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Kim J, Song CH. Stress Granules in Infectious Disease: Cellular Principles and Dynamic Roles in Immunity and Organelles. Int J Mol Sci 2024; 25:12950. [PMID: 39684660 DOI: 10.3390/ijms252312950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 11/29/2024] [Accepted: 12/01/2024] [Indexed: 12/18/2024] Open
Abstract
Stress granules (SGs) are membrane-less aggregates that form in response to various cellular stimuli through a process called liquid-liquid phase separation (LLPS). Stimuli such as heat shock, osmotic stress, oxidative stress, and infections can induce the formation of SGs, which play crucial roles in regulating gene expression to help cells adapt to stress conditions. Various mRNAs and proteins are aggregated into SGs, particularly those associated with the protein translation machinery, which are frequently found in SGs. When induced by infections, SGs modulate immune cell activity, supporting the cellular response against infection. The roles of SGs differ in viral versus microbial infections, and depending on the type of immune cell involved, SGs function differently in response to infection. In this review, we summarize our current understanding of the implication of SGs in immunity and cellular organelles in the context of infectious diseases. Importantly, we explore insights into the regulatory functions of SGs in the context of host cells under infection.
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Affiliation(s)
- Jaewhan Kim
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Chang-Hwa Song
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
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Zhang Y, Kang HR, Jun Y, Kang H, Bang G, Ma R, Ju S, Yoon DE, Kim Y, Kim K, Kim JY, Han K. Neurodevelopmental disorder-associated CYFIP2 regulates membraneless organelles and eIF2α phosphorylation via protein interactors and actin cytoskeleton. Hum Mol Genet 2024; 33:1671-1687. [PMID: 38981622 DOI: 10.1093/hmg/ddae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/10/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
De novo variants in the Cytoplasmic FMR1-interacting protein 2 (CYFIP2) have been repeatedly associated with neurodevelopmental disorders and epilepsy, underscoring its critical role in brain development and function. While CYFIP2's role in regulating actin polymerization as part of the WAVE regulatory complex (WRC) is well-established, its additional molecular functions remain relatively unexplored. In this study, we performed unbiased quantitative proteomic analysis, revealing 278 differentially expressed proteins (DEPs) in the forebrain of Cyfip2 knock-out embryonic mice compared to wild-type mice. Unexpectedly, these DEPs, in conjunction with previously identified CYFIP2 brain interactors, included not only other WRC components but also numerous proteins associated with membraneless organelles (MLOs) involved in mRNA processing and translation within cells, including the nucleolus, stress granules, and processing bodies. Additionally, single-cell transcriptomic analysis of the Cyfip2 knock-out forebrain revealed gene expression changes linked to cellular stress responses and MLOs. We also observed morphological changes in MLOs in Cyfip2 knock-out brains and CYFIP2 knock-down cells under basal and stress conditions. Lastly, we demonstrated that CYFIP2 knock-down in cells, potentially through WRC-dependent actin regulation, suppressed the phosphorylation levels of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α), thereby enhancing protein synthesis. These results suggest a physical and functional connection between CYFIP2 and various MLO proteins and also extend CYFIP2's role within the WRC from actin regulation to influencing eIF2α phosphorylation and protein synthesis. With these dual functions, CYFIP2 may fine-tune the balance between MLO formation/dynamics and protein synthesis, a crucial aspect of proper mRNA processing and translation.
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Affiliation(s)
- Yinhua Zhang
- Department of Neuroscience, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hyae Rim Kang
- Department of Neuroscience, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Yukyung Jun
- Division of National Supercomputing, Korea Institute of Science and Technology Information (KISTI), 245, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyojin Kang
- Division of National Supercomputing, Korea Institute of Science and Technology Information (KISTI), 245, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Geul Bang
- Digital Omics Research Center, Korea Basic Science Institute (KBSI), 162, Yeongudanji-ro, Cheongwon-gu, Ochang 28119, Republic of Korea
| | - Ruiying Ma
- Department of Neuroscience, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sungjin Ju
- Department of Biomedical Sciences, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Physiology, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Da Eun Yoon
- Department of Biomedical Sciences, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Physiology, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Biomedical Sciences, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Physiology, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jin Young Kim
- Digital Omics Research Center, Korea Basic Science Institute (KBSI), 162, Yeongudanji-ro, Cheongwon-gu, Ochang 28119, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125, Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kihoon Han
- Department of Neuroscience, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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Vincek A, Wolf A, Thomas A, Ebel F, Schruefer S. The N-terminus of the Aspergillus fumigatus group III hybrid histidine kinase TcsC is essential for its physiological activity and targets the protein to the nucleus. mBio 2024; 15:e0118424. [PMID: 38832777 PMCID: PMC11253588 DOI: 10.1128/mbio.01184-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
Group III hybrid histidine kinases are fungal-specific proteins and part of the multistep phosphorelay, representing the initial part of the high osmolarity glycerol (HOG) pathway. TcsC, the corresponding kinase in Aspergillus fumigatus, was expected to be a cytosolic protein but is targeted to the nucleus. Activation of TcsC by the antifungal fludioxonil has lethal consequences for the fungus. The agent triggers a fast and TcsC-dependent activation of SakA and later on a redistribution of TcsC to the cytoplasm. High osmolarity also activates TcsC, which then exits the nucleus or concentrates in spot-like, intra-nuclear structures. The sequence corresponding to the N-terminal 208 amino acids of TcsC lacks detectable domains. Its loss renders TcsC cytosolic and non-responsive to hyperosmotic stress, but it has no impact on the antifungal activity of fludioxonil. A point mutation in one of the three putative nuclear localization sequences, which are present in the N-terminus, prevents the nuclear localization of TcsC, but not its ability to respond to hyperosmotic stress. Hence, this striking intracellular localization is no prerequisite for the role of TcsC in the adaptive response to hyperosmotic stress, instead, TcsC proteins that are present in the nuclei seem to modulate the cell wall composition of hyphae, which takes place in the absence of stress. The results of the present study underline that the spatiotemporal dynamics of the individual components of the multistep phosphorelay is a crucial feature of this unique signaling hub. IMPORTANCE Signaling pathways enable pathogens, such as Aspergillus fumigatus, to respond to a changing environment. The TcsC protein is the major sensor of the high osmolarity glycerol (HOG) pathway of A. fumigatus and it is also the target of certain antifungals. Insights in its function are therefore relevant for the pathogenicity and new therapeutic treatment options. TcsC was expected to be cytoplasmic, but we detected it in the nucleus and showed that it translocates to the cytoplasm upon activation. We have identified the motif that guides TcsC to the nucleus. An exchange of a single amino acid in this motif prevents a nuclear localization, but this nuclear targeting is no prerequisite for the TcsC-mediated stress response. Loss of the N-terminal 208 amino acids prevents the nuclear localization and renders TcsC unable to respond to hyperosmotic stress demonstrating that this part of the protein is of crucial importance.
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Affiliation(s)
- Anna Vincek
- Institute for Infectious Diseases and Zoonoses, LMU Munich, Germany
| | - Anja Wolf
- Institute for Infectious Diseases and Zoonoses, LMU Munich, Germany
| | - Astrid Thomas
- Institute for Infectious Diseases and Zoonoses, LMU Munich, Germany
| | - Frank Ebel
- Institute for Infectious Diseases and Zoonoses, LMU Munich, Germany
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Zhang X, Han L, Hou J, Yang H, Xu H, Li G, Shu Q, Zhu D, Zheng Y, Gao C. Stress granule-localized USP8 potentiates cGAS-mediated type I interferonopathies through deubiquitination of DDX3X. Cell Rep 2024; 43:114248. [PMID: 38795350 DOI: 10.1016/j.celrep.2024.114248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/26/2024] [Accepted: 05/02/2024] [Indexed: 05/27/2024] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) undergoes liquid-liquid phase separation (LLPS) to trigger downstream signaling upon double-stranded DNA (dsDNA) stimulation, and the condensed cGAS colocalizes with stress granules (SGs). However, the molecular mechanism underlying the modulation of cGAS activation by SGs remains elusive. In this study, we show that USP8 is localized to SGs upon dsDNA stimulation and potentiates cGAS-stimulator of interferon genes (STING) signaling. A USP8 inhibitor ameliorates pathological inflammation in Trex1-/- mice. Systemic lupus erythematosus (SLE) databases indicate a positive correlation between USP8 expression and SLE. Mechanistic study shows that the SG protein DDX3X promotes cGAS phase separation and activation in a manner dependent on its intrinsic LLPS. USP8 cleaves K27-linked ubiquitin chains from the intrinsically disordered region (IDR) of DDX3X to enhance its condensation. In conclusion, we demonstrate that USP8 catalyzes the deubiquitination of DDX3X to facilitate cGAS condensation and activation and that inhibiting USP8 is a promising strategy for alleviating cGAS-mediated autoimmune diseases.
