151
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Sayago C, Sánchez-Wandelmer J, García F, Hurtado B, Lafarga V, Prieto P, Zarzuela E, Ximénez-Embún P, Ortega S, Megías D, Fernández-Capetillo O, Malumbres M, Munoz J. Decoding protein methylation function with thermal stability analysis. Nat Commun 2023; 14:3016. [PMID: 37230995 DOI: 10.1038/s41467-023-38863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Protein methylation is an important modification beyond epigenetics. However, systems analyses of protein methylation lag behind compared to other modifications. Recently, thermal stability analyses have been developed which provide a proxy of a protein functional status. Here, we show that molecular and functional events closely linked to protein methylation can be revealed by the analysis of thermal stability. Using mouse embryonic stem cells as a model, we show that Prmt5 regulates mRNA binding proteins that are enriched in intrinsically disordered regions and involved in liquid-liquid phase separation mechanisms, including the formation of stress granules. Moreover, we reveal a non-canonical function of Ezh2 in mitotic chromosomes and the perichromosomal layer, and identify Mki67 as a putative Ezh2 substrate. Our approach provides an opportunity to systematically explore protein methylation function and represents a rich resource for understanding its role in pluripotency.
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Affiliation(s)
- Cristina Sayago
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - Fernando García
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Begoña Hurtado
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
- Cancer Cell Cycle group, Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Patricia Prieto
- Mouse Genome Editing Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Eduardo Zarzuela
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Sagrario Ortega
- Mouse Genome Editing Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
- Cancer Cell Cycle group, Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
| | - Javier Munoz
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain.
- Cell Signaling and Clinical Proteomics Group, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain.
- Ikerbasque, Basque foundation for science, 48011, Bilbao, Spain.
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152
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Abstract
Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.
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Affiliation(s)
- Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Sumudu S Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Pei-Qiao Xie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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153
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Gonzalez-Garcia P, Fiorillo Moreno O, Zarate Peñata E, Calderon-Villalba A, Pacheco Lugo L, Acosta Hoyos A, Villarreal Camacho JL, Navarro Quiroz R, Pacheco Londoño L, Aroca Martinez G, Moares N, Gabucio A, Fernandez-Ponce C, Garcia-Cozar F, Navarro Quiroz E. From Cell to Symptoms: The Role of SARS-CoV-2 Cytopathic Effects in the Pathogenesis of COVID-19 and Long COVID. Int J Mol Sci 2023; 24:ijms24098290. [PMID: 37175995 PMCID: PMC10179575 DOI: 10.3390/ijms24098290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection triggers various events from molecular to tissue level, which in turn is given by the intrinsic characteristics of each patient. Given the molecular diversity characteristic of each cellular phenotype, the possible cytopathic, tissue and clinical effects are difficult to predict, which determines the heterogeneity of COVID-19 symptoms. The purpose of this article is to provide a comprehensive review of the cytopathic effects of SARS-CoV-2 on various cell types, focusing on the development of COVID-19, which in turn may lead, in some patients, to a persistence of symptoms after recovery from the disease, a condition known as long COVID. We describe the molecular mechanisms underlying virus-host interactions, including alterations in protein expression, intracellular signaling pathways, and immune responses. In particular, the article highlights the potential impact of these cytopathies on cellular function and clinical outcomes, such as immune dysregulation, neuropsychiatric disorders, and organ damage. The article concludes by discussing future directions for research and implications for the management and treatment of COVID-19 and long COVID.
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Affiliation(s)
| | - Ornella Fiorillo Moreno
- Clínica Iberoamerica, Barranquilla 080001, Colombia
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | - Eloina Zarate Peñata
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | | | - Lisandro Pacheco Lugo
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | - Antonio Acosta Hoyos
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | | | - Roberto Navarro Quiroz
- Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona, Spanish National Research Council, 08028 Barcelona, Spain
| | | | - Gustavo Aroca Martinez
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
- School of Medicine, Universidad del Norte, Barranquilla 080001, Colombia
| | - Noelia Moares
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Antonio Gabucio
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Cecilia Fernandez-Ponce
- Institute of Biomedical Research Cadiz (INIBICA), 11009 Cádiz, Spain
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Francisco Garcia-Cozar
- Institute of Biomedical Research Cadiz (INIBICA), 11009 Cádiz, Spain
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Elkin Navarro Quiroz
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
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154
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Abstract
RNA granules are mesoscale assemblies that form in the absence of limiting membranes. RNA granules contain factors for RNA biogenesis and turnover and are often assumed to represent specialized compartments for RNA biochemistry. Recent evidence suggests that RNA granules assemble by phase separation of subsoluble ribonucleoprotein (RNP) complexes that partially demix from the cytoplasm or nucleoplasm. We explore the possibility that some RNA granules are nonessential condensation by-products that arise when RNP complexes exceed their solubility limit as a consequence of cellular activity, stress, or aging. We describe the use of evolutionary and mutational analyses and single-molecule techniques to distinguish functional RNA granules from "incidental condensates."
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Affiliation(s)
- Andrea Putnam
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Laura Thomas
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Geraldine Seydoux
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, USA
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155
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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156
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Saarikettu J, Lehmusvaara S, Pesu M, Junttila I, Partanen J, Sipilä P, Poutanen M, Yang J, Haikarainen T, Silvennoinen O. The RNA-binding protein Snd1/Tudor-SN regulates hypoxia-responsive gene expression. FASEB Bioadv 2023; 5:183-198. [PMID: 37151849 PMCID: PMC10158624 DOI: 10.1096/fba.2022-00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/29/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Snd1 is an evolutionarily conserved RNA-binding protein implicated in several regulatory processes in gene expression including activation of transcription, mRNA splicing, and microRNA decay. Here, we have investigated the outcome of Snd1 gene deletion in the mouse. The knockout mice are viable showing no gross abnormalities apart from decreased fertility, organ and body size, and decreased number of myeloid cells concomitant with decreased expression of granule protein genes. Deletion of Snd1 affected the expression of relatively small number of genes in spleen and liver. However, mRNA expression changes in the knockout mouse liver showed high similarity to expression profile in adaptation to hypoxia. MicroRNA expression in liver showed upregulation of the hypoxia-induced microRNAs miR-96 and -182. Similar to Snd1 deletion, mimics of miR-96/182 enhanced hypoxia-responsive reporter activity. To further elucidate the function of SND1, BioID biotin proximity ligation assay was performed in HEK-293T cells to identify interacting proteins. Over 50% of the identified interactors were RNA-binding proteins, including stress granule proteins. Taken together, our results show that in normal growth conditions, Snd1 is not a critical factor for mRNA transcription in the mouse, and describe a function for Snd1 in hypoxia adaptation through negatively regulating hypoxia-related miRNAs and hypoxia-induced transcription consistent with a role as stress response regulator.
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Affiliation(s)
- Juha Saarikettu
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life SciencesUniversity of HelsinkiHelsinkiFinland
| | - Saara Lehmusvaara
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - Marko Pesu
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
- Fimlab LaboratoriesTampere University HospitalTampereFinland
| | - Ilkka Junttila
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
- Fimlab LaboratoriesTampere University HospitalTampereFinland
- Northern Finland Laboratory Centre (NordLab)OuluFinland
- Research Unit of BiomedicineUniversity of OuluOuluFinland
| | - Juha Partanen
- Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Petra Sipilä
- Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Matti Poutanen
- Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Jie Yang
- Department of ImmunologyTianjin Medical UniversityTianjinP.R. China
| | - Teemu Haikarainen
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - Olli Silvennoinen
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life SciencesUniversity of HelsinkiHelsinkiFinland
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
- Fimlab LaboratoriesTampere University HospitalTampereFinland
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157
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Fujikawa D, Nakamura T, Yoshioka D, Li Z, Moriizumi H, Taguchi M, Tokai-Nishizumi N, Kozuka-Hata H, Oyama M, Takekawa M. Stress granule formation inhibits stress-induced apoptosis by selectively sequestering executioner caspases. Curr Biol 2023; 33:1967-1981.e8. [PMID: 37119817 DOI: 10.1016/j.cub.2023.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/23/2023] [Accepted: 04/06/2023] [Indexed: 05/01/2023]
Abstract
Cytoplasmic stress granules (SGs) are phase-separated membrane-less organelles that form in response to various stress stimuli. SGs are mainly composed of non-canonical stalled 48S preinitiation complexes. In addition, many other proteins also accumulate into SGs, but the list is still incomplete. SG assembly suppresses apoptosis and promotes cell survival under stress. Furthermore, hyperformation of SGs is frequently observed in various human cancers and accelerates tumor development and progression by reducing stress-induced damage of cancer cells. Therefore, they are of clinical importance. However, the precise mechanism underlying SG-mediated inhibition of apoptosis remains ill-defined. Here, using a proximity-labeling proteomic approach, we comprehensively analyzed SG-resident proteins and identified the executioner caspases, caspase-3 and -7, as SG components. We demonstrate that accumulation of caspase-3/7 into SGs is mediated by evolutionarily conserved amino acid residues within their large catalytic domains and inhibits caspase activities and consequent apoptosis induced by various stresses. Expression of an SG-localization-deficient caspase-3 mutant in cells largely counteracted the anti-apoptotic effect of SGs, whereas enforced relocalization of the caspase-3 mutant to SGs restored it. Thus, SG-mediated sequestration of executioner caspases is a mechanism underlying the broad cytoprotective function of SGs. Furthermore, using a mouse xenograft tumor model, we show that this mechanism prevents cancer cells from apoptosis in tumor tissues, thereby promoting cancer progression. Our results reveal the functional crosstalk between SG-mediated cell survival and caspase-mediated cell death signaling pathways and delineate a molecular mechanism that dictates cell-fate decisions under stress and promotes tumorigenesis.
