrig E, Gobert A, Zuber H, Mutterer J, Chicher J, Kuhn L, Hammann P, Gagliardi D, Garcia D. A NYN domain protein directly interacts with DECAPPING1 and is required for phyllotactic pattern. PLANT PHYSIOLOGY 2022; 188:1174-1188. [PMID: 34791434 PMCID: PMC8825452 DOI: 10.1093/plphys/kiab529] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 06/01/2023]
Abstract
In eukaryotes, general mRNA decay requires the decapping complex. The activity of this complex depends on its catalytic subunit, DECAPPING2 (DCP2), and its interaction with decapping enhancers, including its main partner DECAPPING1 (DCP1). Here, we report that in Arabidopsis thaliana, DCP1 also interacts with a NYN domain endoribonuclease, hence named DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1). Interestingly, we found DNE1 predominantly associated with DCP1, but not with DCP2, and reciprocally, suggesting the existence of two distinct protein complexes. We also showed that the catalytic residues of DNE1 are required to repress the expression of mRNAs in planta upon transient expression. The overexpression of DNE1 in transgenic lines led to growth defects and a similar gene deregulation signature than inactivation of the decapping complex. Finally, the combination of dne1 and dcp2 mutations revealed a functional redundancy between DNE1 and DCP2 in controlling phyllotactic pattern formation. Our work identifies DNE1, a hitherto unknown DCP1 protein partner highly conserved in the plant kingdom and identifies its importance for developmental robustness.
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Affiliation(s)
- Marlene Schiaffini
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Clara Chicois
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Aude Pouclet
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Tiphaine Chartier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jérôme Mutterer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Damien Garcia
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
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18
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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19
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Ibayashi M, Aizawa R, Tsukamoto S. mRNA decapping factor Dcp1a is essential for embryonic growth in mice. Biochem Biophys Res Commun 2021; 555:128-133. [PMID: 33813271 DOI: 10.1016/j.bbrc.2021.03.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022]
Abstract
mRNA decapping is a critical step in posttranscriptional regulation of gene expression in eukaryotes. Although Dcp1a is a well characterized and widely conserved mRNA decapping factor, little is known about its physiological function. To extend our understanding of Dcp1a function in vivo, we employed a transgenic rescue strategy to produce Dcp1a-deficient mice using the CRISPR/Cas9 system. This approach arrowed us to generate heterozygous Dcp1a mice and define the phenotype of Dcp1a-deficient embryos. We found that expression of Dcp1a protein, which is detectable in most mouse tissues, was developmentally regulated through embryonic growth, and that depletion of the Dcp1a gene resulted in embryonic lethality around embryonic day 10.5 (E10.5) concomitant with massive growth retardation and cardiac developmental defects. Moreover, the embryonic lethality was fully rescued by transgenic expression of exogenous human Dcp1a. Together, our results suggest that Dcp1a is required for embryonic growth.
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Affiliation(s)
- Megumi Ibayashi
- Laboratory of Animal and Genome Sciences Section, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Chiba, 263-8555, Japan
| | - Ryutaro Aizawa
- Laboratory of Animal and Genome Sciences Section, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Chiba, 263-8555, Japan
| | - Satoshi Tsukamoto
- Laboratory of Animal and Genome Sciences Section, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Chiba, 263-8555, Japan.
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20
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Tibble RW, Depaix A, Kowalska J, Jemielity J, Gross JD. Biomolecular condensates amplify mRNA decapping by biasing enzyme conformation. Nat Chem Biol 2021; 17:615-623. [PMID: 33767388 PMCID: PMC8476181 DOI: 10.1038/s41589-021-00774-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Cells organize biochemical processes into biological condensates. P-bodies are cytoplasmic condensates that are enriched in enzymes important for mRNA degradation and have been identified as sites of both storage and decay. How these opposing outcomes can be achieved in condensates remains unresolved. mRNA decapping immediately precedes degradation, and the Dcp1/Dcp2 decapping complex is enriched in P-bodies. Here, we show that Dcp1/Dcp2 activity is modulated in condensates and depends on the interactions promoting phase separation. We find that Dcp1/Dcp2 phase separation stabilizes an inactive conformation in Dcp2 to inhibit decapping. The activator Edc3 causes a conformational change in Dcp2 and rewires the protein-protein interactions to stimulate decapping in condensates. Disruption of the inactive conformation dysregulates decapping in condensates. Our results indicate that the regulation of enzymatic activity in condensates relies on a coupling across length scales ranging from microns to ångstroms. We propose that this regulatory mechanism may control the functional state of P-bodies and related phase-separated compartments.