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Affiliation(s)
- Xuejing Zhang
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Lulu Han
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Jinxiu Hou
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Huiyu Yang
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Haiyan Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Guosheng Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qiang Shu
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Deyu Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
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Coronas LE, Van T, Iorio A, Lapidus LJ, Feig M, Sterpone F. Stability and deformation of biomolecular condensates under the action of shear flow. J Chem Phys 2024; 160:215101. [PMID: 38832749 DOI: 10.1063/5.0209119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Biomolecular condensates play a key role in cytoplasmic compartmentalization and cell functioning. Despite extensive research on the physico-chemical, thermodynamic, or crowding aspects of the formation and stabilization of the condensates, one less studied feature is the role of external perturbative fluid flow. In fact, in living cells, shear stress may arise from streaming or active transport processes. Here, we investigate how biomolecular condensates are deformed under different types of shear flows. We first model Couette flow perturbations via two-way coupling between the condensate dynamics and fluid flow by deploying Lattice Boltzmann Molecular Dynamics. We then show that a simplified approach where the shear flow acts as a static perturbation (one-way coupling) reproduces the main features of the condensate deformation and dynamics as a function of the shear rate. With this approach, which can be easily implemented in molecular dynamics simulations, we analyze the behavior of biomolecular condensates described through residue-based coarse-grained models, including intrinsically disordered proteins and protein/RNA mixtures. At lower shear rates, the fluid triggers the deformation of the condensate (spherical to oblated object), while at higher shear rates, it becomes extremely deformed (oblated or elongated object). At very high shear rates, the condensates are fragmented. We also compare how condensates of different sizes and composition respond to shear perturbation, and how their internal structure is altered by external flow. Finally, we consider the Poiseuille flow that realistically models the behavior in microfluidic devices in order to suggest potential experimental designs for investigating fluid perturbations in vitro.
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Affiliation(s)
- Luis E Coronas
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Thong Van
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - Antonio Iorio
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Lisa J Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Fabio Sterpone
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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Belott CJ, Gusev OA, Kikawada T, Menze MA. Membraneless and membrane-bound organelles in an anhydrobiotic cell line are protected from desiccation-induced damage. Cell Stress Chaperones 2024; 29:425-436. [PMID: 38608858 PMCID: PMC11061232 DOI: 10.1016/j.cstres.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Anhydrobiotic species can survive virtually complete water loss by entering a reversible ametabolic glassy state that may persist for years in ambient conditions. The Pv11 cell line was derived from the egg mass of the anhydrobiotic midge, Polypedilum vanderplanki, and is currently the only available anhydrobiotic cell line. Our results demonstrate that the necessary preconditioning for Pv11 cells to enter anhydrobiosis causes autophagy and reduces mitochondrial respiration by over 70%. We speculate that reorganizing cellular bioenergetics to create and conserve energy stores may be valuable to successfully recover after rehydration. Furthermore, mitochondria in preconditioned cells lose their membrane potential during desiccation but rapidly restore it within 30 min upon rehydration, demonstrating that the inner mitochondrial membrane integrity is well-preserved. Strikingly, the nucleolus remains visible immediately upon rehydration in preconditioned cells while absent in control cells. In contrast, a preconditioning-induced membraneless organelle reformed after rehydration, demonstrating that membraneless organelles in Pv11 cells can be either stabilized or recovered. Staining the endoplasmic reticulum and the Golgi apparatus revealed that these organelles fragment during preconditioning. We hypothesize that this process reduces sheering stress caused by rapid changes in cellular volume during desiccation and rehydration. Additionally, preconditioning was found to cause the filamentous-actin (F-actin) network to disassemble significantly and reduce the fusion of adjacent plasma membranes. This study offers several exciting avenues for future studies in the animal model and Pv11 cell line that will further our understanding of anhydrobiosis and may lead to advancements in storing sensitive biologics at ambient temperatures for months or years.
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Affiliation(s)
- Clinton J Belott
- Department of Biology, University of Louisville, Louisville, KY, USA; Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
| | - Oleg A Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan, Russia; Molecular Biomimetics Group, Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia; Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo, Japan.
| | - Takahiro Kikawada
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
| | - Michael A Menze
- Department of Biology, University of Louisville, Louisville, KY, USA
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Pinto CM, Schnepper AP, Trindade PHE, Cardoso LH, Fioretto MN, Justulin LA, Zanelli CF, Valente GT. The joint action of yeast eisosomes and membraneless organelles in response to ethanol stress. Heliyon 2024; 10:e31561. [PMID: 38818138 PMCID: PMC11137566 DOI: 10.1016/j.heliyon.2024.e31561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Elevated ethanol concentrations in yeast affect the plasma membrane. The plasma membrane in yeast has many lipid-protein complexes, such as Pma1 (MCP), Can1 (MCC), and the eisosome complex. We investigated the response of eisosomes, MCPs, and membraneless structures to ethanol stress. We found a correlation between ethanol stress and proton flux with quick acidification of the medium. Moreover, ethanol stress influences the symporter expression in stressed cells. We also suggest that acute stress from ethanol leads to increases in eisosome size and SG number: we hypothesized that eisosomes may protect APC symporters and accumulate an mRNA decay protein in ethanol-stressed cells. Our findings suggest that the joint action of these factors may provide a protective effect on cells under ethanol stress.
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Affiliation(s)
- Camila Moreira Pinto
- Laboratory of Applied Biotechnology. São Paulo State University (UNESP). Botucatu, Brazil
| | | | - Pedro Henrique Esteves Trindade
- Department of Population Health and Pathobiology College of Veterinary Medicine, North Carolina State University (NCSU) Raleigh, USA
| | - Luiz Henrique Cardoso
- Laboratory of Applied Biotechnology. São Paulo State University (UNESP). Botucatu, Brazil
| | - Matheus Naia Fioretto
- Department of Structural and Functional Biology, Institute of Biosciences. São Paulo State University (UNESP). Botucatu, Brazil
| | - Luís Antônio Justulin
- Department of Structural and Functional Biology, Institute of Biosciences. São Paulo State University (UNESP). Botucatu, Brazil
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar EH, Abu Zeid IM, Bouback TA, Bamagoos A, Uversky VN, Rubio-Casillas A, Redwan EM. Intrinsic factors behind long COVID: IV. Hypothetical roles of the SARS-CoV-2 nucleocapsid protein and its liquid-liquid phase separation. J Cell Biochem 2024; 125:e30530. [PMID: 38349116 DOI: 10.1002/jcb.30530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
When the SARS-CoV-2 virus infects humans, it leads to a condition called COVID-19 that has a wide spectrum of clinical manifestations, from no symptoms to acute respiratory distress syndrome. The virus initiates damage by attaching to the ACE-2 protein on the surface of endothelial cells that line the blood vessels and using these cells as hosts for replication. Reactive oxygen species levels are increased during viral replication, which leads to oxidative stress. About three-fifths (~60%) of the people who get infected with the virus eradicate it from their body after 28 days and recover their normal activity. However, a large fraction (~40%) of the people who are infected with the virus suffer from various symptoms (anosmia and/or ageusia, fatigue, cough, myalgia, cognitive impairment, insomnia, dyspnea, and tachycardia) beyond 12 weeks and are diagnosed with a syndrome called long COVID. Long-term clinical studies in a group of people who contracted SARS-CoV-2 have been contrasted with a noninfected matched group of people. A subset of infected people can be distinguished by a set of cytokine markers to have persistent, low-grade inflammation and often self-report two or more bothersome symptoms. No medication can alleviate their symptoms efficiently. Coronavirus nucleocapsid proteins have been investigated extensively as potential drug targets due to their key roles in virus replication, among which is their ability to bind their respective genomic RNAs for incorporation into emerging virions. This review highlights basic studies of the nucleocapsid protein and its ability to undergo liquid-liquid phase separation. We hypothesize that this ability of the nucleocapsid protein for phase separation may contribute to long COVID. This hypothesis unlocks new investigation angles and could potentially open novel avenues for a better understanding of long COVID and treating this condition.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab H Mattar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Moscow Region, Russia
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, Jalisco, Mexico
- Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, Jalisco, Mexico
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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9
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Saaoud F, Lu Y, Xu K, Shao Y, Praticò D, Vazquez-Padron RI, Wang H, Yang X. Protein-rich foods, sea foods, and gut microbiota amplify immune responses in chronic diseases and cancers - Targeting PERK as a novel therapeutic strategy for chronic inflammatory diseases, neurodegenerative disorders, and cancer. Pharmacol Ther 2024; 255:108604. [PMID: 38360205 PMCID: PMC10917129 DOI: 10.1016/j.pharmthera.2024.108604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
The endoplasmic reticulum (ER) is a cellular organelle that is physiologically responsible for protein folding, calcium homeostasis, and lipid biosynthesis. Pathological stimuli such as oxidative stress, ischemia, disruptions in calcium homeostasis, and increased production of normal and/or folding-defective proteins all contribute to the accumulation of misfolded proteins in the ER, causing ER stress. The adaptive response to ER stress is the activation of unfolded protein response (UPR), which affect a wide variety of cellular functions to maintain ER homeostasis or lead to apoptosis. Three different ER transmembrane sensors, including PKR-like ER kinase (PERK), activating transcription factor 6 (ATF6), and inositol-requiring enzyme-1 (IRE1), are responsible for initiating UPR. The UPR involves a variety of signal transduction pathways that reduce unfolded protein accumulation by boosting ER-resident chaperones, limiting protein translation, and accelerating unfolded protein degradation. ER is now acknowledged as a critical organelle in sensing dangers and determining cell life and death. On the other hand, UPR plays a critical role in the development and progression of several diseases such as cardiovascular diseases (CVD), metabolic disorders, chronic kidney diseases, neurological disorders, and cancer. Here, we critically analyze the most current knowledge of the master regulatory roles of ER stress particularly the PERK pathway as a conditional danger receptor, an organelle crosstalk regulator, and a regulator of protein translation. We highlighted that PERK is not only ER stress regulator by sensing UPR and ER stress but also a frontier sensor and direct senses for gut microbiota-generated metabolites. Our work also further highlighted the function of PERK as a central hub that leads to metabolic reprogramming and epigenetic modification which further enhanced inflammatory response and promoted trained immunity. Moreover, we highlighted the contribution of ER stress and PERK in the pathogenesis of several diseases such as cancer, CVD, kidney diseases, and neurodegenerative disorders. Finally, we discuss the therapeutic target of ER stress and PERK for cancer treatment and the potential novel therapeutic targets for CVD, metabolic disorders, and neurodegenerative disorders. Inhibition of ER stress, by the development of small molecules that target the PERK and UPR, represents a promising therapeutic strategy.