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Affiliation(s)
- Daichi Fujikawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takanori Nakamura
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Daisuke Yoshioka
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
| | - Zizheng Li
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
| | - Hisashi Moriizumi
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
| | - Mari Taguchi
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Noriko Tokai-Nishizumi
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan; Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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158
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Sikorski V, Selberg S, Lalowski M, Karelson M, Kankuri E. The structure and function of YTHDF epitranscriptomic m 6A readers. Trends Pharmacol Sci 2023; 44:335-353. [PMID: 37069041 DOI: 10.1016/j.tips.2023.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 04/19/2023]
Abstract
Specific RNA sequences modified by a methylated adenosine, N6-methyladenosine (m6A), contribute to the post-transcriptional regulation of gene expression. The quantity of m6A in RNA is orchestrated by enzymes that write and erase it, while its effects are mediated by proteins that bind to read this modification. Dysfunction of this post-transcriptional regulatory process has been linked to human disease. Although the initial focus has been on pharmacological targeting of the writer and eraser enzymes, interest in the reader proteins has been challenged by a lack of clear understanding of their functional roles and molecular mechanisms of action. Readers of m6A-modified RNA (m6A-RNA) - the YTH (YT521-B homology) domain-containing protein family paralogs 1-3 (YTHDF1-3, referred to here as DF1-DF3) - are emerging as therapeutic targets as their links to pathological processes such as cancer and inflammation and their roles in regulating m6A-RNA fate become clear. We provide an updated understanding of the modes of action of DF1-DF3 and review their structures to unlock insights into drug design approaches for DF paralog-selective inhibition.
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Affiliation(s)
- Vilbert Sikorski
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Finland
| | - Simona Selberg
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Maciej Lalowski
- Helsinki Institute of Life Science (HiLIFE), Meilahti Clinical Proteomics Core Facility, Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Esko Kankuri
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Finland.
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159
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Asano-Inami E, Yokoi A, Sugiyama M, Hyodo T, Hamaguchi T, Kajiyama H. The association of UBAP2L and G3BP1 mediated by small nucleolar RNA is essential for stress granule formation. Commun Biol 2023; 6:415. [PMID: 37059803 PMCID: PMC10104854 DOI: 10.1038/s42003-023-04754-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
Stress granules (SGs) are dynamic, non-membranous structures composed of non-translating mRNAs and various proteins and play critical roles in cell survival under stressed conditions. Extensive proteomics analyses have been performed to identify proteins in SGs; however, the molecular functions of these components in SG formation remain unclear. In this report, we show that ubiquitin-associated protein 2-like (UBAP2L) is a crucial component of SGs. UBAP2L localized to SGs in response to various stresses, and its depletion significantly suppressed SG organization. Proteomics and RNA sequencing analyses found that UBAP2L formed a protein-RNA complex with Ras-GTP-activating protein SH3 domain binding protein 1 (G3BP1) and small nucleolar RNAs (snoRNAs). In vitro binding analysis demonstrated that snoRNAs were required for UBAP2L association with G3BP1. In addition, decreased expression of snoRNAs reduced the interaction between UBAP2L and G3BP1 and suppressed SG formation. Our results reveal a critical role of SG component, the UBAP2L/snoRNA/G3BP1 protein-RNA complex, and provide new insights into the regulation of SG assembly.
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Affiliation(s)
- Eri Asano-Inami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.
| | - Mai Sugiyama
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Aichi, 480-1195, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
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160
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Szwarc MM, Guarnieri AL, Joshi M, Duc HN, Laird MC, Pandey A, Khanal S, Dohm E, Bui AK, Sullivan KD, Galbraith MD, Andrysik Z, Espinosa JM. FAM193A is a positive regulator of p53 activity. Cell Rep 2023; 42:112230. [PMID: 36897777 PMCID: PMC10164416 DOI: 10.1016/j.celrep.2023.112230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2022] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
Inactivation of the p53 tumor suppressor, either by mutations or through hyperactivation of repressors such as MDM2 and MDM4, is a hallmark of cancer. Although many inhibitors of the p53-MDM2/4 interaction have been developed, such as Nutlin, their therapeutic value is limited by highly heterogeneous cellular responses. We report here a multi-omics investigation of the cellular response to MDM2/4 inhibitors, leading to identification of FAM193A as a widespread regulator of p53 function. CRISPR screening identified FAM193A as necessary for the response to Nutlin. FAM193A expression correlates with Nutlin sensitivity across hundreds of cell lines. Furthermore, genetic codependency data highlight FAM193A as a component of the p53 pathway across diverse tumor types. Mechanistically, FAM193A interacts with MDM4, and FAM193A depletion stabilizes MDM4 and inhibits the p53 transcriptional program. Last, FAM193A expression is associated with better prognosis in multiple malignancies. Altogether, these results identify FAM193A as a positive regulator of p53.
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Affiliation(s)
- Maria M Szwarc
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anna L Guarnieri
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Molishree Joshi
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Functional Genomics Facility, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Huy N Duc
- Functional Genomics Facility, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Madison C Laird
- Functional Genomics Facility, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ahwan Pandey
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Santosh Khanal
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emily Dohm
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Aimee K Bui
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kelly D Sullivan
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zdenek Andrysik
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Functional Genomics Facility, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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161
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Tan X, Zheng C, Zhuang Y, Jin P, Wang F. The m6A reader PRRC2A is essential for meiosis I completion during spermatogenesis. Nat Commun 2023; 14:1636. [PMID: 36964127 PMCID: PMC10039029 DOI: 10.1038/s41467-023-37252-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
N6-methyladenosine (m6A) and its reader proteins YTHDC1, YTHDC2, and YTHDF2 have been shown to exert essential functions during spermatogenesis. However, much remains unknown about m6A regulation mechanisms and the functions of specific readers during the meiotic cell cycle. Here, we show that the m6A reader Proline rich coiled-coil 2A (PRRC2A) is essential for male fertility. Germ cell-specific knockout of Prrc2a causes XY asynapsis and impaired meiotic sex chromosome inactivation in late-prophase spermatocytes. Moreover, PRRC2A-null spermatocytes exhibit delayed metaphase entry, chromosome misalignment, and spindle disorganization at metaphase I and are finally arrested at this stage. Sequencing data reveal that PRRC2A decreases the RNA abundance or improves the translation efficiency of targeting transcripts. Specifically, PRRC2A recognizes spermatogonia-specific transcripts and downregulates their RNA abundance to maintain the spermatocyte expression pattern during the meiosis prophase. For genes involved in meiotic cell division, PRRC2A improves the translation efficiency of their transcripts. Further, co-immunoprecipitation data show that PRRC2A interacts with several proteins regulating mRNA metabolism or translation (YBX1, YBX2, PABPC1, FXR1, and EIF4G3). Our study reveals post-transcriptional functions of PRRC2A and demonstrates its critical role in the completion of meiosis I in spermatogenesis.
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Affiliation(s)
- Xinshui Tan
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Caihong Zheng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China
| | - Yinghua Zhuang
- National Institute of Biological Sciences, Beijing, China
| | - Pengpeng Jin
- National Institute of Biological Sciences, Beijing, China
| | - Fengchao Wang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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162
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Kohler V, Andréasson C. Reversible protein assemblies in the proteostasis network in health and disease. Front Mol Biosci 2023; 10:1155521. [PMID: 37021114 PMCID: PMC10067754 DOI: 10.3389/fmolb.2023.1155521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023] Open
Abstract
While proteins populating their native conformations constitute the functional entities of cells, protein aggregates are traditionally associated with cellular dysfunction, stress and disease. During recent years, it has become clear that large aggregate-like protein condensates formed via liquid-liquid phase separation age into more solid aggregate-like particles that harbor misfolded proteins and are decorated by protein quality control factors. The constituent proteins of the condensates/aggregates are disentangled by protein disaggregation systems mainly based on Hsp70 and AAA ATPase Hsp100 chaperones prior to their handover to refolding and degradation systems. Here, we discuss the functional roles that condensate formation/aggregation and disaggregation play in protein quality control to maintain proteostasis and why it matters for understanding health and disease.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Claes Andréasson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
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163
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Segal D, Maier S, Mastromarco GJ, Qian WW, Nabeel-Shah S, Lee H, Moore G, Lacoste J, Larsen B, Lin ZY, Selvabaskaran A, Liu K, Smibert C, Zhang Z, Greenblatt J, Peng J, Lee HO, Gingras AC, Taipale M. A central chaperone-like role for 14-3-3 proteins in human cells. Mol Cell 2023; 83:974-993.e15. [PMID: 36931259 DOI: 10.1016/j.molcel.2023.02.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
14-3-3 proteins are highly conserved regulatory proteins that interact with hundreds of structurally diverse clients and act as central hubs of signaling networks. However, how 14-3-3 paralogs differ in specificity and how they regulate client protein function are not known for most clients. Here, we map the interactomes of all human 14-3-3 paralogs and systematically characterize the effect of disrupting these interactions on client localization. The loss of 14-3-3 binding leads to the coalescence of a large fraction of clients into discrete foci in a client-specific manner, suggesting a central chaperone-like function for 14-3-3 proteins. Congruently, the engraftment of 14-3-3 binding motifs to nonclients can suppress their aggregation or phase separation. Finally, we show that 14-3-3s negatively regulate the localization of the RNA-binding protein SAMD4A to cytoplasmic granules and inhibit its activity as a translational repressor. Our work suggests that 14-3-3s have a more prominent role as chaperone-like molecules than previously thought.