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Affiliation(s)
- Ryan W Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Anaïs Depaix
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
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21
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Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chem Biol 2021; 28:463-474.e7. [PMID: 33357462 PMCID: PMC8052284 DOI: 10.1016/j.chembiol.2020.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/29/2020] [Accepted: 12/04/2020] [Indexed: 01/23/2023]
Abstract
DCP2 is an RNA-decapping enzyme that controls the stability of human RNAs that encode factors functioning in transcription and the immune response. While >1,800 human DCP2 substrates have been identified, compensatory expression changes secondary to genetic ablation of DCP2 have complicated a complete mapping of its regulome. Cell-permeable, selective chemical inhibitors of DCP2 could provide a powerful tool to study DCP2 specificity. Here, we report phage display selection of CP21, a bicyclic peptide ligand to DCP2. CP21 has high affinity and selectivity for DCP2 and inhibits DCP2 decapping activity toward selected RNA substrates in human cells. CP21 increases formation of P-bodies, liquid condensates enriched in intermediates of RNA decay, in a manner that resembles the deletion or mutation of DCP2. We used CP21 to identify 76 previously unreported DCP2 substrates. This work demonstrates that DCP2 inhibition can complement genetic approaches to study RNA decay.
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Affiliation(s)
- Yang Luo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jeremy A Schofield
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Tanja Hann
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06520, USA
| | - Matthew D Simon
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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22
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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: 2.3] [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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23
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Charenton C, Gaudon-Plesse C, Back R, Ulryck N, Cosson L, Séraphin B, Graille M. Pby1 is a direct partner of the Dcp2 decapping enzyme. Nucleic Acids Res 2020; 48:6353-6366. [PMID: 32396195 PMCID: PMC7293026 DOI: 10.1093/nar/gkaa337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Most eukaryotic mRNAs harbor a characteristic 5′ m7GpppN cap that promotes pre-mRNA splicing, mRNA nucleocytoplasmic transport and translation while also protecting mRNAs from exonucleolytic attacks. mRNA caps are eliminated by Dcp2 during mRNA decay, allowing 5′-3′ exonucleases to degrade mRNA bodies. However, the Dcp2 decapping enzyme is poorly active on its own and requires binding to stable or transient protein partners to sever the cap of target mRNAs. Here, we analyse the role of one of these partners, the yeast Pby1 factor, which is known to co-localize into P-bodies together with decapping factors. We report that Pby1 uses its C-terminal domain to directly bind to the decapping enzyme. We solved the structure of this Pby1 domain alone and bound to the Dcp1–Dcp2–Edc3 decapping complex. Structure-based mutant analyses reveal that Pby1 binding to the decapping enzyme is required for its recruitment into P-bodies. Moreover, Pby1 binding to the decapping enzyme stimulates growth in conditions in which decapping activation is compromised. Our results point towards a direct connection of Pby1 with decapping and P-body formation, both stemming from its interaction with the Dcp1–Dcp2 holoenzyme.
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Affiliation(s)
- Clément Charenton
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Claudine Gaudon-Plesse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Régis Back
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Loreline Cosson
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
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24
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Yu X, Li B, Jang GJ, Jiang S, Jiang D, Jang JC, Wu SH, Shan L, He P. Orchestration of Processing Body Dynamics and mRNA Decay in Arabidopsis Immunity. Cell Rep 2020; 28:2194-2205.e6. [PMID: 31433992 DOI: 10.1016/j.celrep.2019.07.054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 06/02/2019] [Accepted: 07/16/2019] [Indexed: 01/14/2023] Open
Abstract
Proper transcriptome reprogramming is critical for hosts to launch an effective defense response upon pathogen attack. How immune-related genes are regulated at the posttranscriptional level remains elusive. We demonstrate here that P-bodies, the non-membranous cytoplasmic ribonucleoprotein foci related to 5'-to-3' mRNA decay, are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns (MAMPs). The DCP1-DCP2 mRNA decapping complex, a hallmark of P-bodies, positively regulates plant MAMP-triggered responses and immunity against pathogenic bacteria. MAMP-activated MAP kinases directly phosphorylate DCP1 at the serine237 residue, which further stimulates its interaction with XRN4, an exonuclease executing 5'-to-3' degradation of decapped mRNA. Consequently, MAMP treatment potentiates DCP1-dependent mRNA decay on a specific group of MAMP-downregulated genes. Thus, the conserved 5'-to-3' mRNA decay elicited by the MAMP-activated MAP kinase cascade is an integral part of plant immunity. This mechanism ensures a rapid posttranscriptional downregulation of certain immune-related genes that may otherwise negatively impact immunity.