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Affiliation(s)
- Fatma Saaoud
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Yifan Lu
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Keman Xu
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Ying Shao
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Domenico Praticò
- Alzheimer's Center, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | | | - Hong Wang
- Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Xiaofeng Yang
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA; Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
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10
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Azam S, Armijo KS, Weindel CG, Chapman MJ, Devigne A, Nakagawa S, Hirose T, Carpenter S, Watson RO, Patrick KL. The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle. Proc Natl Acad Sci U S A 2024; 121:e2312587121. [PMID: 38381785 PMCID: PMC10907238 DOI: 10.1073/pnas.2312587121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the Neat1 lncRNA, in tuning innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophage paraspeckles rapidly aggregate (0.5 h poststimulation) and disaggregate (2 h poststimulation). Paraspeckle maintenance and aggregation require active transcription and MAPK signaling, whereas paraspeckle disaggregation requires degradation of Neat1 via the nuclear RNA exosome. In response to lipopolysaccharide treatment, Neat1 KO macrophages fail to properly express a large cohort of proinflammatory cytokines, chemokines, and antimicrobial mediators. Consequently, Neat1 KO macrophages cannot control replication of Salmonella enterica serovar Typhimurium or vesicular stomatitis virus. These findings highlight a prominent role for MLOs in orchestrating the macrophage response to pathogens and support a model whereby dynamic assembly and disassembly of paraspeckles reorganizes the nuclear landscape to enable inflammatory gene expression following innate stimuli.
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Affiliation(s)
- Sikandar Azam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Kaitlyn S. Armijo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Chi G. Weindel
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Morgan J. Chapman
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Alice Devigne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA95064
| | | | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Osaka565-0871, Japan
| | - Susan Carpenter
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA95064
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Kristin L. Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
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11
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Robinson AO, Lee J, Cameron A, Keating CD, Adamala KP. Cell-Free Expressed Membraneless Organelles Inhibit Translation in Synthetic Cells. ACS Biomater Sci Eng 2024; 10:773-781. [PMID: 38226971 DOI: 10.1021/acsbiomaterials.3c01052] [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: 01/17/2024]
Abstract
Compartments within living cells create specialized microenvironments, allowing multiple reactions to be carried out simultaneously and efficiently. While some organelles are bound by a lipid bilayer, others are formed by liquid-liquid phase separation such as P-granules and nucleoli. Synthetic minimal cells are widely used to study many natural processes, including organelle formation. In this work, synthetic cells expressing artificial membrane-less organelles that inhibit translation are described. RGG-GFP-RGG, a phase-separating protein derived from Caenorhabditis elegans P-granules, is expressed by cell-free transcription and translation, forming artificial membraneless organelles that can sequester RNA and reduce protein expression in synthetic cells. The introduction of artificial membrane-less organelles creates complex microenvironments within the synthetic cell cytoplasm and functions as a tool to inhibit protein expression in synthetic cells. The engineering of compartments within synthetic cells furthers the understanding of the evolution and function of natural organelles and facilitates the creation of more complex and multifaceted synthetic lifelike systems.
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Affiliation(s)
- Abbey O Robinson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
| | - Jessica Lee
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Anders Cameron
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
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12
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Kim N, Kim TH, Kim C, Lee JE, Kang MG, Shin S, Jung M, Kim JS, Mun JY, Rhee HW, Park SY, Shin Y, Yoo JY. Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Dev Cell 2023; 58:1950-1966.e8. [PMID: 37816329 DOI: 10.1016/j.devcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023]
Abstract
Newly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Tae-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghee Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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13
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Ries RJ, Pickering BF, Poh HX, Namkoong S, Jaffrey SR. m 6A governs length-dependent enrichment of mRNAs in stress granules. Nat Struct Mol Biol 2023; 30:1525-1535. [PMID: 37710015 PMCID: PMC10715973 DOI: 10.1038/s41594-023-01089-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/04/2023] [Indexed: 09/16/2023]
Abstract
Stress granules are biomolecular condensates composed of protein and mRNA. One feature of stress granule-enriched mRNAs is that they are often longer than average. Another feature of stress granule-enriched mRNAs is that they often contain multiple N6-methyladenosine (m6A) residues. m6A is bound by the YTHDF proteins, creating mRNA-protein complexes that partition into stress granules in mammalian cells. Here we show that length-dependent enrichment of mRNAs in stress granules is mediated by m6A. Long mRNAs often contain one or more long exons, which are preferential sites of m6A formation. In mammalian cells lacking m6A, long mRNAs no longer show preferential stress granule enrichment. Furthermore, we show that m6A abundance more strongly predicts which short or long mRNAs are enriched in stress granules, rather than length alone. Thus, mRNA length correlates with mRNA enrichment in stress granules owing to the high prevalence of m6A in long mRNAs.
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Affiliation(s)
- Ryan J Ries
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Brian F Pickering
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Hui Xian Poh
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sim Namkoong
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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14
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Singh S, Hu X, Dixelius C. Dynamics of nucleic acid mobility. Genetics 2023; 225:iyad132. [PMID: 37491977 PMCID: PMC10471207 DOI: 10.1093/genetics/iyad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species.
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Affiliation(s)
- Shailja Singh
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| | - Xinyi Hu
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
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15
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Wang Y, Liu R, Wu K, Yang G, Wang Y, Wang H, Rui T. Stress granule activation attenuates lipopolysaccharide-induced cardiomyocyte dysfunction. BMC Cardiovasc Disord 2023; 23:277. [PMID: 37312024 DOI: 10.1186/s12872-023-03281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/07/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Sepsis is the leading cause of death in intensive care units. Sepsis-induced myocardial dysfunction, one of the most serious complications of sepsis, is associated with higher mortality rates. As the pathogenesis of sepsis-induced cardiomyopathy has not been fully elucidated, there is no specific therapeutic approach. Stress granules (SG) are cytoplasmic membrane-less compartments that form in response to cellular stress and play important roles in various cell signaling pathways. The role of SG in sepsis-induced myocardial dysfunction has not been determined. Therefore, this study aimed to determine the effects of SG activation in septic cardiomyocytes (CMs). METHODS Neonatal CMs were treated with lipopolysaccharide (LPS). SG activation was visualized by immunofluorescence staining to detect the co-localization of GTPase-activating protein SH3 domain binding protein 1 (G3BP1) and T cell-restricted intracellular antigen 1 (TIA-1). Eukaryotic translation initiation factor alpha (eIF2α) phosphorylation, an indicator of SG formation, was assessed by western blotting. Tumor necrosis factor alpha (TNF-α) production was assessed by PCR and enzyme-linked immunosorbent assays. CMs function was evaluated by intracellular cyclic adenosine monophosphate (cAMP) levels in response to dobutamine. Pharmacological inhibition (ISRIB), a G3BP1 CRISPR activation plasmid, and a G3BP1 KO plasmid were employed to modulate SG activation. The fluorescence intensity of JC-1 was used to evaluate mitochondrial membrane potential. RESULTS LPS challenge in CMs induced SG activation and resulted in eIF2α phosphorylation, increased TNF-α production, and decreased intracellular cAMP in response to dobutamine. The pharmacological inhibition of SG (ISRIB) increased TNF-α expression and decreased intracellular cAMP levels in CMs treated with LPS. The overexpression of G3BP1 increased SG activation, attenuated the LPS-induced increase in TNF-α expression, and improved CMs contractility (as evidenced by increased intracellular cAMP). Furthermore, SG prevented LPS-induced mitochondrial membrane potential dissipation in CMs. CONCLUSION SG formation plays a protective role in CMs function in sepsis and is a candidate therapeutic target.
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Affiliation(s)
- Yaqiao Wang
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Runmin Liu
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Kehan Wu
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Gaowei Yang
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yusheng Wang
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Wang
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tao Rui
- Division of Cardiology, Department of Medicine, the Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
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16
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Robinson AO, Lee J, Cameron A, Keating CD, Adamala KP. Cell-free expressed membraneless organelles sequester RNA in synthetic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535479. [PMID: 37066403 PMCID: PMC10104018 DOI: 10.1101/2023.04.03.535479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Compartments within living cells create specialized microenvironments, allowing for multiple reactions to be carried out simultaneously and efficiently. While some organelles are bound by a lipid bilayer, others are formed by liquid-liquid phase separation, such as P-granules and nucleoli. Synthetic minimal cells have been widely used to study many natural processes, including organelle formation. Here we describe a synthetic cell expressing RGG-GFP-RGG, a phase-separating protein derived from LAF-1 RGG domains, to form artificial membraneless organelles that can sequester RNA and reduce protein expression. We create complex microenvironments within synthetic cell cytoplasm and introduce a tool to modulate protein expression in synthetic cells. Engineering of compartments within synthetic cells furthers understanding of evolution and function of natural organelles, as well as it facilitates the creation of more complex and multifaceted synthetic life-like systems.