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Affiliation(s)
- Dmitri Segal
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | | | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hyunmin Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Abeeshan Selvabaskaran
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Karen Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Craig Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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164
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The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool. Cell Rep 2023; 42:112242. [PMID: 36924490 DOI: 10.1016/j.celrep.2023.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/19/2023] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Here, we ask how developing precursors maintain the balance between cell genesis for tissue growth and establishment of adult stem cell pools, focusing on postnatal forebrain neural precursor cells (NPCs). We show that these NPCs are transcriptionally primed to differentiate and that the primed mRNAs are associated with the translational repressor 4E-T. 4E-T also broadly associates with other NPC mRNAs encoding transcriptional regulators, and these are preferentially depleted from ribosomes, consistent with repression. By contrast, a second translational regulator, Cpeb4, associates with diverse target mRNAs that are largely ribosome associated. The 4E-T-dependent mRNA association is functionally important because 4E-T knockdown or conditional knockout derepresses proneurogenic mRNA translation and perturbs maintenance versus differentiation of early postnatal NPCs in culture and in vivo. Thus, early postnatal NPCs are primed to differentiate, and 4E-T regulates the balance between cell genesis and stem cell expansion by sequestering and repressing mRNAs encoding transcriptional regulators.
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165
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Comparison of Biomolecular Condensate Localization and Protein Phase Separation Predictors. Biomolecules 2023; 13:biom13030527. [PMID: 36979462 PMCID: PMC10046894 DOI: 10.3390/biom13030527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Research in the field of biochemistry and cellular biology has entered a new phase due to the discovery of phase separation driving the formation of biomolecular condensates, or membraneless organelles, in cells. The implications of this novel principle of cellular organization are vast and can be applied at multiple scales, spawning exciting research questions in numerous directions. Of fundamental importance are the molecular mechanisms that underly biomolecular condensate formation within cells and whether insights gained into these mechanisms provide a gateway for accurate predictions of protein phase behavior. Within the last six years, a significant number of predictors for protein phase separation and condensate localization have emerged. Herein, we compare a collection of state-of-the-art predictors on different tasks related to protein phase behavior. We show that the tested methods achieve high AUCs in the identification of biomolecular condensate drivers and scaffolds, as well as in the identification of proteins able to phase separate in vitro. However, our benchmark tests reveal that their performance is poorer when used to predict protein segments that are involved in phase separation or to classify amino acid substitutions as phase-separation-promoting or -inhibiting mutations. Our results suggest that the phenomenological approach used by most predictors is insufficient to fully grasp the complexity of the phenomenon within biological contexts and make reliable predictions related to protein phase behavior at the residue level.
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166
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Curdy N, Lanvin O, Cerapio JP, Pont F, Tosolini M, Sarot E, Valle C, Saint-Laurent N, Lhuillier E, Laurent C, Fournié JJ, Franchini DM. The proteome and transcriptome of stress granules and P bodies during human T lymphocyte activation. Cell Rep 2023; 42:112211. [PMID: 36884350 DOI: 10.1016/j.celrep.2023.112211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 12/16/2022] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes in terms of formation, constitution, and relationship remains unknown. Here, by combining proteomic, transcriptomic, and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre and post stimulation. The identification of the proteomes and transcriptomes of SGs and PBs indicate an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.
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Affiliation(s)
- Nicolas Curdy
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France; Institut Carnot Lymphome CALYM, Toulouse, France
| | - Olivia Lanvin
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France; Institut Carnot Lymphome CALYM, Toulouse, France
| | - Juan-Pablo Cerapio
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France
| | - Fréderic Pont
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France
| | - Marie Tosolini
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France; Institut Carnot Lymphome CALYM, Toulouse, France
| | - Emeline Sarot
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France
| | - Carine Valle
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Nathalie Saint-Laurent
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Emeline Lhuillier
- Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), INSERM U1048, 31432 Toulouse, France; GeT-Santé, Plateforme Génome et Transcriptome, GenoToul, 31100 Toulouse, France
| | - Camille Laurent
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France; Institut Carnot Lymphome CALYM, Toulouse, France; Centre Hospitalier Universitaire (CHU), 31059 Toulouse, France
| | - Jean-Jacques Fournié
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France; Institut Carnot Lymphome CALYM, Toulouse, France
| | - Don-Marc Franchini
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN-2", Toulouse, France; Institut Carnot Lymphome CALYM, Toulouse, France; Centre Hospitalier Universitaire (CHU), 31059 Toulouse, France.
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167
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Cormier KW, Larsen B, Gingras AC, Woodgett JR. Interactomes of Glycogen Synthase Kinase-3 Isoforms. J Proteome Res 2023; 22:977-989. [PMID: 36779422 PMCID: PMC9990120 DOI: 10.1021/acs.jproteome.2c00825] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Functional differentiation of the two isoforms of the protein-serine/threonine kinase, glycogen synthase kinase-3 (GSK-3), is an unsettled area of research. The isoforms are highly similar in structure and are largely redundant, though there is also evidence for specific roles. Identification of isoform-specific protein interactors may elucidate the differences in function and provide insight into isoform-selective regulation. We therefore sought to identify novel GSK-3 interaction partners and to examine differences in the interactomes of the two isoforms using both affinity purification and proximity-dependent biotinylation (BioID) mass spectrometry methods. While the interactomes of the two isomers are highly similar in HEK293 cells, BioID in HeLa cells yielded a variety of preys that are preferentially associated with one of the two isoforms. DCP1B, which favored GSK-3α, and MISP, which favored GSK-3β, were evaluated for reciprocal interactions. The differences in interactions between isoforms may help in understanding the distinct functions and regulation of the two isoforms as well as offer avenues for the development of isoform-specific strategies.
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Affiliation(s)
- Kevin W Cormier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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168
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Söhnel AC, Brandt R. Neuronal stress granules as dynamic microcompartments: current concepts and open questions. Biol Chem 2023; 404:491-498. [PMID: 36779376 DOI: 10.1515/hsz-2022-0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/18/2023] [Indexed: 02/14/2023]
Abstract
Stress granules are cytosolic, membraneless RNA-protein complexes that form in the cytosol in response to various stressors. Stress granules form through a process termed liquid-liquid phase separation, which increases the local concentration of RNA and protein within the granules, creates dynamic sorting stations for mRNAs and associated proteins, and modulates the availability of mRNA for protein translation. We introduce the concept that neuronal stress granules act as dynamic cytosolic microcompartments in which their components differentially cycle in and out, monitoring the cellular environment. We discuss that neuronal stress granules have distinctive features and contain substructures in which individual components interact transiently. We describe that neuronal stress granules modulate protein expression at multiple levels and affect the proteoform profile of the cytoskeletal protein tau. We argue that a better knowledge of the regulation of stress granule dynamics in neurons and the modulation of their material state is necessary to understand their function during physiological and pathological stress responses. Finally, we delineate approaches to determine the behavior and regulation of critical stress granule organizers and the physical state of stress granules in living neurons.
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Affiliation(s)
| | - Roland Brandt
- Department of Neurobiology, Osnabrück, Germany.,Center for Cellular Nanoanalytics, Osnabrück, Germany.,Institute of Cognitive Science, Osnabrück University, 49076 Osnabrück, Germany
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169
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Xu WQ, Cheah JS, Xu C, Messing J, Freibaum BD, Boeynaems S, Taylor JP, Udeshi ND, Carr SA, Ting AY. Dynamic mapping of proteome trafficking within and between living cells by TransitID. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527548. [PMID: 36798302 PMCID: PMC9934598 DOI: 10.1101/2023.02.07.527548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The ability to map trafficking for thousands of endogenous proteins at once in living cells would reveal biology currently invisible to both microscopy and mass spectrometry. Here we report TransitID, a method for unbiased mapping of endogenous proteome trafficking with nanometer spatial resolution in living cells. Two proximity labeling (PL) enzymes, TurboID and APEX, are targeted to source and destination compartments, and PL with each enzyme is performed in tandem via sequential addition of their small-molecule substrates. Mass spectrometry identifies the proteins tagged by both enzymes. Using TransitID, we mapped proteome trafficking between cytosol and mitochondria, cytosol and nucleus, and nucleolus and stress granules, uncovering a role for stress granules in protecting the transcription factor JUN from oxidative stress. TransitID also identifies proteins that signal intercellularly between macrophages and cancer cells. TransitID introduces a powerful approach for distinguishing protein populations based on compartment or cell type of origin.
