501
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Gwon Y, Maxwell BA, Kolaitis RM, Zhang P, Kim HJ, Taylor JP. Ubiquitination of G3BP1 mediates stress granule disassembly in a context-specific manner. Science 2021; 372:eabf6548. [PMID: 34739333 PMCID: PMC8574224 DOI: 10.1126/science.abf6548] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stress granules are dynamic, reversible condensates composed of RNA and protein that assemble in eukaryotic cells in response to a variety of stressors and are normally disassembled after stress is removed. The composition and assembly of stress granules is well understood, but little is known about the mechanisms that govern disassembly. Impaired disassembly has been implicated in some diseases including amyotrophic lateral sclerosis, frontotemporal dementia, and multisystem proteinopathy. Using cultured human cells, we found that stress granule disassembly was context-dependent: Specifically in the setting of heat shock, disassembly required ubiquitination of G3BP1, the central protein within the stress granule RNA-protein network. We found that ubiquitinated G3BP1 interacted with the endoplasmic reticulum–associated protein FAF2, which engaged the ubiquitin-dependent segregase p97/VCP (valosin-containing protein). Thus, targeting of G3BP1 weakened the stress granule–specific interaction network, resulting in granule disassembly.
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Affiliation(s)
- Youngdae Gwon
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Brian A. Maxwell
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Regina-Maria Kolaitis
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Peipei Zhang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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502
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Maxwell BA, Gwon Y, Mishra A, Peng J, Nakamura H, Zhang K, Kim HJ, Taylor JP. Ubiquitination is essential for recovery of cellular activities after heat shock. Science 2021; 372:eabc3593. [PMID: 34739326 PMCID: PMC8574219 DOI: 10.1126/science.abc3593] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
Eukaryotic cells respond to stress through adaptive programs that include reversible shutdown of key cellular processes, the formation of stress granules, and a global increase in ubiquitination. The primary function of this ubiquitination is thought to be for tagging damaged or misfolded proteins for degradation. Here, working in mammalian cultured cells, we found that different stresses elicited distinct ubiquitination patterns. For heat stress, ubiquitination targeted specific proteins associated with cellular activities that are down-regulated during stress, including nucleocytoplasmic transport and translation, as well as stress granule constituents. Ubiquitination was not required for the shutdown of these processes or for stress granule formation but was essential for the resumption of cellular activities and for stress granule disassembly. Thus, stress-induced ubiquitination primes the cell for recovery after heat stress.
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Affiliation(s)
- Brian A. Maxwell
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Youngdae Gwon
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ashutosh Mishra
- Department of Structural Biology Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Haruko Nakamura
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ke Zhang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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503
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Deviri D, Safran SA. Physical theory of biological noise buffering by multicomponent phase separation. Proc Natl Acad Sci U S A 2021; 118:e2100099118. [PMID: 34135122 PMCID: PMC8237649 DOI: 10.1073/pnas.2100099118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Maintaining homeostasis is a fundamental characteristic of living systems. In cells, this is contributed to by the assembly of biochemically distinct organelles, many of which are not membrane bound but form by the physical process of liquid-liquid phase separation (LLPS). By analogy with LLPS in binary solutions, cellular LLPS was hypothesized to contribute to homeostasis by facilitating "concentration buffering," which renders the local protein concentration within the organelle robust to global variations in the average cellular concentration (e.g., due to expression noise). Interestingly, concentration buffering was experimentally measured in vivo in a simple organelle with a single solute, while it was observed not to be obeyed in one with several solutes. Here, we formulate theoretically and solve analytically a physical model of LLPS in a ternary solution of two solutes (ϕ and ψ) that interact both homotypically (ϕ-ϕ attractions) and heterotypically (ϕ-ψ attractions). Our physical theory predicts how the coexisting concentrations in LLPS are related to expression noise and thus, generalizes the concept of concentration buffering to multicomponent systems. This allows us to reconcile the seemingly contradictory experimental observations. Furthermore, we predict that incremental changes of the homotypic and heterotypic interactions among the molecules that undergo LLPS, such as those that are caused by mutations in the genes encoding the proteins, may increase the efficiency of concentration buffering of a given system. Thus, we hypothesize that evolution may optimize concentration buffering as an efficient mechanism to maintain LLPS homeostasis and suggest experimental approaches to test this in different systems.
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Affiliation(s)
- Dan Deviri
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovet 76100, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovet 76100, Israel
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504
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Samir P, Place DE, Malireddi RKS, Kanneganti TD. TLR and IKK Complex-Mediated Innate Immune Signaling Inhibits Stress Granule Assembly. THE JOURNAL OF IMMUNOLOGY 2021; 207:115-124. [PMID: 34145059 DOI: 10.4049/jimmunol.2100115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/02/2021] [Indexed: 11/19/2022]
Abstract
Cellular stress can induce cytoplasmic ribonucleoprotein complexes called stress granules that allow the cells to survive. Stress granules are also central to cellular responses to infections, in which they can act as platforms for viral sending or modulate innate immune signaling through pattern recognition receptors. However, the effect of innate immune signaling on stress granules is poorly understood. In this study, we report that prior induction of innate immune signaling through TLRs inhibited stress granule assembly in a TLR ligand dose-dependent manner in murine bone marrow-derived macrophages. Time course analysis suggests that TLR stimulation can reverse stress granule assembly even after it has begun. Additionally, both MYD88- and TRIF-mediated TLR signaling inhibited stress granule assembly in response to endoplasmic reticulum stress in bone marrow-derived macrophages and the chemotherapeutic drug oxaliplatin in murine B16 melanoma cells. This inhibition was not due to a decrease in expression of the critical stress granule proteins G3BP1 and DDX3X and was independent of IRAK1/4, JNK, ERK and P38 kinase activity but dependent on IKK complex kinase activity. Overall, we have identified the TLR-IKK complex signaling axis as a regulator of stress granule assembly-disassembly dynamics, highlighting cross-talk between processes that are critical in health and disease.