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Affiliation(s)
- Abbey O Robinson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jessica Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Anders Cameron
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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17
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van Leeuwen W, Nguyen DTM, Grond R, Veenendaal T, Rabouille C, Farías GG. Stress-induced phase separation of ERES components into Sec bodies precedes ER exit inhibition in mammalian cells. J Cell Sci 2022; 135:jcs260294. [PMID: 36325988 PMCID: PMC10112967 DOI: 10.1242/jcs.260294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Phase separation of components of ER exit sites (ERES) into membraneless compartments, the Sec bodies, occurs in Drosophila cells upon exposure to specific cellular stressors, namely, salt stress and amino acid starvation, and their formation is linked to the early secretory pathway inhibition. Here, we show Sec bodies also form in secretory mammalian cells upon the same stress. These reversible and membraneless structures are positive for ERES components, including both Sec16A and Sec16B isoforms and COPII subunits. We find that Sec16A, but not Sec16B, is a driver for Sec body formation, and that the coalescence of ERES components into Sec bodies occurs by fusion. Finally, we show that the stress-induced coalescence of ERES components into Sec bodies precedes ER exit inhibition, leading to their progressive depletion from ERES that become non-functional. Stress relief causes an immediate dissolution of Sec bodies and the concomitant restoration of ER exit. We propose that the dynamic conversion between ERES and Sec body assembly, driven by Sec16A, regulates protein exit from the ER during stress and upon stress relief in mammalian cells, thus providing a conserved pro-survival mechanism in response to stress.
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Affiliation(s)
- Wessel van Leeuwen
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht 3584 CT, The Netherlands
| | - Dan T. M. Nguyen
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Rianne Grond
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht 3584 CT, The Netherlands
| | - Tineke Veenendaal
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht 3584 CT, The Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, Groningen 9713 AV, The Netherlands
| | - Ginny G. Farías
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
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18
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Fefilova AS, Antifeeva IA, Gavrilova AA, Turoverov KK, Kuznetsova IM, Fonin AV. Reorganization of Cell Compartmentalization Induced by Stress. Biomolecules 2022; 12:1441. [PMID: 36291650 PMCID: PMC9599104 DOI: 10.3390/biom12101441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022] Open
Abstract
The discovery of intrinsically disordered proteins (IDPs) that do not have an ordered structure and nevertheless perform essential functions has opened a new era in the understanding of cellular compartmentalization. It threw the bridge from the mostly mechanistic model of the organization of the living matter to the idea of highly dynamic and functional "soft matter". This paradigm is based on the notion of the major role of liquid-liquid phase separation (LLPS) of biopolymers in the spatial-temporal organization of intracellular space. The LLPS leads to the formation of self-assembled membrane-less organelles (MLOs). MLOs are multicomponent and multifunctional biological condensates, highly dynamic in structure and composition, that allow them to fine-tune the regulation of various intracellular processes. IDPs play a central role in the assembly and functioning of MLOs. The LLPS importance for the regulation of chemical reactions inside the cell is clearly illustrated by the reorganization of the intracellular space during stress response. As a reaction to various types of stresses, stress-induced MLOs appear in the cell, enabling the preservation of the genetic and protein material during unfavourable conditions. In addition, stress causes structural, functional, and compositional changes in the MLOs permanently present inside the cells. In this review, we describe the assembly of stress-induced MLOs and the stress-induced modification of existing MLOs in eukaryotes, yeasts, and prokaryotes in response to various stress factors.
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Affiliation(s)
| | | | | | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of RAS, 194064 St. Petersburg, Russia
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19
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Somasundaram K, Gupta B, Jain N, Jana S. LncRNAs divide and rule: The master regulators of phase separation. Front Genet 2022; 13:930792. [PMID: 36035193 PMCID: PMC9399341 DOI: 10.3389/fgene.2022.930792] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Most of the human genome, except for a small region that transcribes protein-coding RNAs, was considered junk. With the advent of RNA sequencing technology, we know that much of the genome codes for RNAs with no protein-coding potential. Long non-coding RNAs (lncRNAs) that form a significant proportion are dynamically expressed and play diverse roles in physiological and pathological processes. Precise spatiotemporal control of their expression is essential to carry out various biochemical reactions inside the cell. Intracellular organelles with membrane-bound compartments are known for creating an independent internal environment for carrying out specific functions. The formation of membrane-free ribonucleoprotein condensates resulting in intracellular compartments is documented in recent times to execute specialized tasks such as DNA replication and repair, chromatin remodeling, transcription, and mRNA splicing. These liquid compartments, called membrane-less organelles (MLOs), are formed by liquid–liquid phase separation (LLPS), selectively partitioning a specific set of macromolecules from others. While RNA binding proteins (RBPs) with low complexity regions (LCRs) appear to play an essential role in this process, the role of RNAs is not well-understood. It appears that short nonspecific RNAs keep the RBPs in a soluble state, while longer RNAs with unique secondary structures promote LLPS formation by specifically binding to RBPs. This review will update the current understanding of phase separation, physio-chemical nature and composition of condensates, regulation of phase separation, the role of lncRNA in the phase separation process, and the relevance to cancer development and progression.
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20
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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21
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Zubaite G, Hindley JW, Ces O, Elani Y. Dynamic Reconfiguration of Subcompartment Architectures in Artificial Cells. ACS NANO 2022; 16:9389-9400. [PMID: 35695383 PMCID: PMC9245354 DOI: 10.1021/acsnano.2c02195] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 06/01/2023]
Abstract
Artificial cells are minimal structures constructed from biomolecular building blocks designed to mimic cellular processes, behaviors, and architectures. One near-ubiquitous feature of cellular life is the spatial organization of internal content. We know from biology that organization of content (including in membrane-bound organelles) is linked to cellular functions and that this feature is dynamic: the presence, location, and degree of compartmentalization changes over time. Vesicle-based artificial cells, however, are not currently able to mimic this fundamental cellular property. Here, we describe an artificial cell design strategy that addresses this technological bottleneck. We create a series of artificial cell architectures which possess multicompartment assemblies localized either on the inner or on the outer surface of the artificial cell membrane. Exploiting liquid-liquid phase separation, we can also engineer spatially segregated regions of condensed subcompartments attached to the cell surface, aligning with coexisting membrane domains. These structures can sense changes in environmental conditions and respond by reversibly transitioning from condensed multicompartment layers on the membrane surface to a dispersed state in the cell lumen, mimicking the dynamic compartmentalization found in biological cells. Likewise, we engineer exosome-like subcompartments that can be released to the environment. We can achieve this by using two types of triggers: chemical (addition of salts) and mechanical (by pulling membrane tethers using optical traps). These approaches allow us to control the compartmentalization state of artificial cells on population and single-cell levels.
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Affiliation(s)
- Greta Zubaite
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Department
of Chemical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - James W. Hindley
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
| | - Oscar Ces
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
| | - Yuval Elani
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Department
of Chemical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, United Kingdom
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22
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Schwed-Gross A, Hamiel H, Faber GP, Angel M, Ben-Yishay R, Benichou JIC, Ishay-Ronen D, Shav-Tal Y. Glucocorticoids enhance chemotherapy-driven stress granule assembly and impair granule dynamics leading to cell death. J Cell Sci 2022; 135:276097. [PMID: 35713120 PMCID: PMC9450892 DOI: 10.1242/jcs.259629] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Stress granules (SGs) can assemble in cancer cells upon chemotoxic stress. Glucocorticoids function during stress responses and are administered with chemotherapies. The roles of glucocorticoids in SG assembly and disassembly pathways are unknown. We examined whether combining glucocorticoids such as cortisone with chemotherapies from the vinca alkaloid family, which dismantle the microtubule network, affects SG assembly and disassembly pathways and influences cell viability in cancer cells and human-derived organoids. Cortisone augmented SG formation when combined with vinorelbine (VRB). Live-cell imaging showed that cortisone increased SG assembly rates but reduced SG clearance rates after stress, by increasing protein residence times within the SGs. Mechanistically, VRB and cortisone signaled through the integrated stress response mediated by eIF2α (also known as EIF2S1), yet induced different kinases, with cortisone activating the GCN2 kinase (also known as EIF2AK4). Cortisone increased VRB-induced cell death and reduced the population of cells trapped in mitotic catastrophe. These effects were mediated by the core SG proteins G3BP1 and G3BP2. In conclusion, glucocorticoids induce SG assembly and cell death when administered with chemotherapies, suggesting that combining glucocorticoids with chemotherapies can enhance cancer cell chemosensitivity. Summary: Combining cortisone with the chemotherapy vinorelbine enhances the assembly of stress granules that are less likely to be cleared from the cells, augmenting vinorelbine-induced cell death.
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Affiliation(s)
- Avital Schwed-Gross
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hila Hamiel
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Gabriel P Faber
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Mor Angel
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Rakefet Ben-Yishay
- Oncology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Jennifer I C Benichou
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dana Ishay-Ronen
- Oncology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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23
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Wang Q, Zhou L, Wang J, Su D, Li D, Du Y, Yang G, Zhang G, Chu B. African Swine Fever Virus K205R Induces ER Stress and Consequently Activates Autophagy and the NF-κB Signaling Pathway. Viruses 2022; 14:v14020394. [PMID: 35215987 PMCID: PMC8880579 DOI: 10.3390/v14020394] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/25/2022] Open
Abstract
African swine fever virus (ASFV) is responsible for enormous economic losses in the global swine industry. The ASFV genome encodes approximate 160 proteins, most of whose functions remain largely unknown. In this study, we examined the roles of ASFV K205R in endoplasmic reticulum (ER) stress, autophagy, and inflammation. We observed that K205R was located in both the cytosolic and membrane fractions, and formed stress granules in cells. Furthermore, K205R triggered ER stress and activated the unfolded protein response through activating the transcription factor 6, ER to nucleus signaling 1, and eukaryotic translation initiation factor 2 alpha kinase 3 (EIF2AK3/PERK) signaling pathways. Moreover, K205R inhibited the serine/threonine kinase 1 and the mechanistic target of the rapamycin kinase signaling pathway, thereby activating unc-51 like autophagy activating kinase 1, and hence autophagy. In addition, K205R stimulated the translocation of P65 into the nucleus and the subsequent activation of the nuclear factor kappa B (NF-κB) signaling pathway. Inhibition of ER stress with a PERK inhibitor attenuated K205R-induced autophagy and NF-κB activation. Our data demonstrated a previously uncharacterized role of ASFV K205R in ER stress, autophagy, and the NF-κB signaling pathway.