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170
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Ramnani B, Powell S, Shetty AG, Manivannan P, Hibbard BR, Leaman DW, Malathi K. Viral Hemorrhagic Septicemia Virus Activates Integrated Stress Response Pathway and Induces Stress Granules to Regulate Virus Replication. Viruses 2023; 15:466. [PMID: 36851680 PMCID: PMC9965902 DOI: 10.3390/v15020466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Virus infection activates integrated stress response (ISR) and stress granule (SG) formation and viruses counteract by interfering with SG assembly, suggesting an important role in antiviral defense. The infection of fish cells by Viral Hemorrhagic Septicemia Virus (VHSV), activates the innate immune recognition pathway and the production of type I interferon (IFN). However, the mechanisms by which VHSV interacts with ISR pathway regulating SG formation is poorly understood. Here, we demonstrate that fish cells respond to heat shock, oxidative stress and VHSV infection by forming SG that localized key SG marker, Ras GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1). We show that PKR-like endoplasmic reticulum kinase (PERK), but not (dsRNA)-dependent protein kinase (PKR), is required for VHSV-induced SG formation. Furthermore, in VHSV Ia infected cells, PERK activity is required for IFN production, antiviral signaling and viral replication. SG formation required active virus replication as individual VHSV Ia proteins or inactive virus did not induce SG. Cells lacking G3BP1 produced increased IFN, antiviral genes and viral mRNA, however viral protein synthesis and viral titers were reduced. We show a critical role of the activation of ISR pathway and SG formation highlighting a novel role of G3BP1 in regulating VHSV protein translation and replication.
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Affiliation(s)
- Barkha Ramnani
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Shelby Powell
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Adarsh G. Shetty
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Praveen Manivannan
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Brian R. Hibbard
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Douglas W. Leaman
- College of Sciences, Auburn University at Montgomery, 7400 East Dr., Montgomery, AL 36117, USA
| | - Krishnamurthy Malathi
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
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171
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Liu C, Mentzelopoulou A, Muhammad A, Volkov A, Weijers D, Gutierrez-Beltran E, Moschou PN. An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome. EMBO J 2023; 42:e111885. [PMID: 36741000 PMCID: PMC10152145 DOI: 10.15252/embj.2022111885] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
Cellular condensates can comprise membrane-less ribonucleoprotein assemblies with liquid-like properties. These cellular condensates influence various biological outcomes, but their liquidity hampers their isolation and characterization. Here, we investigated the composition of the condensates known as processing bodies (PBs) in the model plant Arabidopsis thaliana through a proximity-biotinylation proteomics approach. Using in situ protein-protein interaction approaches, genetics and high-resolution dynamic imaging, we show that processing bodies comprise networks that interface with membranes. Surprisingly, the conserved component of PBs, DECAPPING PROTEIN 1 (DCP1), can localize to unique plasma membrane subdomains including cell edges and vertices. We characterized these plasma membrane interfaces and discovered a developmental module that can control cell shape. This module is regulated by DCP1, independently from its role in decapping, and the actin-nucleating SCAR-WAVE complex, whereby the DCP1-SCAR-WAVE interaction confines and enhances actin nucleation. This study reveals an unexpected function for a conserved condensate at unique membrane interfaces.
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Affiliation(s)
- Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Andriani Mentzelopoulou
- Department of Biology, University of Crete, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Amna Muhammad
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.,University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Andriy Volkov
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain.,Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.,Department of Biology, University of Crete, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
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172
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Li G, Tang Z, Fan W, Wang X, Huang L, Jia Y, Wang M, Hu Z, Zhou Y. Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. CELL INSIGHT 2023; 2:100068. [PMID: 37192911 PMCID: PMC9670597 DOI: 10.1016/j.cellin.2022.100068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
The proteins and RNAs of viruses extensively interact with host proteins after infection. We collected and reanalyzed all available datasets of protein-protein and RNA-protein interactions related to SARS-CoV-2. We investigated the reproducibility of those interactions and made strict filters to identify highly confident interactions. We systematically analyzed the interaction network and identified preferred subcellular localizations of viral proteins, some of which such as ORF8 in ER and ORF7A/B in ER membrane were validated using dual fluorescence imaging. Moreover, we showed that viral proteins frequently interact with host machinery related to protein processing in ER and vesicle-associated processes. Integrating the protein- and RNA-interactomes, we found that SARS-CoV-2 RNA and its N protein closely interacted with stress granules including 40 core factors, of which we specifically validated G3BP1, IGF2BP1, and MOV10 using RIP and Co-IP assays. Combining CRISPR screening results, we further identified 86 antiviral and 62 proviral factors and associated drugs. Using network diffusion, we found additional 44 interacting proteins including two proviral factors previously validated. Furthermore, we showed that this atlas could be applied to identify the complications associated with COVID-19. All data are available in the AIMaP database (https://mvip.whu.edu.cn/aimap/) for users to easily explore the interaction map.
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Affiliation(s)
- Guangnan Li
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China
| | - Zhidong Tang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China
| | - Weiliang Fan
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China
| | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Li Huang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China
| | - Yu Jia
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Institute for Advanced Studies, Wuhan University, Wuhan, China
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173
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525042. [PMID: 36711448 PMCID: PMC9882296 DOI: 10.1101/2023.01.22.525042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Ashley R. Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Andréa B. Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa M. Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Alexandra C. Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Stephanie L. Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Heta S. Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M. Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
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174
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Zou Z, Sepich-Poore C, Zhou X, Wei J, He C. The mechanism underlying redundant functions of the YTHDF proteins. Genome Biol 2023; 24:17. [PMID: 36694229 PMCID: PMC9872407 DOI: 10.1186/s13059-023-02862-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
The YTH N6-methyladenosine RNA binding proteins (YTHDFs) mediate the functional effects of N6-methyladenosine (m6A) on RNA. Recently, a report proposed that all YTHDFs work redundantly to facilitate RNA decay, raising questions about the exact functions of individual YTHDFs, especially YTHDF1 and YTHDF2. We show that YTHDF1 and YTHDF2 differ in their low-complexity domains (LCDs) and exhibit different behaviors in condensate formation and subsequent physiological functions. Biologically, we also find that the global stabilization of RNA after depletion of all YTHDFs is driven by increased P-body formation and is not strictly m6A dependent.
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Affiliation(s)
- Zhongyu Zou
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Caraline Sepich-Poore
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- University of Chicago Medical Scientist Training Program, Chicago, IL, 60637, USA
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
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175
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Millar SR, Huang JQ, Schreiber KJ, Tsai YC, Won J, Zhang J, Moses AM, Youn JY. A New Phase of Networking: The Molecular Composition and Regulatory Dynamics of Mammalian Stress Granules. Chem Rev 2023. [PMID: 36662637 PMCID: PMC10375481 DOI: 10.1021/acs.chemrev.2c00608] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Stress granules (SGs) are cytosolic biomolecular condensates that form in response to cellular stress. Weak, multivalent interactions between their protein and RNA constituents drive their rapid, dynamic assembly through phase separation coupled to percolation. Though a consensus model of SG function has yet to be determined, their perceived implication in cytoprotective processes (e.g., antiviral responses and inhibition of apoptosis) and possible role in the pathogenesis of various neurodegenerative diseases (e.g., amyotrophic lateral sclerosis and frontotemporal dementia) have drawn great interest. Consequently, new studies using numerous cell biological, genetic, and proteomic methods have been performed to unravel the mechanisms underlying SG formation, organization, and function and, with them, a more clearly defined SG proteome. Here, we provide a consensus SG proteome through literature curation and an update of the user-friendly database RNAgranuleDB to version 2.0 (http://rnagranuledb.lunenfeld.ca/). With this updated SG proteome, we use next-generation phase separation prediction tools to assess the predisposition of SG proteins for phase separation and aggregation. Next, we analyze the primary sequence features of intrinsically disordered regions (IDRs) within SG-resident proteins. Finally, we review the protein- and RNA-level determinants, including post-translational modifications (PTMs), that regulate SG composition and assembly/disassembly dynamics.