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Affiliation(s)
- Xiao Yu
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Bo Li
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Geng-Jen Jang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shan Jiang
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Daohong Jiang
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Libo Shan
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Ping He
- Department of Biochemistry and Biophysics and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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25
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Mishra R, Kunar R, Mandal L, Alone DP, Chandrasekharan S, Tiwari AK, Tapadia MG, Mukherjee A, Roy JK. A Forward Genetic Approach to Mapping a P-Element Second Site Mutation Identifies DCP2 as a Novel Tumor Suppressor in Drosophila melanogaster. G3 (BETHESDA, MD.) 2020; 10:2601-2618. [PMID: 32591349 PMCID: PMC7407449 DOI: 10.1534/g3.120.401501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/23/2020] [Indexed: 11/18/2022]
Abstract
The use of transposons to create mutations has been the cornerstone of Drosophila genetics in the past few decades. Second-site mutations caused by transpositions are often devoid of transposons and thereby affect subsequent analyses. In a P-element mutagenesis screen, a second site mutation was identified on chromosome 3, wherein the homozygous mutants exhibit classic hallmarks of tumor suppressor mutants, including brain tumor and lethality; hence the mutant line was initially named as lethal (3) tumorous brain [l(3)tb]. Classical genetic approaches relying on meiotic recombination and subsequent complementation with chromosomal deletions and gene mutations mapped the mutation to CG6169, the mRNA decapping protein 2 (DCP2), on the left arm of the third chromosome (3L). Thus the mutation was renamed as DCP2l(3)tb Fine mapping of the mutation further identified the presence of a Gypsy-LTR like sequence in the 5'UTR coding region of DCP2, along with the expansion of the adjacent upstream intergenic AT-rich sequence. The mutant phenotypes are rescued by the introduction of a functional copy of DCP2 in the mutant background, thereby establishing the causal role of the mutation and providing a genetic validation of the allelism. With the increasing repertoire of genes being associated with tumor biology, this is the first instance of mRNA decapping protein being implicated in Drosophila tumorigenesis. Our findings, therefore, imply a plausible role for the mRNA degradation pathway in tumorigenesis and identify DCP2 as a potential candidate for future explorations of cell cycle regulatory mechanisms.
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Affiliation(s)
- Rakesh Mishra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rohit Kunar
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Lolitika Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Manauli 140306, India
| | - Debasmita Pankaj Alone
- School of Biological Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, 752020 Khurda
| | - Shanti Chandrasekharan
- Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, Delhi, 110012 India
| | - Anand Krishna Tiwari
- School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Koba, Gandhinagar 382 007, India
| | - Madhu Gwaldas Tapadia
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Jagat Kumar Roy
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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26
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Xing W, Muhlrad D, Parker R, Rosen MK. A quantitative inventory of yeast P body proteins reveals principles of composition and specificity. eLife 2020; 9:56525. [PMID: 32553117 PMCID: PMC7373430 DOI: 10.7554/elife.56525] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/18/2020] [Indexed: 01/01/2023] Open
Abstract
P bodies are archetypal biomolecular condensates that concentrate proteins and RNA without a surrounding membrane. While dozens of P body proteins are known, the concentrations of components in the compartment have not been measured. We used live cell imaging to generate a quantitative inventory of the major proteins in yeast P bodies. Only seven proteins are highly concentrated in P bodies (5.1–15µM); the 24 others examined are appreciably lower (most ≤ 2.6µM). P body concentration correlates inversely with cytoplasmic exchange rate. Sequence elements driving Dcp2 concentration into P bodies are distributed across the protein and act synergistically. Our data indicate that P bodies, and probably other condensates, are compositionally simpler than suggested by proteomic analyses, with implications for specificity, reconstitution and evolution.
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Affiliation(s)
- Wenmin Xing
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
| | - Denise Muhlrad
- Department of Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, United States
| | - Roy Parker
- Department of Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, United States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
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27
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Ray A, Frick DN. Fluorescent probe displacement assays reveal unique nucleic acid binding properties of human nudix enzymes. Anal Biochem 2020; 595:113622. [PMID: 32059949 PMCID: PMC7087442 DOI: 10.1016/j.ab.2020.113622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/10/2020] [Indexed: 12/21/2022]
Abstract
Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds. The substrates for a subset of Nudix enzymes are all nucleotides linked to RNA, like the m7G mRNA caps and the more recently discovered NAD(H) RNA caps. However, the RNA affinity and nucleic acid specificity of Nudix proteins has not yet been explored in depth. In this study we designed new fluorescence-based assays to examine the interaction of purified recombinant E. coli NudC and human Nudt1 (aka MTH1) Nudt3, Nudt12, Nudt16, and Nudt20 (aka Dcp2). All Nudix proteins except Nudt1 and Nudt12 bound both RNA and DNA stoichiometrically with high affinity (dissociation constants in the nanomolar range) and no clear sequence specificity. In stark contrast, Nudt12 binds RNA but not similar DNA oligonucleotides. Nudt12 also bound RNAs with 5' NAD+ caps more tightly than those with NADH or m7G cap. NudC was similarly selective against m7G caps but did not differentiate between NAD+ and NADH capped RNA. Nudt3, Nudt16, and Nudt20 bound m7G capped RNA more tightly than RNA with NADH caps.
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Affiliation(s)
- Atreyei Ray
- Department of Chemistry & Biochemistry, The University of Wisconsin- Milwaukee, Milwaukee, WI, 53217, USA
| | - David N Frick
- Department of Chemistry & Biochemistry, The University of Wisconsin- Milwaukee, Milwaukee, WI, 53217, USA.
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28
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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29
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Wurm JP, Sprangers R. Dcp2: an mRNA decapping enzyme that adopts many different shapes and forms. Curr Opin Struct Biol 2019; 59:115-123. [PMID: 31473440 PMCID: PMC6900585 DOI: 10.1016/j.sbi.2019.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/22/2019] [Accepted: 07/30/2019] [Indexed: 02/01/2023]
Abstract
Structure of the active state of the Dcp2 decapping enzyme. Insights into the structural states that are sampled in solution. Details regarding the intermolecular network that Dcp2 is embedded in.