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Affiliation(s)
- Parimal Samir
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - David E Place
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
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505
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Lavalée M, Curdy N, Laurent C, Fournié JJ, Franchini DM. Cancer cell adaptability: turning ribonucleoprotein granules into targets. Trends Cancer 2021; 7:902-915. [PMID: 34144941 DOI: 10.1016/j.trecan.2021.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Stress granules (SGs) and processing bodies (P-bodies) are membraneless cytoplasmic condensates of ribonucleoproteins (RNPs). They both regulate RNA fate under physiological and pathological conditions, and are thereby involved in the regulation and maintenance of cellular integrity. During tumorigenesis, cancer cells use these granules to thrive, to adapt to the harsh conditions of the tumor microenvironment (TME), and to protect themselves from anticancer treatments. This ability to provide multiple outcomes not only makes RNP granules promising targets for cancer therapy but also emphasizes the need for more knowledge about the biology of these granules to achieve clinical use. In this review we focus on the role of RNP granules in cancer, and on how their composition and regulation might be used to elaborate therapeutic strategies.
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Affiliation(s)
- Margot Lavalée
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Nicolas Curdy
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Camille Laurent
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Département de Pathologie, Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France
| | - Jean-Jacques Fournié
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Don-Marc Franchini
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France.
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506
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Fare CM, Villani A, Drake LE, Shorter J. Higher-order organization of biomolecular condensates. Open Biol 2021; 11:210137. [PMID: 34129784 PMCID: PMC8205532 DOI: 10.1098/rsob.210137] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A guiding principle of biology is that biochemical reactions must be organized in space and time. One way this spatio-temporal organization is achieved is through liquid–liquid phase separation (LLPS), which generates biomolecular condensates. These condensates are dynamic and reactive, and often contain a complex mixture of proteins and nucleic acids. In this review, we discuss how underlying physical and chemical processes generate internal condensate architectures. We then outline the diverse condensate architectures that are observed in biological systems. Finally, we discuss how specific condensate organization is critical for specific biological functions.
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Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - James Shorter
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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507
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Riley JF, Fioramonti PJ, Rusnock AK, Hehnly H, Castañeda CA. ALS-linked mutations impair UBQLN2 stress-induced biomolecular condensate assembly in cells. J Neurochem 2021; 159:145-155. [PMID: 34129687 DOI: 10.1111/jnc.15453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/30/2021] [Accepted: 06/13/2021] [Indexed: 11/28/2022]
Abstract
Mutations in Ubiquilin-2 (UBQLN2), a ubiquitin-binding shuttle protein involved in several protein quality control processes, can lead to amyotrophic lateral sclerosis (ALS). We previously found that wild-type UBQLN2 forms dynamic, membraneless biomolecular condensates upon cellular stress, and undergoes liquid-liquid phase separation in vitro. However, the impact of ALS-linked mutations on UBQLN2 condensate formation in cells is unknown. Here, we employ live-cell imaging and photokinetic analysis to investigate how five patient-derived ALS-linked mutations in UBQLN2 impact stress-induced UBQLN2 condensate assembly and condensate material properties. Both wild-type and mutant UBQLN2 condensates are generally cytoplasmic and liquid-like. However, cells transfected with mutant UBQLN2 contain fewer stress-induced UBQLN2 condensates than those with wild-type UBQLN2. Most strikingly, exogenously expressed P506T UBQLN2 forms the lowest number of stress-induced condensates of all UBQLN2 mutants, and these condensates are significantly smaller than those of wild-type UBQLN2. Fluorescence recovery after photobleaching (FRAP) analysis of UBQLN2 condensates revealed higher immobile fractions for UBQLN2 mutants, especially P506T. P497S and P497H mutations differentially impact condensate properties, demonstrating that the effects of ALS-linked mutations are both position- and amino acid-dependent. Collectively, our data show that disease mutations hinder assembly and alter viscoelastic properties of stress-induced UBQLN2 condensates, potentially leading to aggregates commonly observed in ALS.