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Affiliation(s)
- Sean R Millar
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jie Qi Huang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Karl J Schreiber
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Yi-Cheng Tsai
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jiyun Won
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Jianping Zhang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5T 3A1, Canada.,The Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Ji-Young Youn
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
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176
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Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies. PLoS Pathog 2023; 19:e1011080. [PMID: 36634147 PMCID: PMC9876383 DOI: 10.1371/journal.ppat.1011080] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/25/2023] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi's sarcoma (KS). We previously demonstrated that the KSHV Kaposin B (KapB) protein promotes inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). PBs modify gene expression by silencing or degrading labile messenger RNAs (mRNAs), including many transcripts that encode inflammatory or angiogenic proteins associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via phosphorylation of the autophagy regulatory protein, Beclin. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin phosphorylation or autophagic flux. Moreover, we showed that PB disassembly mediated by KSHV or KapB, depended on autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.
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177
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Rodriguez-Calado S, Van Damme P, Avilés FX, Candiota AP, Tanco S, Lorenzo J. Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly. Int J Mol Sci 2023; 24:ijms24021273. [PMID: 36674791 PMCID: PMC9867282 DOI: 10.3390/ijms24021273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
The cytosolic carboxypeptidase 6 (CCP6) catalyzes the deglutamylation of polyglutamate side chains, a post-translational modification that affects proteins such as tubulins or nucleosome assembly proteins. CCP6 is involved in several cell processes, such as spermatogenesis, antiviral activity, embryonic development, and pathologies like renal adenocarcinoma. In the present work, the cellular role of CCP6 has been assessed by BioID, a proximity labeling approach for mapping physiologically relevant protein-protein interactions (PPIs) and bait proximal proteins by mass spectrometry. We used HEK 293 cells stably expressing CCP6-BirA* to identify 37 putative interactors of this enzyme. This list of CCP6 proximal proteins displayed enrichment of proteins associated with the centrosome and centriolar satellites, indicating that CCP6 could be present in the pericentriolar material. In addition, we identified cilium assembly-related proteins as putative interactors of CCP6. In addition, the CCP6 proximal partner list included five proteins associated with the Joubert syndrome, a ciliopathy linked to defects in polyglutamylation. Using the proximity ligation assay (PLA), we show that PCM1, PIBF1, and NudC are true CCP6 physical interactors. Therefore, the BioID methodology confirms the location and possible functional role of CCP6 in centrosomes and centrioles, as well as in the formation and maintenance of primary cilia.
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Affiliation(s)
- Sergi Rodriguez-Calado
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Francesc Xavier Avilés
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Ana Paula Candiota
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Sebastian Tanco
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Correspondence: (S.T.); (J.L.); Tel.: +34-93-586-8938 (S.T.); +34-93-586-8957 (J.L.)
| | - Julia Lorenzo
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Correspondence: (S.T.); (J.L.); Tel.: +34-93-586-8938 (S.T.); +34-93-586-8957 (J.L.)
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178
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Makeeva DS, Riggs CL, Burakov AV, Ivanov PA, Kushchenko AS, Bykov DA, Popenko VI, Prassolov VS, Ivanov PV, Dmitriev SE. Relocalization of Translation Termination and Ribosome Recycling Factors to Stress Granules Coincides with Elevated Stop-Codon Readthrough and Reinitiation Rates upon Oxidative Stress. Cells 2023; 12:259. [PMID: 36672194 PMCID: PMC9856671 DOI: 10.3390/cells12020259] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Upon oxidative stress, mammalian cells rapidly reprogram their translation. This is accompanied by the formation of stress granules (SGs), cytoplasmic ribonucleoprotein condensates containing untranslated mRNA molecules, RNA-binding proteins, 40S ribosomal subunits, and a set of translation initiation factors. Here we show that arsenite-induced stress causes a dramatic increase in the stop-codon readthrough rate and significantly elevates translation reinitiation levels on uORF-containing and bicistronic mRNAs. We also report the recruitment of translation termination factors eRF1 and eRF3, as well as ribosome recycling and translation reinitiation factors ABCE1, eIF2D, MCT-1, and DENR to SGs upon arsenite treatment. Localization of these factors to SGs may contribute to a rapid resumption of mRNA translation after stress relief and SG disassembly. It may also suggest the presence of post-termination, recycling, or reinitiation complexes in SGs. This new layer of translational control under stress conditions, relying on the altered spatial distribution of translation factors between cellular compartments, is discussed.
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Affiliation(s)
- Desislava S. Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Claire L. Riggs
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anton V. Burakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel A. Ivanov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artem S. Kushchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Dmitri A. Bykov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir I. Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel V. Ivanov
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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179
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Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome. Mol Psychiatry 2023; 28:1747-1769. [PMID: 36604605 DOI: 10.1038/s41380-022-01937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
Copy number variations (CNVs) are associated with psychiatric and neurodevelopmental disorders (NDDs), and most, including the recurrent 15q13.3 microdeletion disorder, have unknown disease mechanisms. We used a heterozygous 15q13.3 microdeletion mouse model and patient iPSC-derived neurons to reveal developmental defects in neuronal maturation and network activity. To identify the underlying molecular dysfunction, we developed a neuron-specific proximity-labeling proteomics (BioID2) pipeline, combined with patient mutations, to target the 15q13.3 CNV genetic driver OTUD7A. OTUD7A is an emerging independent NDD risk gene with no known function in the brain, but has putative deubiquitinase function. The OTUD7A protein-protein interaction network included synaptic, axonal, and cytoskeletal proteins and was enriched for ASD and epilepsy risk genes (Ank3, Ank2, SPTAN1, SPTBN1). The interactions between OTUD7A and Ankyrin-G (Ank3) and Ankyrin-B (Ank2) were disrupted by an epilepsy-associated OTUD7A L233F variant. Further investigation of Ankyrin-G in mouse and human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed protein instability, increased polyubiquitination, and decreased levels in the axon initial segment, while structured illumination microscopy identified reduced Ankyrin-G nanodomains in dendritic spines. Functional analysis of human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed shared and distinct impairments to axonal growth and intrinsic excitability. Importantly, restoring OTUD7A or Ankyrin-G expression in 15q13.3 microdeletion neurons led to a reversal of abnormalities. These data reveal a critical OTUD7A-Ankyrin pathway in neuronal development, which is impaired in the 15q13.3 microdeletion syndrome, leading to neuronal dysfunction. Furthermore, our study highlights the utility of targeting CNV genes using cell type-specific proteomics to identify shared and unexplored disease mechanisms across NDDs.
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180
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Samson R, Zangari F, Gingras AC. Studying Cellular Dynamics Using Proximity-Dependent Biotinylation: Somatic Cell Reprogramming. Methods Mol Biol 2023; 2718:23-52. [PMID: 37665453 DOI: 10.1007/978-1-0716-3457-8_3] [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] [Indexed: 09/05/2023]
Abstract
Assessing the reorganization of proteins and organelles following the induction of reprogramming and differentiation programs is crucial to understand the mechanistic underpinning of morphological and fate changes associated with these processes. The advent of proximity-dependent biotinylation (PDB) methods has overcome some of the limitations of biochemical purification methods, enabling proteomic characterization of most subcellular compartments. The first-generation PDB enzyme, the biotin ligase BirA* used in BioID, has now been used in multiple studies determining the cellular context in which proteins reside, typically under standard growth conditions and using long labeling (usually 8-24 h) times. Capitalizing on the generation of more active PDB enzymes such as miniTurbo that can generate strong biotinylation signals in minutes rather than hours, as well as the development of an inducible lentiviral toolkit for BioID, we define here protocols for time-resolved PDB in primary cells. Here, we report the optimization and application of lentivirally delivered miniTurbo constructs to a mouse fibroblast model of somatic cell reprogramming, allowing the study of this dynamic process. This detailed protocol also provides a baseline reference for researchers who wish to adapt these techniques to other dynamic cellular processes.
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Affiliation(s)
- Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Francesco Zangari
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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181
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Alexander EJ, Wang J. An Optimized Stress Granule Detection Method: Investigation of UBQLN2 Effect on Stress Granule Formation. Methods Mol Biol 2023; 2551:543-560. [PMID: 36310224 DOI: 10.1007/978-1-0716-2597-2_33] [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] [Indexed: 06/16/2023]
Abstract
Stress granules (SGs) are cytosolic ribonucleoprotein granules that form via a liquid-liquid phase separation in response to environmental stresses such as heat, oxidative, and osmotic changes. Due to the condensation of low complexity, hydrophobic regions in core SG components in these highly dynamic granules, defects in SG maintenance and formation have been linked to toxic aggregate formation in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. However, efforts to dissect mechanisms regulating SG formation and maintenance have been limited by methods of tracking protein-SG localization. Here we describe a method for detecting and quantifying recruitment of cytosolically enriched proteins to SGs by indirect immunofluorescence microscopy. Using this method, we tracked the transient recruitment of the cytosolically enriched ubiquitin-like protein, ubiquilin 2 (UBQLN2), and a number of other factors into SGs, demonstrating its utility (Alexander et al., Proc Natl Acad Sci U S A 115:E11485-E11494, 2018).