Eukaryotic mRNAs contain a 5’ cap structure that protects the transcript against rapid exonucleolytic degradation. The regulation of cellular mRNA levels therefore depends on a precise control of the mRNA decapping pathways. The major mRNA decapping enzyme in eukaryotic cells is Dcp2. It is regulated by interactions with several activators, including Dcp1, Edc1, and Edc3, as well as by an autoinhibition mechanism. The structural and mechanistical characterization of Dcp2 complexes has long been impeded by the high flexibility and dynamic nature of the enzyme. Here we review recent insights into the catalytically active conformation of the mRNA decapping complex, the mode of action of decapping activators and the large interactions network that Dcp2 is embedded in.
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Affiliation(s)
- Jan Philip Wurm
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany.
| | - Remco Sprangers
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany.
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30
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Wang Q, Zhang D, Guan Z, Li D, Pei K, Liu J, Zou T, Yin P. DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli. Nucleic Acids Res 2019; 46:6880-6892. [PMID: 29931175 PMCID: PMC6061791 DOI: 10.1093/nar/gky528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/28/2018] [Indexed: 11/30/2022] Open
Abstract
mRNA decay is an important strategy by which bacteria can rapidly adapt to their ever-changing surroundings. The 5′-terminus state of mRNA determines the velocity of decay of many types of RNA. In Escherichia coli, RNA pyrophosphohydrolase (RppH) is responsible for the removal of the 5′-terminal triphosphate from hundreds of mRNAs and triggers its rapid degradation by ribonucleases. A diaminopimelate epimerase, DapF, can directly interact with RppH and stimulate its hydrolysis activity in vivo and in vitro. However, the molecular mechanism remains to be elucidated. Here, we determined the complex structure of DapF–RppH as a heterotetramer in a 2:2 molar ratio. DapF-bound RppH exhibits an RNA-favorable conformation similar to the RNA-bound state, suggesting that association with DapF promotes and stabilizes RppH in a conformation that facilitates substrate RNA binding and thus stimulates the activity of RppH. To our knowledge, this is the first published structure of an RNA–pyrophosphohydrolysis complex in bacteria. Our study provides a framework for further investigation of the potential regulators involved in the RNA–pyrophosphohydrolysis process in prokaryotes.
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Affiliation(s)
- Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Pei
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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31
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Paquette DR, Tibble RW, Daifuku TS, Gross JD. Control of mRNA decapping by autoinhibition. Nucleic Acids Res 2019; 46:6318-6329. [PMID: 29618050 PMCID: PMC6158755 DOI: 10.1093/nar/gky233] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
5′ mediated cytoplasmic RNA decay is a conserved cellular process in eukaryotes. While the functions of the structured core domains in this pathway are well-studied, the role of abundant intrinsically disordered regions (IDRs) is lacking. Here we reconstitute the Dcp1:Dcp2 complex containing a portion of the disordered C-terminus and show its activity is autoinhibited by linear interaction motifs. Enhancers of decapping (Edc) 1 and 3 cooperate to activate decapping by different mechanisms: Edc3 alleviates autoinhibition by binding IDRs and destabilizing an inactive form of the enzyme, whereas Edc1 stabilizes the transition state for catalysis. Both activators are required to fully stimulate an autoinhibited Dcp1:Dcp2 as Edc1 alone cannot overcome the decrease in activity attributed to the C-terminal extension. Our data provide a mechanistic framework for combinatorial control of decapping by protein cofactors, a principle that is likely conserved in multiple 5′ mRNA decay pathways.
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Affiliation(s)
- David R Paquette
- Integrative Program in Quantitative Biology, Graduate Group in Biophysics, University of California, San Francisco, CA 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94158, USA
| | - Tristan S Daifuku
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - John D Gross
- Integrative Program in Quantitative Biology, Graduate Group in Biophysics, University of California, San Francisco, CA 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94158, USA
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32
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He F, Celik A, Wu C, Jacobson A. General decapping activators target different subsets of inefficiently translated mRNAs. eLife 2018; 7:34409. [PMID: 30520724 PMCID: PMC6300357 DOI: 10.7554/elife.34409] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/04/2018] [Indexed: 12/18/2022] Open
Abstract
The Dcp1-Dcp2 decapping enzyme and the decapping activators Pat1, Dhh1, and Lsm1 regulate mRNA decapping, but their mechanistic integration is unknown. We analyzed the gene expression consequences of deleting PAT1, LSM1, or DHH1, or the DCP2 C-terminal domain, and found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap, are generally translated inefficiently, and, as expected, are targeted to decapping-dependent decay. Our results define the roles of Pat1, Lsm1, and Dhh1 in decapping of general mRNAs and suggest that these factors may monitor mRNA translation and target unique features of individual mRNAs.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Massachusetts, United States
| | - Alper Celik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Massachusetts, United States
| | - Chan Wu
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Massachusetts, United States
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Massachusetts, United States
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33
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Mugridge JS, Coller J, Gross JD. Structural and molecular mechanisms for the control of eukaryotic 5'-3' mRNA decay. Nat Struct Mol Biol 2018; 25:1077-1085. [PMID: 30518847 DOI: 10.1038/s41594-018-0164-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022]