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Affiliation(s)
- Julia F Riley
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.,Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
| | | | - Amber K Rusnock
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Heidi Hehnly
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Carlos A Castañeda
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.,Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
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508
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Sanchez II, Nguyen TB, England WE, Lim RG, Vu AQ, Miramontes R, Byrne LM, Markmiller S, Lau AL, Orellana I, Curtis MA, Faull RLM, Yeo GW, Fowler CD, Reidling JC, Wild EJ, Spitale RC, Thompson LM. Huntington's disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization. J Clin Invest 2021; 131:140723. [PMID: 33945510 DOI: 10.1172/jci140723] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 04/28/2021] [Indexed: 01/01/2023] Open
Abstract
Chronic cellular stress associated with neurodegenerative disease can result in the persistence of stress granule (SG) structures, membraneless organelles that form in response to cellular stress. In Huntington's disease (HD), chronic expression of mutant huntingtin generates various forms of cellular stress, including activation of the unfolded protein response and oxidative stress. However, it has yet to be determined whether SGs are a feature of HD neuropathology. We examined the miRNA composition of extracellular vesicles (EVs) present in the cerebrospinal fluid (CSF) of patients with HD and show that a subset of their target mRNAs were differentially expressed in the prefrontal cortex. Of these targets, SG components were enriched, including the SG-nucleating Ras GTPase-activating protein-binding protein 1 (G3BP1). We investigated localization and levels of G3BP1 and found a significant increase in the density of G3BP1-positive granules in the cortex and hippocampus of R6/2 transgenic mice and in the superior frontal cortex of the brains of patients with HD. Intriguingly, we also observed that the SG-associated TAR DNA-binding protein 43 (TDP43), a nuclear RNA/DNA binding protein, was mislocalized to the cytoplasm of G3BP1 granule-positive HD cortical neurons. These findings suggest that G3BP1 SG dynamics may play a role in the pathophysiology of HD.
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Affiliation(s)
| | | | | | - Ryan G Lim
- Institute for Memory Impairment and Neurological Disorders, University of California, Irvine, California, USA
| | - Anthony Q Vu
- Department of Cellular and Molecular Medicine, and.,Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, California, USA
| | - Ricardo Miramontes
- Institute for Memory Impairment and Neurological Disorders, University of California, Irvine, California, USA
| | - Lauren M Byrne
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, and.,Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, California, USA
| | - Alice L Lau
- Department of Psychiatry & Human Behavior, and
| | - Iliana Orellana
- Sue and Bill Gross Stem Cell Center, University of California, Irvine, California, USA
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Science, and.,Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Richard Lewis Maxwell Faull
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Science, and.,Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, and.,Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, California, USA
| | | | - Jack C Reidling
- Institute for Memory Impairment and Neurological Disorders, University of California, Irvine, California, USA
| | - Edward J Wild
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, and.,Department of Chemistry, University of California, Irvine, California, USA
| | - Leslie M Thompson
- Department of Neurobiology & Behavior.,Institute for Memory Impairment and Neurological Disorders, University of California, Irvine, California, USA.,Department of Psychiatry & Human Behavior, and.,Sue and Bill Gross Stem Cell Center, University of California, Irvine, California, USA
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509
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Arabidopsis thaliana G3BP Ortholog Rescues Mammalian Stress Granule Phenotype across Kingdoms. Int J Mol Sci 2021; 22:ijms22126287. [PMID: 34208100 PMCID: PMC8230867 DOI: 10.3390/ijms22126287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
Stress granules (SGs) are dynamic RNA–protein complexes localized in the cytoplasm that rapidly form under stress conditions and disperse when normal conditions are restored. The formation of SGs depends on the Ras-GAP SH3 domain-binding protein (G3BP). Formations, interactions and functions of plant and human SGs are strikingly similar, suggesting a conserved mechanism. However, functional analyses of plant G3BPs are missing. Thus, members of the Arabidopsis thaliana G3BP (AtG3BP) protein family were investigated in a complementation assay in a human G3BP knock-out cell line. It was shown that two out of seven AtG3BPs were able to complement the function of their human homolog. GFP-AtG3BP fusion proteins co-localized with human SG marker proteins Caprin-1 and eIF4G1 and restored SG formation in G3BP double KO cells. Interaction between AtG3BP-1 and -7 and known human G3BP interaction partners such as Caprin-1 and USP10 was also demonstrated by co-immunoprecipitation. In addition, an RG/RGG domain exchange from Arabidopsis G3BP into the human G3BP background showed the ability for complementation. In summary, our results support a conserved mechanism of SG function over the kingdoms, which will help to further elucidate the biological function of the Arabidopsis G3BP protein family.
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510
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Posey AE, Ruff KM, Lalmansingh JM, Kandola TS, Lange JJ, Halfmann R, Pappu RV. Mechanistic Inferences From Analysis of Measurements of Protein Phase Transitions in Live Cells. J Mol Biol 2021; 433:166848. [PMID: 33539877 PMCID: PMC8561728 DOI: 10.1016/j.jmb.2021.166848] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023]
Abstract
The combination of phase separation and disorder-to-order transitions can give rise to ordered, semi-crystalline fibrillar assemblies that underlie prion phenomena namely, the non-Mendelian transfer of information across cells. Recently, a method known as Distributed Amphifluoric Förster Resonance Energy Transfer (DAmFRET) was developed to study the convolution of phase separation and disorder-to-order transitions in live cells. In this assay, a protein of interest is expressed to a broad range of concentrations and the acquisition of local density and order, measured by changes in FRET, is used to map phase transitions for different proteins. The high-throughput nature of this assay affords the promise of uncovering sequence-to-phase behavior relationships in live cells. Here, we report the development of a supervised method to obtain automated and accurate classifications of phase transitions quantified using the DAmFRET assay. Systems that we classify as undergoing two-state discontinuous transitions are consistent with prion-like behaviors, although the converse is not always true. We uncover well-established and surprising new sequence features that contribute to two-state phase behavior of prion-like domains. Additionally, our method enables quantitative, comparative assessments of sequence-specific driving forces for phase transitions in live cells. Finally, we demonstrate that a modest augmentation of DAmFRET measurements, specifically time-dependent protein expression profiles, can allow one to apply classical nucleation theory to extract sequence-specific lower bounds on the probability of nucleating ordered assemblies. Taken together, our approaches lead to a useful analysis pipeline that enables the extraction of mechanistic inferences regarding phase transitions in live cells.