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Affiliation(s)
- Elizabeth J Alexander
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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182
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Martinez De La Cruz B, Darsinou M, Riccio A. From form to function: m 6A methylation links mRNA structure to metabolism. Adv Biol Regul 2023; 87:100926. [PMID: 36513580 PMCID: PMC10585597 DOI: 10.1016/j.jbior.2022.100926] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Reversible N6-methyladenosine (m6A) RNA modification is a posttranscriptional epigenetic modification of the RNA that regulates many key aspects of RNA metabolism and function. In this review, we highlight major recent advances in the field, with special emphasis on the potential link between m6A modifications and RNA structure. We will also discuss the role of RNA methylation of neuronal transcripts, and the emerging evidence of a potential role in RNA transport and local translation in dendrites and axons of transcripts involved in synaptic functions and axon growth.
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Affiliation(s)
| | - Marousa Darsinou
- UCL Laboratory for Molecular Cell Biology - University College London, Gower Street, WC1E 6BT, London, UK
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology - University College London, Gower Street, WC1E 6BT, London, UK.
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183
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Ito-Kureha T, Heissmeyer V. Critical functions of N 6-adenosine methylation of mRNAs in T cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119380. [PMID: 36228837 DOI: 10.1016/j.bbamcr.2022.119380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022]
Abstract
The existence of N6-adenosine methylation (m6A) of mRNA has been known for a long time, but only recently its regulatory potential was uncovered. Current research deciphers the molecular determinants leading to the deposition of this modification and consequences for modified mRNAs. It also evaluates the importance of such modifications for specific cell types and programs. In this review, we summarize the current knowledge on m6A modification of mRNAs in conventional and regulatory T cells and T-cell-driven immune responses and pathology. We discuss the impact of m6A modification on T cell activation including cytokine and antigen receptor signaling or sensing of double-stranded RNAs (dsRNA).
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Affiliation(s)
- Taku Ito-Kureha
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, 82152 Planegg-Martinsried, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, 82152 Planegg-Martinsried, Germany; Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, 81377 Munich, Germany.
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184
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Baskaran P, Mihaylov SR, Vinsland E, Shah K, Granat L, Ultanir SK, Tee AR, Murn J, Bateman JM. Phosphorylation of the novel mTOR substrate Unkempt regulates cellular morphogenesis. J Biol Chem 2023; 299:102788. [PMID: 36509146 PMCID: PMC9852543 DOI: 10.1016/j.jbc.2022.102788] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Mechanistic target of rapamycin (mTOR) is a protein kinase that integrates multiple inputs to regulate anabolic cellular processes. For example, mTOR complex 1 (mTORC1) has key functions in growth control, autophagy, and metabolism. However, much less is known about the signaling components that act downstream of mTORC1 to regulate cellular morphogenesis. Here, we show that the RNA-binding protein Unkempt, a key regulator of cellular morphogenesis, is a novel substrate of mTORC1. We show that Unkempt phosphorylation is regulated by nutrient levels and growth factors via mTORC1. To analyze Unkempt phosphorylation, we immunoprecipitated Unkempt from cells in the presence or the absence of the mTORC1 inhibitor rapamycin and used mass spectrometry to identify mTORC1-dependent phosphorylated residues. This analysis showed that mTORC1-dependent phosphorylation is concentrated in a serine-rich intrinsically disordered region in the C-terminal half of Unkempt. We also found that Unkempt physically interacts with and is directly phosphorylated by mTORC1 through binding to the regulatory-associated protein of mTOR, Raptor. Furthermore, analysis in the developing brain of mice lacking TSC1 expression showed that phosphorylation of Unkempt is mTORC1 dependent in vivo. Finally, mutation analysis of key serine/threonine residues in the serine-rich region indicates that phosphorylation inhibits the ability of Unkempt to induce a bipolar morphology. Phosphorylation within this serine-rich region thus profoundly affects the ability of Unkempt to regulate cellular morphogenesis. Taken together, our findings reveal a novel molecular link between mTORC1 signaling and cellular morphogenesis.
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Affiliation(s)
- Pranetha Baskaran
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Simeon R Mihaylov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; Kinases and Brain Development Lab, The Francis Crick Institute, London, UK
| | - Elin Vinsland
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Kriti Shah
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Lucy Granat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sila K Ultanir
- Kinases and Brain Development Lab, The Francis Crick Institute, London, UK
| | - Andrew R Tee
- Cancer and Genetics Building, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park Way, Cardiff, UK
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, California, USA.
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
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185
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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186
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Yu T, Wu F, Jia Y, Zhang X, Qi X, Jin Z, Hao T, Zhao J, Liu Z, Wang C, Niu M, Yue Q, Li M, Liu Y. RNA N 6-methyladenosine modification mediates downregulation of NR4A1 to facilitate malignancy of cervical cancer. Cell Biosci 2022; 12:207. [PMID: 36566195 DOI: 10.1186/s13578-022-00937-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/05/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND N6-methyladenosine is the most abundant eukaryotic mRNA modification and alters a wide range of cellular processes in cancer. Therefore, defining the molecular details are critical for understanding the regulatory mechanism of m6A modification. RESULTS We found that METTL3, a core m6A methyltransferase component, is upregulated and functions as an oncogene in cervical cancer. Mechanistically, METTL3 induces the degradation of m6A-modified transcripts of NR4A1 though YTHDF2-DDX6 pathway. In addition, NR4A1 overexpression attenuates the malignant progression through recruiting the LSD1/HDAC1/CoREST transcriptional repression complex to AKT1 promoter. CONCLUSIONS Our findings reveal that m6A regulates cervical cancer cellular progression through manipulating NR4A1 pathway.
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Affiliation(s)
- Tao Yu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Fuxia Wu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yan Jia
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xue Zhang
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaozhen Qi
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zeyuan Jin
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Tongxin Hao
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jianing Zhao
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ziyu Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chaokun Wang
- Department of Integrative Chinese and Western Medicine, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Minmin Niu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Qin Yue
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Min Li
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yankun Liu
- Department of Molecular Diagnosis, Tangshan People's Hospital, Tangshan, 063001, China.
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187
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PARP1 Activation Controls Stress Granule Assembly after Oxidative Stress and DNA Damage. Cells 2022; 11:cells11233932. [PMID: 36497190 PMCID: PMC9740212 DOI: 10.3390/cells11233932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
DNA damage causes PARP1 activation in the nucleus to set up the machinery responsible for the DNA damage response. Here, we report that, in contrast to cytoplasmic PARPs, the synthesis of poly(ADP-ribose) by PARP1 opposes the formation of cytoplasmic mRNA-rich granules after arsenite exposure by reducing polysome dissociation. However, when mRNA-rich granules are pre-formed, whether in the cytoplasm or nucleus, PARP1 activation positively regulates their assembly, though without additional recruitment of poly(ADP-ribose) in stress granules. In addition, PARP1 promotes the formation of TDP-43- and FUS-rich granules in the cytoplasm, two RNA-binding proteins which form neuronal cytoplasmic inclusions observed in certain neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Together, the results therefore reveal a dual role of PARP1 activation which, on the one hand, prevents the early stage of stress granule assembly and, on the other hand, enables the persistence of cytoplasmic mRNA-rich granules in cells which may be detrimental in aging neurons.
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188
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Sadasivan J, Vlok M, Wang X, Nayak A, Andino R, Jan E. Targeting Nup358/RanBP2 by a viral protein disrupts stress granule formation. PLoS Pathog 2022; 18:e1010598. [PMID: 36455064 PMCID: PMC9746944 DOI: 10.1371/journal.ppat.1010598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Viruses have evolved mechanisms to modulate cellular pathways to facilitate infection. One such pathway is the formation of stress granules (SG), which are ribonucleoprotein complexes that assemble during translation inhibition following cellular stress. Inhibition of SG assembly has been observed under numerous virus infections across species, suggesting a conserved fundamental viral strategy. However, the significance of SG modulation during virus infection is not fully understood. The 1A protein encoded by the model dicistrovirus, Cricket paralysis virus (CrPV), is a multifunctional protein that can bind to and degrade Ago-2 in an E3 ubiquitin ligase-dependent manner to block the antiviral RNA interference pathway and inhibit SG formation. Moreover, the R146 residue of 1A is necessary for SG inhibition and CrPV infection in both Drosophila S2 cells and adult flies. Here, we uncoupled CrPV-1A's functions and provide insight into its underlying mechanism for SG inhibition. CrPV-1A mediated inhibition of SGs requires the E3 ubiquitin-ligase binding domain and the R146 residue, but not the Ago-2 binding domain. Wild-type but not mutant CrPV-1A R146A localizes to the nuclear membrane which correlates with nuclear enrichment of poly(A)+ RNA. Transcriptome changes in CrPV-infected cells are dependent on the R146 residue. Finally, Nup358/RanBP2 is targeted and degraded in CrPV-infected cells in an R146-dependent manner and the depletion of Nup358 blocks SG formation. We propose that CrPV utilizes a multiprong strategy whereby the CrPV-1A protein interferes with a nuclear event that contributes to SG inhibition in order to promote infection.