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Affiliation(s)
- Qi Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
| | - Luyu Zhou
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
| | - Dan Su
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
| | - Dahua Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
| | - Yongkun Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China
| | - Guoyu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China
- College of Animal Science & Techmology, Henan University of Animal Husbandry and Economy, Zhengzhou 450047, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: (G.Z.); (B.C.)
| | - Beibei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Q.W.); (L.Z.); (J.W.); (D.S.); (D.L.); (Y.D.)
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China;
- Key Laboratory of Animal Growth and Development, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: (G.Z.); (B.C.)
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24
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Su Y, Maimaitiyiming Y, Wang L, Cheng X, Hsu CH. Modulation of Phase Separation by RNA: A Glimpse on N 6-Methyladenosine Modification. Front Cell Dev Biol 2021; 9:786454. [PMID: 34957114 PMCID: PMC8703171 DOI: 10.3389/fcell.2021.786454] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
Phase separation is the driving force behind formation of various biomolecular condensates (BioMCs), which sub-compartmentalize certain cellular components in a membraneless manner to orchestrate numerous biological processes. Many BioMCs are composed of proteins and RNAs. While the features and functions of proteins are well studied, less attention was paid to the other essential component RNAs. Here, we describe how RNA contributes to the biogenesis, dissolution, and properties of BioMCs as a multivalence providing scaffold for proteins/RNA to undergo phase separation. Specifically, we focus on N6-methyladenosine (m6A), the most widely distributed dynamic post-transcriptional modification, which would change the charge, conformation, and RNA-binding protein (RBP) anchoring of modified RNA. m6A RNA-modulated phase separation is a new perspective to illustrate m6A-mediated various biological processes. We summarize m6A main functions as “beacon” to recruit reader proteins and “structural switcher” to alter RNA–protein and RNA–RNA interactions to modulate phase separation and regulate the related biological processes.
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Affiliation(s)
- Yingfeng Su
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yasen Maimaitiyiming
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingfang Wang
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaodong Cheng
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chih-Hung Hsu
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
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25
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Sołtys K, Ożyhar A. Transcription Regulators and Membraneless Organelles Challenges to Investigate Them. Int J Mol Sci 2021; 22:12758. [PMID: 34884563 PMCID: PMC8657783 DOI: 10.3390/ijms222312758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic cells are composed of different bio-macromolecules that are divided into compartments called organelles providing optimal microenvironments for many cellular processes. A specific type of organelles is membraneless organelles. They are formed via a process called liquid-liquid phase separation that is driven by weak multivalent interactions between particular bio-macromolecules. In this review, we gather crucial information regarding different classes of transcription regulators with the propensity to undergo liquid-liquid phase separation and stress the role of intrinsically disordered regions in this phenomenon. We also discuss recently developed experimental systems for studying formation and properties of membraneless organelles.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland;
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26
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Kusumaatmaja H, May AI, Knorr RL. Intracellular wetting mediates contacts between liquid compartments and membrane-bound organelles. J Cell Biol 2021; 220:212595. [PMID: 34427635 PMCID: PMC8404468 DOI: 10.1083/jcb.202103175] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/14/2021] [Accepted: 08/05/2021] [Indexed: 12/29/2022] Open
Abstract
Protein-rich droplets, such as stress granules, P-bodies, and the nucleolus, perform diverse and specialized cellular functions. Recent evidence has shown the droplets, which are also known as biomolecular condensates or membrane-less compartments, form by phase separation. Many droplets also contact membrane-bound organelles, thereby functioning in development, intracellular degradation, and organization. These underappreciated interactions have major implications for our fundamental understanding of cells. Starting with a brief introduction to wetting phenomena, we summarize recent progress in the emerging field of droplet-membrane contact. We describe the physical mechanism of droplet-membrane interactions, discuss how these interactions remodel droplets and membranes, and introduce "membrane scaffolding" by liquids as a novel reshaping mechanism, thereby demonstrating that droplet-membrane interactions are elastic wetting phenomena. "Membrane-less" and "membrane-bound" condensates likely represent distinct wetting states that together link phase separation with mechanosensitivity and explain key structures observed during embryogenesis, during autophagy, and at synapses. We therefore contend that droplet wetting on membranes provides a robust and intricate means of intracellular organization.
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Affiliation(s)
| | - Alexander I May
- Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Roland L Knorr
- Graduate School and Faculty of Medicine, University of Tokyo, Tokyo, Japan.,Integrative Research Institute for the Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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27
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Lee J, Le LTHL, Kim E, Lee MJ. Formation of Non-Nucleoplasmic Proteasome Foci during the Late Stage of Hyperosmotic Stress. Cells 2021; 10:cells10092493. [PMID: 34572142 PMCID: PMC8467775 DOI: 10.3390/cells10092493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Cellular stress induces the formation of membraneless protein condensates in both the nucleus and cytoplasm. The nucleocytoplasmic transport of proteins mainly occurs through nuclear pore complexes (NPCs), whose efficiency is affected by various stress conditions. Here, we report that hyperosmotic stress compartmentalizes nuclear 26S proteasomes into dense nuclear foci, independent of signaling cascades. Most of the proteasome foci were detected between the condensed chromatin mass and inner nuclear membrane. The proteasome-positive puncta were not colocalized with other types of nuclear bodies and were reversibly dispersed when cells were returned to the isotonic medium. The structural integrity of 26S proteasomes in the nucleus was slightly affected under the hyperosmotic condition. We also found that these insulator-body-like proteasome foci were possibly formed through disrupted nucleus-to-cytosol transport, which was mediated by the sequestration of NPC components into osmostress-responding stress granules. These data suggest that phase separation in both the nucleus and cytosol may be a major cell survival mechanism during hyperosmotic stress conditions.
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Affiliation(s)
- Jeeyoung Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Ly Thi Huong Luu Le
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Eunkyoung Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Correspondence:
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28
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Zhang C, van Leeuwen W, Blotenburg M, Aguilera-Gomez A, Brussee S, Grond R, Kampinga HH, Rabouille C. Activation of salt Inducible Kinases, IRE1 and PERK leads to Sec bodies formation in Drosophila S2 cells. J Cell Sci 2021; 134:272062. [PMID: 34350957 PMCID: PMC8445602 DOI: 10.1242/jcs.258685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
The phase separation of the non-membrane bound Sec bodies occurs in Drosophila S2 cells by coalescence of components of the endoplasmic reticulum (ER) exit sites under the stress of amino acid starvation. Here, we address which signaling pathways cause Sec body formation and find that two pathways are critical. The first is the activation of the salt-inducible kinases (SIKs; SIK2 and SIK3) by Na+ stress, which, when it is strong, is sufficient. The second is activation of IRE1 and PERK (also known as PEK in flies) downstream of ER stress induced by the absence of amino acids, which needs to be combined with moderate salt stress to induce Sec body formation. SIK, and IRE1 and PERK activation appear to potentiate each other through the stimulation of the unfolded protein response, a key parameter in Sec body formation. This work shows the role of SIKs in phase transition and re-enforces the role of IRE1 and PERK as a metabolic sensor for the level of circulating amino acids and salt. This article has an associated First Person interview with the first author of the paper. Summary: In S2 cells, the phase-separated Sec bodies form upon the combined activation of salt-inducible kinases, IRE1 and PERK.
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Affiliation(s)
- Chujun Zhang
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Sem Brussee
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Rianne Grond
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Harm H Kampinga
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands.,Department of Biomedical Sciences in Cells and Systems, UMC Groningen, The Netherlands.,Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
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29
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Wang E, Thombre R, Shah Y, Latanich R, Wang J. G-Quadruplexes as pathogenic drivers in neurodegenerative disorders. Nucleic Acids Res 2021; 49:4816-4830. [PMID: 33784396 PMCID: PMC8136783 DOI: 10.1093/nar/gkab164] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/20/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplexes (G4s), higher-order DNA and RNA secondary structures featuring guanine-rich nucleic acid sequences with various conformations, are widely distributed in the human genome. These structural motifs are known to participate in basic cellular processes, including transcription, splicing, and translation, and their functions related to health and disease are becoming increasingly recognized. In this review, we summarize the landscape of G4s involved in major neurodegenerative disorders, describing the genes that contain G4-forming sequences and proteins that have high affinity for G4-containing elements. The functions of G4s are diverse, with potentially protective or deleterious effects in the pathogenic cascades of various neurological diseases. While the studies of the functions of G4s in vivo, including those involved in pathophysiology, are still in their early stages, we will nevertheless discuss the evidence pointing to their biological relevance. A better understanding of this unique structural element in the biological context is important for unveiling its potential roles in the pathogenesis of diseases such as neurodegeneration and for designing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Ernest Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ravi Thombre
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yajas Shah
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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30
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Thioesterase superfamily member 1 undergoes stimulus-coupled conformational reorganization to regulate metabolism in mice. Nat Commun 2021; 12:3493. [PMID: 34108467 PMCID: PMC8190112 DOI: 10.1038/s41467-021-23595-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/29/2021] [Indexed: 01/21/2023] Open
Abstract
In brown adipose tissue, thermogenesis is suppressed by thioesterase superfamily member 1 (Them1), a long chain fatty acyl-CoA thioesterase. Them1 is highly upregulated by cold ambient temperature, where it reduces fatty acid availability and limits thermogenesis. Here, we show that Them1 regulates metabolism by undergoing conformational changes in response to β-adrenergic stimulation that alter Them1 intracellular distribution. Them1 forms metabolically active puncta near lipid droplets and mitochondria. Upon stimulation, Them1 is phosphorylated at the N-terminus, inhibiting puncta formation and activity and resulting in a diffuse intracellular localization. We show by correlative light and electron microscopy that Them1 puncta are biomolecular condensates that are inhibited by phosphorylation. Thus, Them1 forms intracellular biomolecular condensates that limit fatty acid oxidation and suppress thermogenesis. During a period of energy demand, the condensates are disrupted by phosphorylation to allow for maximal thermogenesis. The stimulus-coupled reorganization of Them1 provides fine-tuning of thermogenesis and energy expenditure.