Abstract
5'-3' RNA decay pathways are critical for quality control and regulation of gene expression. Structural and biochemical studies have provided insights into the key nucleases that carry out deadenylation, decapping, and exonucleolysis during 5'-3' decay, but detailed understanding of how these activities are coordinated is only beginning to emerge. Here we review recent mechanistic insights into the control of 5'-3' RNA decay, including coupling between translation and decay, coordination between the complexes and activities that process 5' and 3' RNA termini, conformational control of enzymatic activity, liquid phase separation, and RNA modifications.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jeff Coller
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
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34
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Charenton C, Graille M. mRNA decapping: finding the right structures. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0164. [PMID: 30397101 DOI: 10.1098/rstb.2018.0164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
In eukaryotes, the elimination of the m7GpppN mRNA cap, a process known as decapping, is a critical, largely irreversible and highly regulated step of mRNA decay that withdraws the targeted mRNAs from the pool of translatable templates. The decapping reaction is catalysed by a multi-protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor, a holoenzyme that is poorly active on its own and needs several accessory proteins (Lsm1-7 complex, Pat1, Edc1-2, Edc3 and/or EDC4) to be fully efficient. Here, we discuss the several crystal structures of Dcp2 domains bound to various partners (proteins or small molecules) determined in the last couple of years that have considerably improved our current understanding of how Dcp2, assisted by its various activators, is recruited to its mRNA targets and adopts its active conformation upon substrate recognition. We also describe how, over the years, elegant integrative structural biology approaches combined to biochemistry and genetics led to the identification of the correct structure of the active Dcp1-Dcp2 holoenzyme among the many available conformations trapped by X-ray crystallography.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Clément Charenton
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
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35
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Valdés-Flores J, López-Rosas I, López-Camarillo C, Ramírez-Moreno E, Ospina-Villa JD, Marchat LA. Life and Death of mRNA Molecules in Entamoeba histolytica. Front Cell Infect Microbiol 2018; 8:199. [PMID: 29971219 PMCID: PMC6018208 DOI: 10.3389/fcimb.2018.00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/28/2018] [Indexed: 02/05/2023] Open
Abstract
In eukaryotic cells, the life cycle of mRNA molecules is modulated in response to environmental signals and cell-cell communication in order to support cellular homeostasis. Capping, splicing and polyadenylation in the nucleus lead to the formation of transcripts that are suitable for translation in cytoplasm, until mRNA decay occurs in P-bodies. Although pre-mRNA processing and degradation mechanisms have usually been studied separately, they occur simultaneously and in a coordinated manner through protein-protein interactions, maintaining the integrity of gene expression. In the past few years, the availability of the genome sequence of Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, coupled to the development of the so-called "omics" technologies provided new opportunities for the study of mRNA processing and turnover in this pathogen. Here, we review the current knowledge about the molecular basis for splicing, 3' end formation and mRNA degradation in amoeba, which suggest the conservation of events related to mRNA life throughout evolution. We also present the functional characterization of some key proteins and describe some interactions that indicate the relevance of cooperative regulatory events for gene expression in this human parasite.
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Affiliation(s)
- Jesús Valdés-Flores
- Departamento de Bioquímica, CINVESTAV, Ciudad de Mexico, Mexico City, Mexico
| | - Itzel López-Rosas
- CONACyT Research Fellow – Colegio de Postgraduados Campus Campeche, Campeche, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México Ciudad de Mexico, Mexico City, Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Juan D. Ospina-Villa
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Laurence A. Marchat
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
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36
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Falcone C, Mazzoni C. RNA stability and metabolism in regulated cell death, aging and diseases. FEMS Yeast Res 2018; 18:4978431. [DOI: 10.1093/femsyr/foy050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Claudio Falcone
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
| | - Cristina Mazzoni
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
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IL-17-receptor-associated adaptor Act1 directly stabilizes mRNAs to mediate IL-17 inflammatory signaling. Nat Immunol 2018; 19:354-365. [PMID: 29563620 PMCID: PMC6082628 DOI: 10.1038/s41590-018-0071-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 02/16/2018] [Indexed: 12/15/2022]
Abstract
Mechanisms that degrade inflammatory mRNAs are well-known, however
stabilizing mechanisms are poorly understood. Here we show that Act1, an
interleukin-17 (IL-17) receptor complex adaptor, binds and stabilizes mRNAs
encoding key inflammatory proteins. The Act1 SEFIR domain binds a stem-loop
structure, SBE (SEFIR-binding element), in the inflammatory chemokine
Cxcl1 3’ UTR. mRNA-bound Act1 directs formation of
three compartmentally-distinct protein-RNA complexes (RNPs) that regulate three
disparate events in inflammatory mRNA metabolism: preventing mRNA decay in the
nucleus, inhibiting mRNA decapping in P-bodies, and promoting translation. SBE
RNA aptamers reduced IL-17-mediated mRNA stabilization in
vitro, IL-17-induced skin inflammation and airway inflammation in a
mouse asthma model, providing a therapeutic strategy for autoimmune diseases.