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Affiliation(s)
- Ammon E Posey
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Kiersten M Ruff
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tejbir S Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; The Open University, Milton Keynes MK7 6AA, United Kingdom
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA.
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511
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Schmidt H, Putnam A, Rasoloson D, Seydoux G. Protein-based condensation mechanisms drive the assembly of RNA-rich P granules. eLife 2021; 10:63698. [PMID: 34106046 PMCID: PMC8238508 DOI: 10.7554/elife.63698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Germ granules are protein-RNA condensates that segregate with the embryonic germline. In Caenorhabditis elegans embryos, germ (P) granule assembly requires MEG-3, an intrinsically disordered protein that forms RNA-rich condensates on the surface of PGL condensates at the core of P granules. MEG-3 is related to the GCNA family and contains an N-terminal disordered region (IDR) and a predicted ordered C-terminus featuring an HMG-like motif (HMGL). We find that MEG-3 is a modular protein that uses its IDR to bind RNA and its C-terminus to drive condensation. The HMGL motif mediates binding to PGL-3 and is required for co-assembly of MEG-3 and PGL-3 condensates in vivo. Mutations in HMGL cause MEG-3 and PGL-3 to form separate condensates that no longer co-segregate to the germline or recruit RNA. Our findings highlight the importance of protein-based condensation mechanisms and condensate-condensate interactions in the assembly of RNA-rich germ granules.
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Affiliation(s)
- Helen Schmidt
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Andrea Putnam
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Dominique Rasoloson
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
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512
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Emenecker RJ, Holehouse AS, Strader LC. Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis. Cell Commun Signal 2021; 19:65. [PMID: 34090478 PMCID: PMC8178893 DOI: 10.1186/s12964-021-00744-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/20/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. METHODS In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), a transcription factor integral to the auxin signaling pathway in plants. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. RESULTS Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. CONCLUSIONS IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate. Video Abstract.
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Affiliation(s)
- Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130 USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
| | - Lucia C. Strader
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130 USA
- Department of Biology, Duke University, Durham, NC 27708 USA
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513
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Ruff KM, Dar F, Pappu RV. Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates. BIOPHYSICS REVIEWS 2021; 2:021302. [PMID: 34179888 PMCID: PMC8211317 DOI: 10.1063/5.0050059] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022]
Abstract
Cellular matter can be spatially and temporally organized into membraneless biomolecular condensates. The current thinking is that these condensates form and dissolve via phase transitions driven by one or more condensate-specific multivalent macromolecules known as scaffolds. Cells likely regulate condensate formation and dissolution by exerting control over the concentrations of regulatory molecules, which we refer to as ligands. Wyman and Gill introduced the framework of polyphasic linkage to explain how ligands can exert thermodynamic control over phase transitions. This review focuses on describing the concepts of polyphasic linkage and the relevance of such a mechanism for controlling condensate formation and dissolution. We describe how ligand-mediated control over scaffold phase behavior can be quantified experimentally. Further, we build on recent studies to highlight features of ligands that make them suppressors vs drivers of phase separation. Finally, we highlight areas where advances are needed to further understand ligand-mediated control of condensates in complex cellular environments. These advances include understanding the effects of networks of ligands on condensate behavior and how ligands modulate phase transitions controlled by different combinations of homotypic and heterotypic interactions among scaffold macromolecules. Insights gained from the application of polyphasic linkage concepts should be useful for designing novel pharmaceutical ligands to regulate condensates.
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Affiliation(s)
- Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
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514
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Generic nature of the condensed states of proteins. Nat Cell Biol 2021; 23:587-594. [PMID: 34108660 DOI: 10.1038/s41556-021-00697-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/07/2021] [Indexed: 02/05/2023]
Abstract
Proteins undergoing liquid-liquid phase separation are being discovered at an increasing rate. Since at the high concentrations present in the cell most proteins would be expected to form a liquid condensed state, this state should be considered to be a fundamental state of proteins along with the native state and the amyloid state. Here we discuss the generic nature of the liquid-like and solid-like condensed states, and describe a wide variety of biological functions conferred by these condensed states.
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515
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Peeples W, Rosen MK. Mechanistic dissection of increased enzymatic rate in a phase-separated compartment. Nat Chem Biol 2021; 17:693-702. [PMID: 34035521 PMCID: PMC8635274 DOI: 10.1038/s41589-021-00801-x] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/18/2021] [Indexed: 02/08/2023]
Abstract
Biomolecular condensates concentrate macromolecules into discrete cellular foci without an encapsulating membrane. Condensates are often presumed to increase enzymatic reaction rates through increased concentrations of enzymes and substrates (mass action), although this idea has not been widely tested and other mechanisms of modulation are possible. Here we describe a synthetic system where the SUMOylation enzyme cascade is recruited into engineered condensates generated by liquid-liquid phase separation of multidomain scaffolding proteins. SUMOylation rates can be increased up to 36-fold in these droplets compared to the surrounding bulk, depending on substrate KM. This dependency produces substantial specificity among different substrates. Analyses of reactions above and below the phase-separation threshold lead to a quantitative model in which reactions in condensates are accelerated by mass action and changes in substrate KM, probaby due to scaffold-induced molecular organization. Thus, condensates can modulate reaction rates both by concentrating molecules and physically organizing them.