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31
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Reversible protein aggregation as cytoprotective mechanism against heat stress. Curr Genet 2021; 67:849-855. [PMID: 34091720 PMCID: PMC8592950 DOI: 10.1007/s00294-021-01191-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 01/01/2023]
Abstract
Temperature fluctuation is one of the most frequent threats to which organisms are exposed in nature. The activation of gene expression programs that trigger the transcription of heat stress-protective genes is the main cellular response to resist high temperatures. In addition, reversible accumulation and compartmentalization of thermosensitive proteins in high-order molecular assemblies are emerging as critical mechanisms to ensure cellular protection upon heat stress. Here, we summarize representative examples of membrane-less intracellular bodies formed upon heat stress in yeasts and human cells and highlight how protein aggregation can be turned into a cytoprotective mechanism.
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32
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Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
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Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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33
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Campos-Melo D, Hawley ZCE, Droppelmann CA, Strong MJ. The Integral Role of RNA in Stress Granule Formation and Function. Front Cell Dev Biol 2021; 9:621779. [PMID: 34095105 PMCID: PMC8173143 DOI: 10.3389/fcell.2021.621779] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are phase-separated, membraneless, cytoplasmic ribonucleoprotein (RNP) assemblies whose primary function is to promote cell survival by condensing translationally stalled mRNAs, ribosomal components, translation initiation factors, and RNA-binding proteins (RBPs). While the protein composition and the function of proteins in the compartmentalization and the dynamics of assembly and disassembly of SGs has been a matter of study for several years, the role of RNA in these structures had remained largely unknown. RNA species are, however, not passive members of RNA granules in that RNA by itself can form homo and heterotypic interactions with other RNA molecules leading to phase separation and nucleation of RNA granules. RNA can also function as molecular scaffolds recruiting multivalent RBPs and their interactors to form higher-order structures. With the development of SG purification techniques coupled to RNA-seq, the transcriptomic landscape of SGs is becoming increasingly understood, revealing the enormous potential of RNA to guide the assembly and disassembly of these transient organelles. SGs are not only formed under acute stress conditions but also in response to different diseases such as viral infections, cancer, and neurodegeneration. Importantly, these granules are increasingly being recognized as potential precursors of pathological aggregates in neurodegenerative diseases. In this review, we examine the current evidence in support of RNA playing a significant role in the formation of SGs and explore the concept of SGs as therapeutic targets.
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Affiliation(s)
- Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Zachary C E Hawley
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Pathology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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Verma A, Sumi S, Seervi M. Heat shock proteins-driven stress granule dynamics: yet another avenue for cell survival. Apoptosis 2021; 26:371-384. [PMID: 33978921 DOI: 10.1007/s10495-021-01678-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/24/2022]
Abstract
Heat shock proteins (HSPs) are evolutionary conserved 'stress-response' proteins that facilitate cell survival against various adverse conditions. HSP-mediated cytoprotection was hitherto reported to occur principally in two ways. Firstly, HSPs interact directly or indirectly with apoptosis signaling components and suppress apoptosis. Secondly, through chaperon activity, HSPs suppress proteotoxicity and maintain protein-homeostasis. Recent studies highlight the interaction of HSPs with cytoplasmic stress granules (SGs). SGs are conserved cytoplasmic mRNPs granules that aid in cell survival under stressful conditions. We primarily aim to describe the distinct cell survival strategy mediated by HSPs as the crucial regulators of SGs assembly and disassembly. Based on the growing evidence, HSPs and associated co-chaperones act as important determinants of SG assembly, composition and dissolution. Under cellular stress, as a 'stress-coping mechanism', the formation of SGs reprograms protein translation machinery and modulates signaling pathways indispensable for cell survival. Besides their role in suppressing apoptosis, HSPs also regulate protein-homeostasis by their chaperone activity as well as by their tight regulation of SG dynamics. The intricate molecular signaling in and around the nexus of HSPs-SGs and its importance in diseases has to be unearthed. These studies have significant implications in the management of chronic diseases such as cancer and neurodegenerative diseases where SGs possess pathological functions.
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Affiliation(s)
- Akanksha Verma
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India
| | - S Sumi
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
| | - Mahendra Seervi
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.
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Pantoja-Uceda D, Stuani C, Laurents DV, McDermott AE, Buratti E, Mompeán M. Phe-Gly motifs drive fibrillization of TDP-43's prion-like domain condensates. PLoS Biol 2021; 19:e3001198. [PMID: 33909608 PMCID: PMC8109789 DOI: 10.1371/journal.pbio.3001198] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 05/10/2021] [Accepted: 03/20/2021] [Indexed: 11/30/2022] Open
Abstract
Transactive response DNA-binding Protein of 43 kDa (TDP-43) assembles various aggregate forms, including biomolecular condensates or functional and pathological amyloids, with roles in disparate scenarios (e.g., muscle regeneration versus neurodegeneration). The link between condensates and fibrils remains unclear, just as the factors controlling conformational transitions within these aggregate species: Salt- or RNA-induced droplets may evolve into fibrils or remain in the droplet form, suggesting distinct end point species of different aggregation pathways. Using microscopy and NMR methods, we unexpectedly observed in vitro droplet formation in the absence of salts or RNAs and provided visual evidence for fibrillization at the droplet surface/solvent interface but not the droplet interior. Our NMR analyses unambiguously uncovered a distinct amyloid conformation in which Phe-Gly motifs are key elements of the reconstituted fibril form, suggesting a pivotal role for these residues in creating the fibril core. This contrasts the minor participation of Phe-Gly motifs in initiation of the droplet form. Our results point to an intrinsic (i.e., non-induced) aggregation pathway that may exist over a broad range of conditions and illustrate structural features that distinguishes between aggregate forms. The prion-like domain of TDP-43 assembles biomolecular condensates which mature into amyloid fibrils that accumulate at the condensate/solvent interface. In vitro reconstitution of these fibrils reveals an amyloid core stabilized by residues that are not necessarily essential to create the droplet form.
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Affiliation(s)
- David Pantoja-Uceda
- Rocasolano Institute of Physical Chemistry, Spanish National Research Council, Madrid, Spain
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Douglas V. Laurents
- Rocasolano Institute of Physical Chemistry, Spanish National Research Council, Madrid, Spain
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Miguel Mompeán
- Rocasolano Institute of Physical Chemistry, Spanish National Research Council, Madrid, Spain
- Department of Chemistry, Columbia University, New York, New York, United States of America
- * E-mail:
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36
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O'Flynn BG, Mittag T. The role of liquid-liquid phase separation in regulating enzyme activity. Curr Opin Cell Biol 2021; 69:70-79. [PMID: 33503539 PMCID: PMC8058252 DOI: 10.1016/j.ceb.2020.12.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
Liquid-liquid phase separation (LLPS) is now recognized as a common mechanism underlying regulation of enzyme activity in cells. Insights from studies in cells are complemented by in vitro studies aimed at developing a better understanding of mechanisms underlying such control. These mechanisms are often based on the influence of LLPS on the physicochemical properties of the enzyme's environment. Biochemical mechanisms underlying such regulation include the potential for concentrating reactants together, tuning reaction rates, and controlling competing metabolic pathways. LLPS is thus a powerful tool with extensive utilities at the cell's disposal, e.g. for consolidating cell survival under stress or rerouting metabolic pathways in response to the energy state of the cell. Here, we examin the evidence for how LLPS affects enzyme catalysis and begin to understand emerging concepts and expand our understanding of enzyme catalysis in living cells.
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Affiliation(s)
- Brian G O'Flynn
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Pantoja-Uceda D, Stuani C, Laurents DV, McDermott AE, Buratti E, Mompeán M. NMR assignments for the C-terminal domain of human TDP-43. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:177-181. [PMID: 33417141 DOI: 10.1007/s12104-020-10002-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Transactive response DNA-binding protein of 43 kDa (TDP-43) is a 414-residue protein whose aberrant aggregation is implicated in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) or frontotemporal lobar degeneration (FTLD). Intriguingly, TDP-43 has also been shown to functionally oligomerize to carry out physiological functions. TDP-43 also exists in mixed condensates or granules with other proteins (e.g. neuronal or stress granules), and its large C-terminal domain (CTD, residues 267-414) seems responsible for TDP-43 both homo- and heterotypic interactions underlying such diverse functional and pathological aggregation events. A myriad of distinct triggers may drive TDP-43 oligomerization, including interaction partners or changes in pH or salinity. In this Assignment Note, we report the complete backbone and a wealth of side chain chemical shift assignments for the CTD of TDP-43 at pH 4. The assignments presented here provide a solid starting point to study the aggregation pathway of TDP-43 at pH values below those considered physiological but relevant in pathological settings, and to contrast the aggregation behaviour under distinct conditions and in the presence of interacting partners.
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Affiliation(s)
- David Pantoja-Uceda
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149, Trieste, Italy
| | - Douglas V Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149, Trieste, Italy
| | - Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain.