These results reveal a network in which Act1 assembles RNPs on the 3’
UTRs of select mRNAs to control receptor-mediated mRNA stabilization and
translation during inflammation.
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38
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Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross JD. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun 2018; 9:1152. [PMID: 29559651 PMCID: PMC5861098 DOI: 10.1038/s41467-018-03536-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/22/2018] [Indexed: 11/17/2022] Open
Abstract
The conserved decapping enzyme Dcp2 recognizes and removes the 5′ eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis. The decapping enzyme Dcp2 removes the 5′ eukaryotic cap from mRNA transcripts and acts in concert with its essential activator Dcp1 and various coactivators. Here the authors present the structure of the fully-activated mRNA decapping complex, which reveals how Dcp2 recognizes the cap substrate and coactivators Edc1 and Edc3 activate catalysis.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.,Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA.
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Quintas A, Pérez-Núñez D, Sánchez EG, Nogal ML, Hentze MW, Castelló A, Revilla Y. Characterization of the African Swine Fever Virus Decapping Enzyme during Infection. J Virol 2017; 91:e00990-17. [PMID: 29021398 PMCID: PMC5709586 DOI: 10.1128/jvi.00990-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/03/2017] [Indexed: 01/13/2023] Open
Abstract
African swine fever virus (ASFV) infection is characterized by a progressive decrease in cellular protein synthesis with a concomitant increase in viral protein synthesis, though the mechanism by which the virus achieves this is still unknown. Decrease of cellular mRNA is observed during ASFV infection, suggesting that inhibition of cellular proteins is due to an active mRNA degradation process. ASFV carries a gene (Ba71V D250R/Malawi g5R) that encodes a decapping protein (ASFV-DP) that has a Nudix hydrolase motif and decapping activity in vitro Here, we show that ASFV-DP was expressed from early times and accumulated throughout the infection with a subcellular localization typical of the endoplasmic reticulum, colocalizing with the cap structure and interacting with the ribosomal protein L23a. ASFV-DP was capable of interaction with poly(A) RNA in cultured cells, primarily mediated by the N-terminal region of the protein. ASFV-DP also interacted with viral and cellular RNAs in the context of infection, and its overexpression in infected cells resulted in decreased levels of both types of transcripts. This study points to ASFV-DP as a viral decapping enzyme involved in both the degradation of cellular mRNA and the regulation of viral transcripts.IMPORTANCE Virulent ASFV strains cause a highly infectious and lethal disease in domestic pigs for which there is no vaccine. Since 2007, an outbreak in the Caucasus region has spread to Russia, jeopardizing the European pig population and making it essential to deepen knowledge about the virus. Here, we demonstrate that ASFV-DP is a novel RNA-binding protein implicated in the regulation of mRNA metabolism during infection, making it a good target for vaccine development.
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Affiliation(s)
- Ana Quintas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Pérez-Núñez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elena G Sánchez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria L Nogal
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Alfredo Castelló
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Yolanda Revilla
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Madrid, Spain
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40
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Adachi T, Nagahama K, Izumi S. The C. elegans mRNA decapping enzyme shapes morphology of cilia. Biochem Biophys Res Commun 2017; 493:382-387. [PMID: 28887031 DOI: 10.1016/j.bbrc.2017.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 10/18/2022]
Abstract
Cilia and flagella are evolutionarily conserved organelles that protrude from cell surfaces. Most cilia and flagella are single rod-shaped but some cilia show a variety of shapes. For example, human airway epithelial cells are multiciliated, flagella of crayfish spermatozoon are star-like shaped, and fruit fly spermatozoon extends long flagella. In Caenorhabditis elegans, cilia display morphological diversity of shapes (single, dual rod-type and wing-like and highly-branched shapes). Here we show that DCAP-1 and DCAP-2, which are the homologues of mammalian DCP1 and DCP2 mRNA decapping enzymes, respectively, are involved in formation of dual rod-type and wing-like shaped cilia in C. elegans. mRNA decapping enzyme catalyzes hydrolysis of 5' cap structure of mRNA, which leads to degradation of mRNA. Rescue experiments showed that DCAP-2 acts not in glial cells surrounding cilia but in neurons. This is the first evidence to demonstrate that mRNA decapping is involved in ciliary shape formation.
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Affiliation(s)
- Takeshi Adachi
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka City, Kanagawa 259-1293, Japan.
| | - Keigo Nagahama
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka City, Kanagawa 259-1293, Japan
| | - Susumu Izumi
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka City, Kanagawa 259-1293, Japan
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41
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Cheng J, Maier KC, Avsec Ž, Rus P, Gagneur J. Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. RNA (NEW YORK, N.Y.) 2017; 23:1648-1659. [PMID: 28802259 PMCID: PMC5648033 DOI: 10.1261/rna.062224.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/31/2017] [Indexed: 05/09/2023]
Abstract
The stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model for Saccharomyces cerevisiae based on functional mRNA sequence features that explains 59% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3' UTR motif, ATATTC, which we functionally validated. Codon usage proves to be the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3' UTR motifs or upstream AUGs. Analyzing mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5'-to-3' exonuclease Xrn1, the nonsense-mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.