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Affiliation(s)
- William Peeples
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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516
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Wiedner HJ, Giudice J. It's not just a phase: function and characteristics of RNA-binding proteins in phase separation. Nat Struct Mol Biol 2021; 28:465-473. [PMID: 34099940 PMCID: PMC8787349 DOI: 10.1038/s41594-021-00601-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/30/2021] [Indexed: 12/31/2022]
Abstract
Biomolecular condensates that form via phase separation are increasingly regarded as coordinators of cellular reactions that regulate a wide variety of biological phenomena. Mounting evidence suggests that multiple steps of the RNA life cycle are organized within RNA-binding protein-rich condensates. In this Review, we discuss recent insights into the influence of phase separation on RNA biology, which has implications for basic cell biology, the pathogenesis of human diseases and the development of novel therapies.
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Affiliation(s)
- Hannah J Wiedner
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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517
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Amen T, Kaganovich D. Stress granules inhibit fatty acid oxidation by modulating mitochondrial permeability. Cell Rep 2021; 35:109237. [PMID: 34133922 PMCID: PMC8220302 DOI: 10.1016/j.celrep.2021.109237] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/29/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
The formation of stress granules (SGs) is an essential aspect of the cellular response to many kinds of stress, but its adaptive role is far from clear. SG dysfunction is implicated in aging-onset neurodegenerative diseases, prompting interest in their physiological function. Here, we report that during starvation stress, SGs interact with mitochondria and regulate metabolic remodeling. We show that SG formation leads to a downregulation of fatty acid β-oxidation (FAO) through the modulation of mitochondrial voltage-dependent anion channels (VDACs), which import fatty acids (FAs) into mitochondria. The subsequent decrease in FAO during long-term starvation reduces oxidative damage and rations FAs for longer use. Failure to form SGs, whether caused by the genetic deletion of SG components or an amyotrophic lateral sclerosis (ALS)-associated mutation, translates into an inability to downregulate FAO. Because metabolic dysfunction is a common pathological element of neurodegenerative diseases, including ALS, our findings provide a direction for studying the clinical relevance of SGs. Stress granules inhibit fatty acid oxidation Stress granules regulate VDAC levels Stress granules control mitochondrial permeability to fatty acids Stress granules redirect fatty acids to lipid droplets
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany
| | - Daniel Kaganovich
- 1Base Pharmaceuticals, Boston, MA 02129, USA; Department of Experimental Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany.
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518
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Floris E, Piras A, Dall’Asta L, Gamba A, Hirsch E, Campa CC. Physics of compartmentalization: How phase separation and signaling shape membrane and organelle identity. Comput Struct Biotechnol J 2021; 19:3225-3233. [PMID: 34141141 PMCID: PMC8190439 DOI: 10.1016/j.csbj.2021.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/15/2021] [Indexed: 11/29/2022] Open
Abstract
Compartmentalization of cellular functions is at the core of the physiology of eukaryotic cells. Recent evidences indicate that a universal organizing process - phase separation - supports the partitioning of biomolecules in distinct phases from a single homogeneous mixture, a landmark event in both the biogenesis and the maintenance of membrane and non-membrane-bound organelles. In the cell, 'passive' (non energy-consuming) mechanisms are flanked by 'active' mechanisms of separation into phases of distinct density and stoichiometry, that allow for increased partitioning flexibility and programmability. A convergence of physical and biological approaches is leading to new insights into the inner functioning of this driver of intracellular order, holding promises for future advances in both biological research and biotechnological applications.
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Affiliation(s)
- Elisa Floris
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Andrea Piras
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Luca Dall’Asta
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Collegio Carlo Alberto, Piazza Arbarello 8, 10122 Torino, Italy
| | - Andrea Gamba
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), sezione di Torino, Via Giuria 1, 10125 Torino, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
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519
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Embarc-Buh A, Francisco-Velilla R, Martinez-Salas E. RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements. Viruses 2021; 13:952. [PMID: 34064059 PMCID: PMC8224014 DOI: 10.3390/v13060952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is largely achieved by the concerted action of regulatory structural elements on viral RNAs and a subset of host proteins, whose dedicated function across all stages of the infection steps is critical to complete the viral cycle. Importantly, not only the RNA sequence but also the RNA architecture imposed by the presence of specific structural domains mediates the interaction with host RNA-binding proteins (RBPs), ultimately affecting virus multiplication and spreading. In marked difference with other biological systems, the genome of positive strand RNA viruses is also the mRNA. Here we focus on distinct types of positive strand RNA viruses that differ in the regulatory elements used to promote translation of the viral RNA, as well as in the mechanisms used to evade the series of events connected to antiviral response, including translation shutoff induced in infected cells, assembly of stress granules, and trafficking stress.
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Affiliation(s)
| | | | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, 28049 Madrid, Spain; (A.E.-B.); (R.F.-V.)