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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Schnell HM, Jochem M, Micoogullari Y, Riggs CL, Ivanov P, Welsch H, Ravindran R, Anderson P, Robinson LC, Tatchell K, Hanna J. Reg1 and Snf1 regulate stress-induced relocalization of protein phosphatase-1 to cytoplasmic granules. FEBS J 2021; 288:4833-4848. [PMID: 33682330 DOI: 10.1111/febs.15802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
The compartmentalization of cellular function is achieved largely through the existence of membrane-bound organelles. However, recent work suggests a novel mechanism of compartmentalization mediated by membraneless structures that have liquid droplet-like properties and arise through phase separation. Cytoplasmic stress granules (SGs) are the best characterized and are induced by various stressors including arsenite, heat shock, and glucose deprivation. Current models suggest that SGs play an important role in protein homeostasis by mediating reversible translation attenuation. Protein phosphatase-1 (PP1) is a central cellular regulator responsible for most serine/threonine dephosphorylation. Here, we show that upon arsenite stress, PP1's catalytic subunit Glc7 relocalizes to punctate cytoplasmic granules. This altered localization requires PP1's recently described maturation pathway mediated by the multifunctional ATPase Cdc48 and PP1's regulatory subunit Ypi1. Glc7 relocalization is mediated by its regulatory subunit Reg1 and its target Snf1, the AMP-dependent protein kinase. Surprisingly, Glc7 granules are highly specific to arsenite and appear distinct from canonical SGs. Arsenite induces potent translational inhibition, and translational recovery is strongly dependent on Glc7, but independent of Glc7's well-established role in regulating eIF2α. These results suggest a novel form of stress-induced cytoplasmic granule and a new mode of translational control by Glc7.
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Affiliation(s)
- Helena Maria Schnell
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Marco Jochem
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Yagmur Micoogullari
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Claire Louise Riggs
- Department of Rheumatology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Pavel Ivanov
- Department of Rheumatology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Hendrik Welsch
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Rini Ravindran
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Paul Anderson
- Department of Rheumatology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Lucy Christina Robinson
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Kelly Tatchell
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
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Lin KL, Chen SD, Lin KJ, Liou CW, Chuang YC, Wang PW, Chuang JH, Lin TK. Quality Matters? The Involvement of Mitochondrial Quality Control in Cardiovascular Disease. Front Cell Dev Biol 2021; 9:636295. [PMID: 33829016 PMCID: PMC8019794 DOI: 10.3389/fcell.2021.636295] [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: 12/01/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases are one of the leading causes of death and global health problems worldwide. Multiple factors are known to affect the cardiovascular system from lifestyles, genes, underlying comorbidities, and age. Requiring high workload, metabolism of the heart is largely dependent on continuous power supply via mitochondria through effective oxidative respiration. Mitochondria not only serve as cellular power plants, but are also involved in many critical cellular processes, including the generation of intracellular reactive oxygen species (ROS) and regulating cellular survival. To cope with environmental stress, mitochondrial function has been suggested to be essential during bioenergetics adaptation resulting in cardiac pathological remodeling. Thus, mitochondrial dysfunction has been advocated in various aspects of cardiovascular pathology including the response to ischemia/reperfusion (I/R) injury, hypertension (HTN), and cardiovascular complications related to type 2 diabetes mellitus (DM). Therefore, mitochondrial homeostasis through mitochondrial dynamics and quality control is pivotal in the maintenance of cardiac health. Impairment of the segregation of damaged components and degradation of unhealthy mitochondria through autophagic mechanisms may play a crucial role in the pathogenesis of various cardiac disorders. This article provides in-depth understanding of the current literature regarding mitochondrial remodeling and dynamics in cardiovascular diseases.
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Affiliation(s)
- Kai-Lieh Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shang-Der Chen
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Jung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yao-Chung Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Wen Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Metabolism, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jiin-Haur Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Pediatric Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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40
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Kim J, Lee G. Metabolic Control of m 6A RNA Modification. Metabolites 2021; 11:metabo11020080. [PMID: 33573224 PMCID: PMC7911930 DOI: 10.3390/metabo11020080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/30/2022] Open
Abstract
Nutrients and metabolic pathways regulate cell growth and cell fate decisions via epigenetic modification of DNA and histones. Another key genetic material, RNA, also contains diverse chemical modifications. Among these, N6-methyladenosine (m6A) is the most prevalent and evolutionarily conserved RNA modification. It functions in various aspects of developmental and disease states, by controlling RNA metabolism, such as stability and translation. Similar to other epigenetic processes, m6A modification is regulated by specific enzymes, including writers (methyltransferases), erasers (demethylases), and readers (m6A-binding proteins). As this is a reversible enzymatic process, metabolites can directly influence the flux of this reaction by serving as substrates and/or allosteric regulators. In this review, we will discuss recent understanding of the regulation of m6A RNA modification by metabolites, nutrients, and cellular metabolic pathways.
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Affiliation(s)
- Joohwan Kim
- Department of Microbiology and Molecular Genetics, University of California Irvine School of Medicine, Irvine, CA 92697, USA;
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Irvine, CA 92697, USA
- Correspondence:
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Bai Q, Zhang Q, Jing H, Chen J, Liang D. Liquid-Liquid Phase Separation of Peptide/Oligonucleotide Complexes in Crowded Macromolecular Media. J Phys Chem B 2020; 125:49-57. [PMID: 33373232 DOI: 10.1021/acs.jpcb.0c09225] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The membraneless organelles (MLOs) and coacervates of oppositely charged polyelectrolytes are both formed by liquid-liquid phase separation. To reveal how the crowded cell interior regulates the MLOs, we chose the coacervates formed by peptide S5 and single-stranded oligonucleotide (ss-oligo) at 1:1 charge ratio and investigated the phase separation processes in polyacrylamide (PAM) and poly(ethylene oxide) (PEO) media at varying concentrations. Results show that the droplet formation unit is the neutral primary complex, instead of individual S5 or ss-oligo. Therefore, the coacervation process can be described by the classic theory of nucleation and growth. The dynamic scaling relationships show that S5/ss-oligo coacervation undergoes in sequence the heterogeneous nucleation, diffusion-limited growth, and Brownian motion coalescence with time. The inert crowders generate multiple effects, including accelerating the growth of droplets, weakening the electrostatic attraction, and slowing down or even trapping the droplets in the crowder network. The overall effect is that both the size and size distribution of the droplets decrease with increasing crowder concentration, and the effect of PEO is stronger than that of PAM. Our study provides a further step toward a deeper understanding of the kinetics of MLOs in crowded living cells.
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Affiliation(s)
- Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Qiufen Zhang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Hairong Jing
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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42
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Tarczewska A, Wycisk K, Orłowski M, Waligórska A, Dobrucki J, Drewniak-Świtalska M, Berlicki Ł, Ożyhar A. Nuclear immunophilin FKBP39 from Drosophila melanogaster drives spontaneous liquid-liquid phase separation. Int J Biol Macromol 2020; 163:108-119. [PMID: 32615218 DOI: 10.1016/j.ijbiomac.2020.06.255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/27/2022]
Abstract
The FKBP39 from Drosophila melanogaster is a multifunctional regulatory immunophilin. It contains two globular domains linked by a highly charged disordered region. The N-terminal domain shows homology to the nucleoplasmin core domain, and the C-terminal domain is characteristic for the family of the FKBP immunophilin ligand binding domain. The specific partially disordered structure of the protein inspired us to investigate whether FKBP39 can drive spontaneous liquid-liquid phase separation (LLPS). Preliminary analyses using CatGranule and Pi-Pi contact predictors suggested a propensity for LLPS. Microscopy observations revealed that FKBP39 can self-concentrate to form liquid condensates. We also found that FKBP39 can lead to LLPS in the presence of RNA and peptides containing Arg-rich linear motifs derived from selected nuclear and nucleolar proteins. These heterotypic interactions have a stronger propensity for driving LLPS when compared to the interactions mediated by self-associating FKBP39 molecules. To investigate whether FKBP39 can drive LLPS in the cellular environment, we analysed it in fusion with YFP in COS-7 cells. The specific distribution and diffusion kinetics of FKBP39 examined by FRAP experiments provided evidence that immunophilin is an important driver of phase separation. The ability of FKBP39 to go into heterotypic interaction may be fundamental for ribosome subunits assembly.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Marek Orłowski
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Agnieszka Waligórska
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Magda Drewniak-Świtalska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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Abstract
Proteinaceous liquid-liquid phase separation (LLPS) occurs when a polypeptide coalesces into a dense phase to form a liquid droplet (i.e., condensate) in aqueous solution. In vivo, functional protein-based condensates are often referred to as membraneless organelles (MLOs), which have roles in cellular processes ranging from stress responses to regulation of gene expression. Late embryogenesis abundant (LEA) proteins containing seed maturation protein domains (SMP; PF04927) have been linked to storage tolerance of orthodox seeds. The mechanism by which anhydrobiotic longevity is improved is unknown. Interestingly, the brine shrimp Artemia franciscana is the only animal known to express such a protein (AfrLEA6) in its anhydrobiotic embryos. Ectopic expression of AfrLEA6 (AWM11684) in insect cells improves their desiccation tolerance and a fraction of the protein is sequestered into MLOs, while aqueous AfrLEA6 raises the viscosity of the cytoplasm. LLPS of AfrLEA6 is driven by the SMP domain, while the size of formed MLOs is regulated by a domain predicted to engage in protein binding. AfrLEA6 condensates formed in vitro selectively incorporate target proteins based on their surface charge, while cytoplasmic MLOs formed in AfrLEA6-transfected insect cells behave like stress granules. We suggest that AfrLEA6 promotes desiccation tolerance by engaging in two distinct molecular mechanisms: by raising cytoplasmic viscosity at even modest levels of water loss to promote cell integrity during drying and by forming condensates that may act as protective compartments for desiccation-sensitive proteins. Identifying and understanding the molecular mechanisms that govern anhydrobiosis will lead to significant advancements in preserving biological samples.