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Affiliation(s)
- Jun Cheng
- Department of Informatics, Technical University of Munich, 85748 Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Žiga Avsec
- Department of Informatics, Technical University of Munich, 85748 Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Petra Rus
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, 85748 Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 München, Germany
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42
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A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast. Proc Natl Acad Sci U S A 2017; 114:E9493-E9501. [PMID: 29078363 DOI: 10.1073/pnas.1711680114] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Pat1 protein is a central player of eukaryotic mRNA decay that has also been implicated in translational control. It is commonly considered a central platform responsible for the recruitment of several RNA decay factors. We demonstrate here that a yeast-specific C-terminal region from Pat1 interacts with several short motifs, named helical leucine-rich motifs (HLMs), spread in the long C-terminal region of yeast Dcp2 decapping enzyme. Structures of Pat1-HLM complexes reveal the basis for HLM recognition by Pat1. We also identify a HLM present in yeast Xrn1, the main 5'-3' exonuclease involved in mRNA decay. We show further that the ability of yeast Pat1 to bind HLMs is required for efficient growth and normal mRNA decay. Overall, our analyses indicate that yeast Pat1 uses a single binding surface to successively recruit several mRNA decay factors and show that interaction between those factors is highly polymorphic between species.
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43
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Tenekeci U, Poppe M, Beuerlein K, Buro C, Müller H, Weiser H, Kettner-Buhrow D, Porada K, Newel D, Xu M, Chen ZJ, Busch J, Schmitz ML, Kracht M. K63-Ubiquitylation and TRAF6 Pathways Regulate Mammalian P-Body Formation and mRNA Decapping. Mol Cell 2017; 62:943-957. [PMID: 27315556 DOI: 10.1016/j.molcel.2016.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 01/22/2016] [Accepted: 05/13/2016] [Indexed: 01/09/2023]
Abstract
Signals and posttranslational modifications regulating the decapping step in mRNA degradation pathways are poorly defined. In this study we reveal the importance of K63-linked ubiquitylation for the assembly of decapping factors, P-body formation, and constitutive decay of instable mRNAs encoding mediators of inflammation by various experimental approaches. K63-branched ubiquitin chains also regulate IL-1-inducible phosphorylation of the P-body component DCP1a. The E3 ligase TRAF6 binds to DCP1a and indirectly regulates DCP1a phosphorylation, expression of decapping factors, and gene-specific mRNA decay. Mutation of six C-terminal lysines of DCP1a suppresses decapping activity and impairs the interaction with the mRNA decay factors DCP2, EDC4, and XRN1, but not EDC3, thus remodeling P-body architecture. The usage of ubiquitin chains for the proper assembly and function of the decay-competent mammalian decapping complex suggests an additional layer of control to allow a coordinated function of decapping activities and mRNA metabolism in higher eukaryotes.
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Affiliation(s)
- Ulas Tenekeci
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Poppe
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Knut Beuerlein
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Christin Buro
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Helmut Müller
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Hendrik Weiser
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Daniela Kettner-Buhrow
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Katharina Porada
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Doris Newel
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ming Xu
- Department of Molecular Biology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Zhijian J Chen
- Department of Molecular Biology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Julia Busch
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
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44
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Affiliation(s)
- Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio USA
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45
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Das S, Sarkar D, Das B. The interplay between transcription and mRNA degradation in Saccharomyces cerevisiae. MICROBIAL CELL 2017; 4:212-228. [PMID: 28706937 PMCID: PMC5507684 DOI: 10.15698/mic2017.07.580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The cellular transcriptome is shaped by both the rates of mRNA synthesis in the nucleus and mRNA degradation in the cytoplasm under a specified condition. The last decade witnessed an exciting development in the field of post-transcriptional regulation of gene expression which underscored a strong functional coupling between the transcription and mRNA degradation. The functional integration is principally mediated by a group of specialized promoters and transcription factors that govern the stability of their cognate transcripts by “marking” them with a specific factor termed “coordinator.” The “mark” carried by the message is later decoded in the cytoplasm which involves the stimulation of one or more mRNA-decay factors, either directly by the “coordinator” itself or in an indirect manner. Activation of the decay factor(s), in turn, leads to the alteration of the stability of the marked message in a selective fashion. Thus, the integration between mRNA synthesis and decay plays a potentially significant role to shape appropriate gene expression profiles during cell cycle progression, cell division, cellular differentiation and proliferation, stress, immune and inflammatory responses, and may enhance the rate of biological evolution.
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Affiliation(s)
- Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Debasish Sarkar
- Present Address: Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201-2002, USA
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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46
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Abstract
5’-3’ decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5’-3’ exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5’-3’ degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1) as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5’-3’ exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5’-3’ decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5’ polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA’s 5’ end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap. Eukaryotic mRNAs are stabilised by a 5’ cap and one important step in mRNA decay is the removal of this cap by the nudix domain protein Dcp2 of the decapping complex. The decapping complex is highly conserved throughout eukaryotes, with the exception of trypanosomes that lack the entire complex. Here, I show that trypanosomes have evolved to use an ApaH-like phosphatase instead of a nudix domain protein as their major decapping enzyme. This work closes an important gap in the knowledge of trypanosome mRNA metabolism. Moreover, this is the first reported function of an ApaH-like phosphatase, a bacterial derived class of enzymes that are widespread throughout eukaryotes.