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520
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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: 58] [Impact Index Per Article: 19.3] [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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521
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Cai H, Liu X, Zhang F, Han QY, Liu ZS, Xue W, Guo ZL, Zhao JM, Sun LM, Wang N, Mao J, He K, Xia T, Chen Y, Chen L, Li AL, Zhou T, Zhang XM, Li WH, Li T. G3BP1 Inhibition Alleviates Intracellular Nucleic Acid-Induced Autoimmune Responses. THE JOURNAL OF IMMUNOLOGY 2021; 206:2453-2467. [PMID: 33941659 DOI: 10.4049/jimmunol.2001111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/15/2021] [Indexed: 12/20/2022]
Abstract
The detection of intracellular nucleic acids is a fundamental mechanism of host defense against infections. The dysregulated nucleic acid sensing, however, is a major cause for a number of autoimmune diseases. In this study, we report that GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) is critical for both intracellular DNA- and RNA-induced immune responses. We found that in both human and mouse cells, the deletion of G3BP1 led to the dampened cGAS activation by DNA and the insufficient binding of RNA by RIG-I. We further found that resveratrol (RSVL), a natural compound found in grape skin, suppressed both intracellular DNA- and RNA-induced type I IFN production through inhibiting G3BP1. Importantly, using experimental mouse models for Aicardi-Goutières syndrome, an autoimmune disorder found in humans, we demonstrated that RSVL effectively alleviated intracellular nucleic acid-stimulated autoimmune responses. Thus, our study demonstrated a broader role of G3BP1 in sensing different kinds of intracellular nucleic acids and presented RSVL as a potential treatment for autoimmune conditions caused by dysregulated nucleic acid sensing.
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Affiliation(s)
- Hong Cai
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Xin Liu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Feng Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Qiu-Ying Han
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Zhao-Shan Liu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Wen Xue
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Zeng-Lin Guo
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Jiang-Man Zhao
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Li-Ming Sun
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Na Wang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Jie Mao
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Kun He
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Tian Xia
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Yuan Chen
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Liang Chen
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Ai-Ling Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Tao Zhou
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Xue-Min Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, China.,School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei-Hua Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China .,Nanhu Laboratory, Jiaxing, Zhejiang Province, China
| | - Tao Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China .,Nanhu Laboratory, Jiaxing, Zhejiang Province, China.,School of Basic Medical Sciences, Fudan University, Shanghai, China
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522
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Sidibé H, Dubinski A, Vande Velde C. The multi-functional RNA-binding protein G3BP1 and its potential implication in neurodegenerative disease. J Neurochem 2021; 157:944-962. [PMID: 33349931 PMCID: PMC8248322 DOI: 10.1111/jnc.15280] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
Ras-GTPase-activating protein (GAP)-binding protein 1 (G3BP1) is a multi-functional protein that is best known for its role in the assembly and dynamics of stress granules. Recent studies have highlighted that G3BP1 also has other functions related to RNA metabolism. In the context of disease, G3BP1 has been therapeutically targeted in cancers because its over-expression is correlated with proliferation of cancerous cells and metastasis. However, evidence suggests that G3BP1 is essential for neuronal development and possibly neuronal maintenance. In this review, we will examine the many functions that are carried out by G3BP1 in the context of neurons and speculate how these functions are critical to the progression of neurodegenerative diseases. Additionally, we will highlight the similarities and differences between G3BP1 and the closely related protein G3BP2, which is frequently overlooked. Although G3BP1 and G3BP2 have both been deemed important for stress granule assembly, their roles may differ in other cellular pathways, some of which are specific to the CNS, and presents an opportunity for further exploration.
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Affiliation(s)
- Hadjara Sidibé
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
| | - Alicia Dubinski
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
| | - Christine Vande Velde
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
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523
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Tweedie A, Nissan T. Hiding in Plain Sight: Formation and Function of Stress Granules During Microbial Infection of Mammalian Cells. Front Mol Biosci 2021; 8:647884. [PMID: 33996904 PMCID: PMC8116797 DOI: 10.3389/fmolb.2021.647884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/01/2021] [Indexed: 01/21/2023] Open
Abstract
Stress granule (SG) formation is a host cell response to stress-induced translational repression. SGs assemble with RNA-binding proteins and translationally silent mRNA. SGs have been demonstrated to be both inhibitory to viruses, as well as being subverted for viral roles. In contrast, the function of SGs during non-viral microbial infections remains largely unexplored. A handful of microbial infections have been shown to result in host SG assembly. Nevertheless, a large body of evidence suggests SG formation in hosts is a widespread response to microbial infection. Diverse stresses caused by microbes and their products can activate the integrated stress response in order to inhibit translation initiation through phosphorylation of the eukaryotic translation initiation factor 2α (eIF2α). This translational response in other contexts results in SG assembly, suggesting that SG assembly can be a general phenomenon during microbial infection. This review explores evidence for host SG formation in response to bacterial, fungal, and protozoan infection and potential functions of SGs in the host and for adaptations of the pathogen.
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Affiliation(s)
- Alistair Tweedie
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tracy Nissan
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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524
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Guo Q, Shi X, Wang X. RNA and liquid-liquid phase separation. Noncoding RNA Res 2021; 6:92-99. [PMID: 33997539 PMCID: PMC8111091 DOI: 10.1016/j.ncrna.2021.04.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/09/2023] Open
Abstract
Liquid-Liquid Phase Separation (LLPS) is a biological phenomenon that refers to the components of similar properties form droplets condensate in cells. These droplets play an important role in maintaining the stability of order in cells. In the studies of phase separation, weak multivalent interactions between proteins have always been the focus of attentions. With the deepening research of phase separation, more and more evidences show that RNA, especially long noncoding RNA (lncRNA), also plays an important regulatory role in the phase separation. We summarized recent researches between phase separation and RNA, and focused on the function of non-coding RNA (ncRNA) in the process of phase separation. In fact, phase separation and RNA have a two-way regulation relationship. Noncoding RNA usually recruits proteins as molecular scaffolds to drive phase separation. On the other hand, phase separation is also involved in RNA transcription, transport, metabolism and other processes.