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Affiliation(s)
- Jibin Sadasivan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xinying Wang
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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189
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Kurosaki T, Mitsutomi S, Hewko A, Akimitsu N, Maquat LE. Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells. Mol Cell 2022; 82:4564-4581.e11. [PMID: 36356584 PMCID: PMC9753132 DOI: 10.1016/j.molcel.2022.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/17/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
How fragile X syndrome protein (FMRP) binds mRNAs and regulates mRNA metabolism remains unclear. Our previous work using human neuronal cells focused on mRNAs targeted for nonsense-mediated mRNA decay (NMD), which we showed are generally bound by FMRP and destabilized upon FMRP loss. Here, we identify >400 high-confidence FMRP-bound mRNAs, only ∼35% of which are NMD targets. Integrative transcriptomics together with SILAC-LC-MS/MS reveal that FMRP loss generally results in mRNA destabilization and more protein produced per FMRP target. We use our established RIP-seq technology to show that FMRP footprints are independent of protein-coding potential, target GC-rich and structured sequences, and are densest in 5' UTRs. Regardless of where within an mRNA FMRP binds, we find that FMRP protects mRNAs from deadenylation and directly binds the cytoplasmic poly(A)-binding protein. Our results reveal how FMRP sequesters polyadenylated mRNAs into stabilized and translationally repressed complexes, whose regulation is critical for neurogenesis and synaptic plasticity.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| | - Shuhei Mitsutomi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA; Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Alexander Hewko
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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190
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Zhang T, Su S, Altouma V, Zhu X, Xue Y, Shen W, Wilgenburg B, Wang W. Topoisomerase 3b is dispensable for replication of a positive-sense RNA virus--murine coronavirus. Antiviral Res 2022; 208:105451. [PMID: 36328071 PMCID: PMC9618458 DOI: 10.1016/j.antiviral.2022.105451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/02/2022]
Abstract
A recent study demonstrated that a DNA-RNA dual-activity topoisomerase complex, TOP3B-TDRD3, is required for normal replication of positive-sense RNA viruses, including several human flaviviruses and coronaviruses; and the authors proposed that TOP3B is a target of antiviral drugs. Here we examined this hypothesis by investigating whether inactivation of Top3b can inhibit the replication of a mouse coronavirus, MHV, using cell lines and mice that are inactivated of Top3b or Tdrd3. We found that Top3b-KO or Tdrd3-KO cell lines generated by different CRISPR-CAS9 guide RNAs have variable effects on MHV replication. In addition, we did not find significant changes of MHV replication in brains or lungs in Top3B-KO mice. Moreover, immunostaining showed that Top3b proteins are not co-localized with MHV replication complexes but rather, localized in stress granules in the MHV-infected cells. Our results suggest that Top3b does not have a universal role in promoting replication of positive-sense RNA virus, and cautions should be taken when targeting it to develop anti-viral drugs.
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Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Xingliang Zhu
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Brian Wilgenburg
- Comparative Medicine Section, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA.
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191
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Prokofeva P, Höfer S, Hornisch M, Abele M, Kuster B, Médard G. Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors. ACS Chem Biol 2022; 17:3100-3109. [PMID: 36302507 PMCID: PMC9680877 DOI: 10.1021/acschembio.2c00500] [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: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 01/20/2023]
Abstract
Finding the targets of natural products is of key importance in both chemical biology and drug discovery, and deconvolution of cofactor interactomes contributes to the functional annotation of the proteome. Identifying the proteins that underlie natural compound activity in phenotypic screens helps to validate the respective targets and, potentially, expand the druggable proteome. Here, we present a generally applicable protocol for the photoactivated immobilization of unmodified and microgram quantities of natural products on diazirine-decorated beads and their use for systematic affinity-based proteome profiling. We show that among 31 molecules of very diverse reported activity and biosynthetic origin, 25 could indeed be immobilized. Dose-response competition binding experiments using lysates of human or bacterial cells followed by quantitative mass spectrometry recapitulated targets of 9 molecules with <100 μM affinity. Among them, immobilization of coenzyme A produced a tool to interrogate proteins containing a HotDog domain. Surprisingly, immobilization of the cofactor flavin adenine dinucleotide (FAD) led to the identification of nanomolar interactions with dozens of RNA-binding proteins.
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Affiliation(s)
- Polina Prokofeva
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Höfer
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Maximilian Hornisch
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Miriam Abele
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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192
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Jia J, Wang F, Bhujabal Z, Peters R, Mudd M, Duque T, Allers L, Javed R, Salemi M, Behrends C, Phinney B, Johansen T, Deretic V. Stress granules and mTOR are regulated by membrane atg8ylation during lysosomal damage. J Cell Biol 2022; 221:e202207091. [PMID: 36179369 PMCID: PMC9533235 DOI: 10.1083/jcb.202207091] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 01/22/2023] Open
Abstract
We report that lysosomal damage is a hitherto unknown inducer of stress granule (SG) formation and that the process termed membrane atg8ylation coordinates SG formation with mTOR inactivation during lysosomal stress. SGs were induced by lysosome-damaging agents including SARS-CoV-2ORF3a, Mycobacterium tuberculosis, and proteopathic tau. During damage, mammalian ATG8s directly interacted with the core SG proteins NUFIP2 and G3BP1. Atg8ylation was needed for their recruitment to damaged lysosomes independently of SG condensates whereupon NUFIP2 contributed to mTOR inactivation via the Ragulator-RagA/B complex. Thus, cells employ membrane atg8ylation to control and coordinate SG and mTOR responses to lysosomal damage.
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Affiliation(s)
- Jingyue Jia
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Fulong Wang
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zambarlal Bhujabal
- Autophagy Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ryan Peters
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michal Mudd
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Thabata Duque
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Lee Allers
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michelle Salemi
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, Davis, CA
| | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Brett Phinney
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, Davis, CA
| | - Terje Johansen
- Autophagy Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
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193
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Xia M, Wang S, Ye Y, Tu Y, Huang T, Gao L. Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy. Front Immunol 2022; 13:995645. [PMID: 36389678 PMCID: PMC9664221 DOI: 10.3389/fimmu.2022.995645] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/17/2022] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Accumulating evidence suggests that N6-methyladenosine (m6A) RNA methylation plays an important role in tumor proliferation and growth. However, its effect on the clinical prognosis, immune infiltration, and immunotherapy response of thyroid cancer patients has not been investigated in detail. METHODS Clinical data and RNA expression profiles of thyroid cancer were extracted from the Cancer Genome Atlas-thyroid carcinoma (TCGA-THCA) and preprocessed for consensus clustering. The risk model was constructed based on differentially expressed genes (DEGs) using Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression analyses. The associations between risk score and clinical traits, immune infiltration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), immune infiltration, and immunotherapy were assessed. Immunohistochemistry was used to substantiate the clinical traits of our samples. RESULTS Gene expression analysis showed that 17 genes, except YHTDF2, had significant differences (vs healthy control, P<0.001). Consensus clustering yielded 2 clusters according to their clinical features and estimated a poorer prognosis for Cluster 1 (P=0.03). The heatmap between the 2 clusters showed differences in T (P<0.01), N (P<0.001) and stage (P<0.01). Based on univariate Cox and LASSO regression, a risk model consisting of three high-risk genes (KIAA1429, RBM15, FTO) was established, and the expression difference between normal and tumor tissues of three genes was confirmed by immunohistochemical results of our clinical tissues. KEGG and GSEA analyses showed that the risk DEGs were related mainly to proteolysis, immune response, and cancer pathways. The levels of immune infiltration in the high- and low-risk groups were different mainly in iDCs (P<0.05), NK cells (P<0.05), and type-INF-II (P<0.001). Immunotherapy analysis yielded 30 drugs associated with the expression of each gene and 20 drugs associated with the risk score. CONCLUSIONS Our risk model can act as an independent marker for thyroid cancer and provides promising immunotherapy targets for its treatment.