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Affiliation(s)
- Susanne Kramer
- Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- * E-mail:
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47
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Valkov E, Jonas S, Weichenrieder O. Mille viae in eukaryotic mRNA decapping. Curr Opin Struct Biol 2017; 47:40-51. [PMID: 28591671 DOI: 10.1016/j.sbi.2017.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2. Together with structure-based insight into decapping network assembly, we propose that DCP2-mediated decapping follows more than one path.
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Affiliation(s)
- Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zürich, Otto-Stern Weg 3, 8093 Zürich, Switzerland.
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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48
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Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme. Proc Natl Acad Sci U S A 2017; 114:6034-6039. [PMID: 28533364 DOI: 10.1073/pnas.1704496114] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crystal structures of enzymes are indispensable to understanding their mechanisms on a molecular level. It, however, remains challenging to determine which structures are adopted in solution, especially for dynamic complexes. Here, we study the bilobed decapping enzyme Dcp2 that removes the 5' cap structure from eukaryotic mRNA and thereby efficiently terminates gene expression. The numerous Dcp2 structures can be grouped into six states where the domain orientation between the catalytic and regulatory domains significantly differs. Despite this wealth of structural information it is not possible to correlate these states with the catalytic cycle or the activity of the enzyme. Using methyl transverse relaxation-optimized NMR spectroscopy, we demonstrate that only three of the six domain orientations are present in solution, where Dcp2 adopts an open, a closed, or a catalytically active state. We show how mRNA substrate and the activator proteins Dcp1 and Edc1 influence the dynamic equilibria between these states and how this modulates catalytic activity. Importantly, the active state of the complex is only stably formed in the presence of both activators and the mRNA substrate or the m7GDP decapping product, which we rationalize based on a crystal structure of the Dcp1:Dcp2:Edc1:m7GDP complex. Interestingly, we find that the activating mechanisms in Dcp2 also result in a shift of the substrate specificity from bacterial to eukaryotic mRNA.
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Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. The evolution of function within the Nudix homology clan. Proteins 2017; 85:775-811. [PMID: 27936487 PMCID: PMC5389931 DOI: 10.1002/prot.25223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/15/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), and nonenzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed a structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775-811. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John R. Srouji
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Present address: Molecular and Cellular Biology DepartmentHarvard UniversityCambridgeMassachusetts02138
| | - Anting Xu
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Annsea Park
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
| | - Jack F. Kirsch
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Steven E. Brenner
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
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Bischler T, Hsieh PK, Resch M, Liu Q, Tan HS, Foley PL, Hartleib A, Sharma CM, Belasco JG. Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets. J Biol Chem 2016; 292:1934-1950. [PMID: 27974459 DOI: 10.1074/jbc.m116.761171] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/02/2016] [Indexed: 12/20/2022] Open
Abstract
RNA degradation is crucial for regulating gene expression in all organisms. Like the decapping of eukaryotic mRNAs, the conversion of the 5'-terminal triphosphate of bacterial transcripts to a monophosphate can trigger RNA decay by exposing the transcript to attack by 5'-monophosphate-dependent ribonucleases. In both biological realms, this deprotection step is catalyzed by members of the Nudix hydrolase family. The genome of the gastric pathogen Helicobacter pylori, a Gram-negative epsilonproteobacterium, encodes two proteins resembling Nudix enzymes. Here we present evidence that one of them, HP1228 (renamed HpRppH), is an RNA pyrophosphohydrolase that triggers RNA degradation in H. pylori, whereas the other, HP0507, lacks such activity. In vitro, HpRppH converts RNA 5'-triphosphates and diphosphates to monophosphates. It requires at least two unpaired nucleotides at the 5' end of its substrates and prefers three or more but has only modest sequence preferences. The influence of HpRppH on RNA degradation in vivo was examined by using RNA-seq to search the H. pylori transcriptome for RNAs whose 5'-phosphorylation state and cellular concentration are governed by this enzyme. Analysis of cDNA libraries specific for transcripts bearing a 5'-triphosphate and/or monophosphate revealed at least 63 potential HpRppH targets. These included mRNAs and sRNAs, several of which were validated individually by half-life measurements and quantification of their 5'-terminal phosphorylation state in wild-type and mutant cells. These findings demonstrate an important role for RppH in post-transcriptional gene regulation in pathogenic Epsilonproteobacteria and suggest a possible basis for the phenotypes of H. pylori mutants lacking this enzyme.
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Affiliation(s)
- Thorsten Bischler
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Ping-Kun Hsieh
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Marcus Resch
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Quansheng Liu
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Hock Siew Tan
- the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Patricia L Foley
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Anika Hartleib
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Cynthia M Sharma
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and.
| | - Joel G Belasco
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016.
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