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Affiliation(s)
- Qi Guo
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangmin Shi
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
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525
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Jin X, Cao X, Liu S, Liu B. Functional Roles of Poly(ADP-Ribose) in Stress Granule Formation and Dynamics. Front Cell Dev Biol 2021; 9:671780. [PMID: 33981709 PMCID: PMC8107429 DOI: 10.3389/fcell.2021.671780] [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: 02/24/2021] [Accepted: 04/06/2021] [Indexed: 12/03/2022] Open
Abstract
Stress granules (SGs) are highly dynamic cytoplasmic foci formed in response to stress. The formation of SGs is reported to be regulated by diverse post-translational protein modifications (PTMs). Among them, ADP-ribosylation is of emerging interest due to its recently identified roles in SG organization. In this review, we summarized the latest advances on the roles of poly(ADP-ribose) (PAR) in the regulation of SG formation and dynamics, including its function in modulating nucleocytoplasmic trafficking and SG recruitment of SG components, as well as its effects on protein phase separation behavior. Moreover, the functional role of PAR chain diversity on dynamic of SG composition is also introduced. Potential future developments on investigating global ADP-ribosylation networks, individual roles of different PARPs, and interactions between ADP-ribosylation and other PTMs in SGs are also discussed.
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Affiliation(s)
- Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Xiuling Cao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Faculty of Science, Center for Large-Scale Cell-Based Screening, University of Gothenburg, Gothenburg, Sweden
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526
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Amen T, Kaganovich D. Small Molecule Screen Reveals Joint Regulation of Stress Granule Formation and Lipid Droplet Biogenesis. Front Cell Dev Biol 2021; 8:606111. [PMID: 33972926 PMCID: PMC8105174 DOI: 10.3389/fcell.2020.606111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/21/2020] [Indexed: 01/22/2023] Open
Abstract
Metabolic regulation is a necessary component of all stress response pathways, because all different mechanisms of stress-adaptation place high-energy demands on the cell. Mechanisms that integrate diverse stress response pathways with their metabolic components are therefore of great interest, but few are known. We show that stress granule (SG) formation, a common adaptive response to a variety of stresses, is reciprocally regulated by the pathways inducing lipid droplet accumulation. Inability to upregulate lipid droplets reduces stress granule formation. Stress granule formation in turn drives lipid droplet clustering and fatty acid accumulation. Our findings reveal a novel connection between stress response pathways and new modifiers of stress granule formation.
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.,1Base Pharmaceuticals, Boston, MA, United States
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527
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Hamey JJ, Nguyen A, Wilkins MR. Discovery of Arginine Methylation, Phosphorylation, and Their Co-occurrence in Condensate-Associated Proteins in Saccharomyces cerevisiae. J Proteome Res 2021; 20:2420-2434. [PMID: 33856219 DOI: 10.1021/acs.jproteome.0c00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The formation of condensates in membraneless organelles is thought to be driven by protein phase separation. Arginine methylation and serine/threonine phosphorylation are important in the phase separation process; however, these post-translational modifications are often present in intrinsically disordered regions that are difficult to analyze with standard proteomic techniques. To understand their presence and co-occurrence in condensate-associated proteins, here, we use a multiprotease and multi-tandem mass spectrometry (MS/MS) fragmentation approach, coupled with heavy methyl stable isotope labeling of amino acids in cell culture (SILAC) and phospho- or methyl-peptide enrichment. For Saccharomyces cerevisiae, we report a 50% increase in the known arginine methylproteome, involving 15 proteins that are all condensate-associated. Importantly, some of these proteins have arginine methylation on all predicted sites-providing evidence that this modification can be pervasive. We explored whether arginine-methylated, condensate-associated proteins are also phosphorylated and found 12 such proteins to carry phosphorylated serine or threonine. In Npl3, Ded1, and Sbp1, single peptides were found to carry both modifications, indicating a co-occurrence in close proximity and on the same protein molecule. These co-modifications occur in regions of disorder, whereas arginine methylation is typically on regions of disorder that are also basic. For phosphorylation, its association with charged regions of condensate-associated proteins was less consistent, although some regions with multisite phosphorylation sites were strongly acidic. We conclude that arginine-methylated proteins associated with condensates are typically also modified with protein phosphorylation.