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Affiliation(s)
- Minqi Xia
- Department of Endocrinology and Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shuo Wang
- Department of Endocrinology and Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yingchun Ye
- Department of Endocrinology and Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Tu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tiantian Huang
- Department of Endocrinology and Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ling Gao
- Department of Endocrinology and Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
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Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, Bader GD, Scherer SW, Lu Y, Singh KK. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Cell Rep 2022; 41:111678. [DOI: 10.1016/j.celrep.2022.111678] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
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195
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Essential Functions of Calmodulin and Identification of Its Proximal Interacting Proteins in Tachyzoite-Stage Toxoplasma gondii via BioID Technology. Microbiol Spectr 2022; 10:e0136322. [PMID: 36214684 PMCID: PMC9602672 DOI: 10.1128/spectrum.01363-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Toxoplasma gondii (T. gondii) is a pathogen belonging to the apicomplexan phylum, and it threatens human and animal health. Calcium ions, a critical second messenger in cells, can regulate important biological processes, including parasite invasion and egress. Calmodulin (CaM) is a small, highly conserved, Ca2+-binding protein found in all eukaryotic cells. After binding to Ca2+, CaM can be activated to interact with various proteins. However, little is known about CaM's function and its interacting proteins in T. gondii. In this study, we successfully knocked down CaM in the T. gondii parent strain TATI using a tetracycline-off system with the Toxoplasma CaM promoter. The results indicated that CaM was required for tachyzoite proliferation, invasion, and egress and that CaM depletion resulted in apicoplast loss, thus threatening parasite survival in the next lytic cycle. In the tachyzoite stage, CaM loss caused significant anomalies in the parasite's basal constriction, motility, and parasite rosette-like arrangement in the parasitophorous vacuole (PV). These phenotypic defects caused by CaM depletion indicate the importance of CaM in T. gondii. Therefore, it is important to identify the CaM-interacting proteins in T. gondii. Applying BioID technology, more than 300 CaM's proximal interacting proteins were identified from T. gondii. These CaM partners were broadly distributed throughout the parasite. Furthermore, the protein interactome and transcriptome analyses indicated the potential role of CaM in ion binding, cation binding, metal ion binding, calcium ion binding, and oxidation-reduction. Our findings shed light on the CaM function and CaM-interactome in T. gondii and other eukaryotes. IMPORTANCE Toxoplasma gondii is an intracellular pathogen that threatens human and animal health. This unicellular parasite is active in many biological processes, such as egress and invasion. The implementation efficiency of T. gondii biological processes is dependent on signal transmission. Ca2+, as a second messenger, is essential for the parasite's life cycle. Calmodulin, a ubiquitous Ca2+ receptor protein, is highly conserved and mediates numerous Ca2+-dependent events in eukaryotes. Few CaM functions or regulated partners have been characterized in T. gondii tachyzoites. Here, we reported the essential functions of calmodulin in T. gondii tachyzoite and the identification of its interacting partners using BioID technology, shedding light on the CaM function and CaM-interactome in Toxoplasma gondii and other eukaryotes.
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196
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Ying Z, Wang K, Wu J, Wang M, Yang J, Wang X, Zhou G, Chen H, Xu H, Sze SCW, Gao F, Li C, Sha O. CCHCR1-astrin interaction promotes centriole duplication through recruitment of CEP72. BMC Biol 2022; 20:240. [PMID: 36280838 PMCID: PMC9590400 DOI: 10.1186/s12915-022-01437-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/14/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The centrosome is one of the most important non-membranous organelles regulating microtubule organization and progression of cell mitosis. The coiled-coil alpha-helical rod protein 1 (CCHCR1, also known as HCR) gene is considered to be a psoriasis susceptibility gene, and the protein is suggested to be localized to the P-bodies and centrosomes in mammalian cells. However, the exact cellular function of HCR and its potential regulatory role in the centrosomes remain unexplored. RESULTS We found that HCR interacts directly with astrin, a key factor in centrosome maturation and mitosis. Immunoprecipitation assays showed that the coiled-coil region present in the C-terminus of HCR and astrin respectively mediated the interaction between them. Astrin not only recruits HCR to the centrosome, but also protects HCR from ubiquitin-proteasome-mediated degradation. In addition, depletion of either HCR or astrin significantly reduced centrosome localization of CEP72 and subsequent MCPH proteins, including CEP152, CDK5RAP2, and CEP63. The absence of HCR also caused centriole duplication defects and mitotic errors, resulting in multipolar spindle formation, genomic instability, and DNA damage. CONCLUSION We conclude that HCR is localized and stabilized at the centrosome by directly binding to astrin. HCR are required for the centrosomal recruitment of MCPH proteins and centriolar duplication. Both HCR and astrin play key roles in keeping normal microtubule assembly and maintaining genomic stability.
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Affiliation(s)
- Zhenguang Ying
- Department of Anatomy, Histology and Developmental Biology, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Kaifang Wang
- Department of Anatomy, Histology and Developmental Biology, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Junfeng Wu
- Department of Anatomy, Histology and Developmental Biology, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Mingyu Wang
- Medical AI Laboratory, School of Biomedical Engineering, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Jing Yang
- Department of Anatomy, Histology and Developmental Biology, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Xia Wang
- Department of Anatomy, Histology and Developmental Biology, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Guowei Zhou
- Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Haibin Chen
- Department of Histology and Embryology, Shantou University Medical College, Shantou, 515000, China
| | - Hongwu Xu
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
- Department of Clinically Oriented Anatomy, Shantou University Medical College, Shantou, 515000, China
| | - Stephen Cho Wing Sze
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hongkong, 999077, China
- Golden Meditech Centre for NeuroRegeneration Sciences, Hong Kong Baptist University, Hongkong, 999077, China
| | - Feng Gao
- School of Dentistry, Shenzhen University Health Science Centre, Shenzhen, 518000, China
| | - Chunman Li
- Department of Anatomy, Shantou University Medical College, Shantou, 515000, China.
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515000, China.
| | - Ou Sha
- Department of Anatomy, Histology and Developmental Biology, Shenzhen University Health Science Centre, Shenzhen, 518000, China.
- School of Dentistry, Shenzhen University Health Science Centre, Shenzhen, 518000, China.
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197
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mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading. Cell Rep 2022; 41:111548. [DOI: 10.1016/j.celrep.2022.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
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198
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Kokot T, Köhn M. Emerging insights into serine/threonine-specific phosphoprotein phosphatase function and selectivity. J Cell Sci 2022; 135:277104. [DOI: 10.1242/jcs.259618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ABSTRACT
Protein phosphorylation on serine and threonine residues is a widely distributed post-translational modification on proteins that acts to regulate their function. Phosphoprotein phosphatases (PPPs) contribute significantly to a plethora of cellular functions through the accurate dephosphorylation of phosphorylated residues. Most PPPs accomplish their purpose through the formation of complex holoenzymes composed of a catalytic subunit with various regulatory subunits. PPP holoenzymes then bind and dephosphorylate substrates in a highly specific manner. Despite the high prevalence of PPPs and their important role for cellular function, their mechanisms of action in the cell are still not well understood. Nevertheless, substantial experimental advancements in (phospho-)proteomics, structural and computational biology have contributed significantly to a better understanding of PPP biology in recent years. This Review focuses on recent approaches and provides an overview of substantial new insights into the complex mechanism of PPP holoenzyme regulation and substrate selectivity.
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Affiliation(s)
- Thomas Kokot
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg 1 , Freiburg 79104 , Germany
- University of Freiburg, 2 Faculty of Biology , Freiburg 79104 , Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg 1 , Freiburg 79104 , Germany
- University of Freiburg, 2 Faculty of Biology , Freiburg 79104 , Germany
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199
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Delle Vedove A, Natarajan J, Zanni G, Eckenweiler M, Muiños-Bühl A, Storbeck M, Guillén Boixet J, Barresi S, Pizzi S, Hölker I, Körber F, Franzmann TM, Bertini ES, Kirschner J, Alberti S, Tartaglia M, Wirth B. CAPRIN1 P512L causes aberrant protein aggregation and associates with early-onset ataxia. Cell Mol Life Sci 2022; 79:526. [PMID: 36136249 PMCID: PMC9499908 DOI: 10.1007/s00018-022-04544-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/15/2022] [Accepted: 08/31/2022] [Indexed: 12/26/2022]
Abstract
CAPRIN1 is a ubiquitously expressed protein, abundant in the brain, where it regulates the transport and translation of mRNAs of genes involved in synaptic plasticity. Here we describe two unrelated children, who developed early-onset ataxia, dysarthria, cognitive decline and muscle weakness. Trio exome sequencing unraveled the identical de novo c.1535C > T (p.Pro512Leu) missense variant in CAPRIN1, affecting a highly conserved residue. In silico analyses predict an increased aggregation propensity of the mutated protein. Indeed, overexpressed CAPRIN1P512L forms insoluble ubiquitinated aggregates, sequestrating proteins associated with neurodegenerative disorders (ATXN2, GEMIN5, SNRNP200 and SNCA). Moreover, the CAPRIN1P512L mutation in isogenic iPSC-derived cortical neurons causes reduced neuronal activity and altered stress granule dynamics. Furthermore, nano-differential scanning fluorimetry reveals that CAPRIN1P512L aggregation is strongly enhanced by RNA in vitro. These findings associate the gain-of-function Pro512Leu mutation to early-onset ataxia and neurodegeneration, unveiling a critical residue of CAPRIN1 and a key role of RNA–protein interactions.
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Affiliation(s)
- Andrea Delle Vedove
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Janani Natarajan
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Ginevra Zanni
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Matthias Eckenweiler
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, 79106, Freiburg, Germany
| | - Anixa Muiños-Bühl
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Jordina Guillén Boixet
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Irmgard Hölker
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Friederike Körber
- Institute of Diagnostic and Interventional Radiology, 50937, Cologne, Germany
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Enrico S Bertini
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, 79106, Freiburg, Germany
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany. .,Institute for Genetics, University of Cologne, 50674, Cologne, Germany. .,Center for Rare Diseases, University Hospital of Cologne, 50931, Cologne, Germany.
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200
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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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