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44
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Shears SB, Wang H. Metabolism and Functions of Inositol Pyrophosphates: Insights Gained from the Application of Synthetic Analogues. Molecules 2020; 25:E4515. [PMID: 33023101 PMCID: PMC7583957 DOI: 10.3390/molecules25194515] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Inositol pyrophosphates (PP-InsPs) comprise an important group of intracellular, diffusible cellular signals that a wide range of biological processes throughout the yeast, plant, and animal kingdoms. It has been difficult to gain a molecular-level mechanistic understanding of the actions of these molecules, due to their highly phosphorylated nature, their low levels, and their rapid metabolic turnover. More recently, these obstacles to success are being surmounted by the chemical synthesis of a number of insightful PP-InsP analogs. This review will describe these analogs and will indicate the important chemical and biological information gained by using them.
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Affiliation(s)
- Stephen B. Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA;
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McQuail J, Switzer A, Burchell L, Wigneshweraraj S. The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starved Escherichia coli. J Biol Chem 2020; 295:12355-12367. [PMID: 32532816 PMCID: PMC7458820 DOI: 10.1074/jbc.ra120.014107] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Indexed: 11/13/2022] Open
Abstract
The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.
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Affiliation(s)
- Josh McQuail
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Amy Switzer
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Lynn Burchell
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Sivaramesh Wigneshweraraj
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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InsP 7 is a small-molecule regulator of NUDT3-mediated mRNA decapping and processing-body dynamics. Proc Natl Acad Sci U S A 2020; 117:19245-19253. [PMID: 32727897 DOI: 10.1073/pnas.1922284117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Regulation of enzymatic 5' decapping of messenger RNA (mRNA), which normally commits transcripts to their destruction, has the capacity to dynamically reshape the transcriptome. For example, protection from 5' decapping promotes accumulation of mRNAs into processing (P) bodies-membraneless, biomolecular condensates. Such compartmentalization of mRNAs temporarily removes them from the translatable pool; these repressed transcripts are stabilized and stored until P-body dissolution permits transcript reentry into the cytosol. Here, we describe regulation of mRNA stability and P-body dynamics by the inositol pyrophosphate signaling molecule 5-InsP7 (5-diphosphoinositol pentakisphosphate). First, we demonstrate 5-InsP7 inhibits decapping by recombinant NUDT3 (Nudix [nucleoside diphosphate linked moiety X]-type hydrolase 3) in vitro. Next, in intact HEK293 and HCT116 cells, we monitored the stability of a cadre of NUDT3 mRNA substrates following CRISPR-Cas9 knockout of PPIP5Ks (diphosphoinositol pentakisphosphate 5-kinases type 1 and 2, i.e., PPIP5K KO), which elevates cellular 5-InsP7 levels by two- to threefold (i.e., within the physiological rheostatic range). The PPIP5K KO cells exhibited elevated levels of NUDT3 mRNA substrates and increased P-body abundance. Pharmacological and genetic attenuation of 5-InsP7 synthesis in the KO background reverted both NUDT3 mRNA substrate levels and P-body counts to those of wild-type cells. Furthermore, liposomal delivery of a metabolically resistant 5-InsP7 analog into wild-type cells elevated levels of NUDT3 mRNA substrates and raised P-body abundance. In the context that cellular 5-InsP7 levels normally fluctuate in response to changes in the bioenergetic environment, regulation of mRNA structure by this inositol pyrophosphate represents an epitranscriptomic control process. The associated impact on P-body dynamics has relevance to regulation of stem cell differentiation, stress responses, and, potentially, amelioration of neurodegenerative diseases and aging.
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Buddika K, Ariyapala IS, Hazuga MA, Riffert D, Sokol NS. Canonical nucleators are dispensable for stress granule assembly in Drosophila intestinal progenitors. J Cell Sci 2020; 133:jcs243451. [PMID: 32265270 PMCID: PMC7325430 DOI: 10.1242/jcs.243451] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
Stressed cells downregulate translation initiation and assemble membrane-less foci termed stress granules (SGs). Although SGs have been extensively characterized in cultured cells, the existence of such structures in stressed adult stem cell pools remains poorly characterized. Here, we report that the Drosophila orthologs of the mammalian SG components AGO1, ATX2, CAPRIN, eIF4E, FMRP, G3BP, LIN-28, PABP and TIAR are enriched in adult fly intestinal progenitor cells, where they accumulate in small cytoplasmic messenger ribonucleoprotein complexes (mRNPs). Treatment with sodium arsenite or rapamycin reorganized these mRNPs into large cytoplasmic granules. Formation of these intestinal progenitor stress granules (IPSGs) depended on polysome disassembly, led to translational downregulation and was reversible. Although the canonical SG nucleators ATX2 and G3BP were sufficient for IPSG formation in the absence of stress, neither of them, nor TIAR, either individually or collectively, were required for stress-induced IPSG formation. This work therefore finds that IPSGs do not assemble via a canonical mechanism, raising the possibility that other stem cell populations employ a similar stress-response mechanism.
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Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Mary A Hazuga
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Derek Riffert
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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48
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B. Domènech E, Marfany G. The Relevance of Oxidative Stress in the Pathogenesis and Therapy of Retinal Dystrophies. Antioxidants (Basel) 2020; 9:E347. [PMID: 32340220 PMCID: PMC7222416 DOI: 10.3390/antiox9040347] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Retinal cell survival requires an equilibrium between oxygen, reactive oxygen species, and antioxidant molecules that counteract oxidative stress damage. Oxidative stress alters cell homeostasis and elicits a protective cell response, which is most relevant in photoreceptors and retinal ganglion cells, neurons with a high metabolic rate that are continuously subject to light/oxidative stress insults. We analyze how the alteration of cellular endogenous pathways for protection against oxidative stress leads to retinal dysfunction in prevalent (age-related macular degeneration, glaucoma) as well as in rare genetic visual disorders (Retinitis pigmentosa, Leber hereditary optic neuropathy). We also highlight some of the key molecular actors and discuss potential therapies using antioxidants agents, modulators of gene expression and inducers of cytoprotective signaling pathways to treat damaging oxidative stress effects and ameliorate severe phenotypic symptoms in multifactorial and rare retinal dystrophies.
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Affiliation(s)
- Elena B. Domènech
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, 08028 Barcelona, Spain;
- CIBERER, ISCIII, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, 08028 Barcelona, Spain;
- CIBERER, ISCIII, Universitat de Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine (IBUB, IBUB-IRSJD), Universitat de Barcelona, 08028 Barcelona, Spain
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van Leeuwen W, Rabouille C. Cellular stress leads to the formation of membraneless stress assemblies in eukaryotic cells. Traffic 2019; 20:623-638. [PMID: 31152627 PMCID: PMC6771618 DOI: 10.1111/tra.12669] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/10/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022]
Abstract
In cells at steady state, two forms of cell compartmentalization coexist: membrane-bound organelles and phase-separated membraneless organelles that are present in both the nucleus and the cytoplasm. Strikingly, cellular stress is a strong inducer of the reversible membraneless compartments referred to as stress assemblies. Stress assemblies play key roles in survival during cell stress and in thriving of cells upon stress relief. The two best studied stress assemblies are the RNA-based processing-bodies (P-bodies) and stress granules that form in response to oxidative, endoplasmic reticulum (ER), osmotic and nutrient stress as well as many others. Interestingly, P-bodies and stress granules are heterogeneous with respect to both the pathways that lead to their formation and their protein and RNA content. Furthermore, in yeast and Drosophila, nutrient stress also leads to the formation of many other types of prosurvival cytoplasmic stress assemblies, such as metabolic enzymes foci, proteasome storage granules, EIF2B bodies, U-bodies and Sec bodies, some of which are not RNA-based. Nutrient stress leads to a drop in cytoplasmic pH, which combined with posttranslational modifications of granule contents, induces phase separation.
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Affiliation(s)
- Wessel van Leeuwen
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciencesand University Medical Center UtrechtUtrechtthe Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciencesand University Medical Center UtrechtUtrechtthe Netherlands
- Department of Biomedical Science of Cells and SystemsUniversity Medical Center GroningenGroningenthe Netherlands
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50
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Zhang C, Rabouille C. Membrane-Bound Meet Membraneless in Health and Disease. Cells 2019; 8:cells8091000. [PMID: 31470564 PMCID: PMC6770257 DOI: 10.3390/cells8091000] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
Membraneless organelles (MLOs) are defined as cellular structures that are not sealed by a lipidic membrane and are shown to form by phase separation. They exist in both the nucleus and the cytoplasm that is also heavily populated by numerous membrane-bound organelles. Even though the name membraneless suggests that MLOs are free of membrane, both membrane and factors regulating membrane trafficking steps are emerging as important components of MLO formation and function. As a result, we name them biocondensates. In this review, we examine the relationships between biocondensates and membrane. First, inhibition of membrane trafficking in the early secretory pathway leads to the formation of biocondensates (P-bodies and Sec bodies). In the same vein, stress granules have a complex relationship with the cyto-nuclear transport machinery. Second, membrane contributes to the regulated formation of phase separation in the cells and we will present examples including clustering at the plasma membrane and at the synapse. Finally, the whole cell appears to transit from an interphase phase-separated state to a mitotic diffuse state in a DYRK3 dependent manner. This firmly establishes a crosstalk between the two types of cell organization that will need to be further explored.
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Affiliation(s)
- Chujun Zhang
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
- Department of Biomedical Science of Cells and Systems, University Medical Center Groningen, 9713 AV Groningen, The Netherlands.
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