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Affiliation(s)
- Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Amy Nguyen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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528
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Liu Y, Cheng A, Wang M, Mao S, Ou X, Yang Q, Wu Y, Gao Q, Liu M, Zhang S, Huang J, Jia R, Zhu D, Chen S, Zhao X, Yu Y, Liu Y, Zhang L, Tian B, Pan L. Duck Hepatitis A Virus Type 1 Induces eIF2α Phosphorylation-Dependent Cellular Translation Shutoff via PERK/GCN2. Front Microbiol 2021; 12:624540. [PMID: 33912143 PMCID: PMC8072014 DOI: 10.3389/fmicb.2021.624540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/12/2021] [Indexed: 11/20/2022] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) is one of the most deadly pathogens that endanger the duck industry. Most viruses usually turn off host translation after infection to facilitate viral replication and translation. For the first time report to our knowledge, DHAV-1 can induce eIF2α phosphorylation and inhibit cellular translation in duck embryo fibroblasts (DEFs). Moreover, the activity of DHAV-1 in the cells caused obvious eIF2α phosphorylation, which has nothing to do with the viral protein. Subsequently, we screened two kinases (PERK and GCN2) that affect eIF2α phosphorylation through inhibitors and shRNA. Notably, the role of GCN2 in other picornaviruses has not been reported. In addition, when the phosphorylation of eIF2α induced by DHAV-1 is inhibited, the translation efficiency of DEFs restores to a normal level, indicating that DHAV-1 induced cellular translation shutoff is dependent on eIF2α phosphorylation.
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Affiliation(s)
- Yuanzhi Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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529
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Porcine Epidemic Diarrhea Virus Infection Induces Caspase-8-Mediated G3BP1 Cleavage and Subverts Stress Granules To Promote Viral Replication. J Virol 2021; 95:JVI.02344-20. [PMID: 33568512 DOI: 10.1128/jvi.02344-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is an α-coronavirus causing severe diarrhea and high mortality rates in suckling piglets and posing significant economic impact. PEDV replication is completed and results in a large amount of RNA in the cytoplasm. Stress granules (SGs) are dynamic cytosolic RNA granules formed under various stress conditions, including viral infections. Several previous studies suggested that SGs were involved in the antiviral activity of host cells to limit viral propagation. However, the underlying mechanisms are poorly understood. This study aimed to delineate the molecular mechanisms regulating the SG response to PEDV infection. SG formation is induced early during PEDV infection, but as infection proceeds, this ability is lost and SGs disappear at late stages of infection (>18 h postinfection). PEDV infection resulted in the cleavage of Ras-GTPase-activating protein-binding protein 1 (G3BP1) mediated by caspase-8. Using mutational analysis, the PEDV-induced cleavage site within G3BP1 was identified, which differed from the 3C protease cleavage site previously identified. Furthermore, G3BP1 cleavage by caspase-8 at D168 and D169 was confirmed in vitro as well as in vivo The overexpression of cleavage-resistant G3BP1 conferred persistent SG formation and suppression of viral replication. Additionally, the knockdown of endogenous G3BP1 abolished SG formation and potentiated viral replication. Taken together, these data provide new insights into novel strategies in which PEDV limits the host stress response and antiviral responses and indicate that caspase-8-mediated G3BP1 cleavage is important in the failure of host defense against PEDV infection.IMPORTANCE Coronaviruses (CoVs) are drawing extensive attention again since the outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019. CoVs are prone to variation and own the transmission capability by crossing the species barrier resulting in reemergence. How CoVs manipulate the antiviral responses of their hosts needs to be explored. Overall, the study provides new insight into how porcine epidemic diarrhea virus (PEDV) impaired SG assembly by targeting G3BP1 via the host proteinase caspase-8. These findings enhanced the understanding of PEDV infection and might help identify new antiviral targets that could inhibit viral replication and limit the pathogenesis of PEDV.
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530
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Zhao M, Yu Y, Sun LM, Xing JQ, Li T, Zhu Y, Wang M, Yu Y, Xue W, Xia T, Cai H, Han QY, Yin X, Li WH, Li AL, Cui J, Yuan Z, Zhang R, Zhou T, Zhang XM, Li T. GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Nat Commun 2021; 12:2114. [PMID: 33837182 PMCID: PMC8035206 DOI: 10.1038/s41467-021-22297-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
Lack of detailed knowledge of SARS-CoV-2 infection has been hampering the development of treatments for coronavirus disease 2019 (COVID-19). Here, we report that RNA triggers the liquid-liquid phase separation (LLPS) of the SARS-CoV-2 nucleocapsid protein, N. By analyzing all 29 proteins of SARS-CoV-2, we find that only N is predicted as an LLPS protein. We further confirm the LLPS of N during SARS-CoV-2 infection. Among the 100,849 genome variants of SARS-CoV-2 in the GISAID database, we identify that ~37% (36,941) of the genomes contain a specific trio-nucleotide polymorphism (GGG-to-AAC) in the coding sequence of N, which leads to the amino acid substitutions, R203K/G204R. Interestingly, NR203K/G204R exhibits a higher propensity to undergo LLPS and a greater effect on IFN inhibition. By screening the chemicals known to interfere with N-RNA binding in other viruses, we find that (-)-gallocatechin gallate (GCG), a polyphenol from green tea, disrupts the LLPS of N and inhibits SARS-CoV-2 replication. Thus, our study reveals that targeting N-RNA condensation with GCG could be a potential treatment for COVID-19.
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Affiliation(s)
- Ming Zhao
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, 314002, China
| | - Yu Yu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China.,Cancer Research Institute of Jilin University, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Li-Ming Sun
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Jia-Qing Xing
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Tingting Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Yunkai Zhu
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Miao Wang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Yin Yu
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wen Xue
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Tian Xia
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Hong Cai
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Qiu-Ying Han
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Xiaoyao Yin
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Wei-Hua Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Ai-Ling Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Jiuwei Cui
- Cancer Research Institute of Jilin University, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Zhenghong Yuan
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Rong Zhang
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Tao Zhou
- Nanhu Laboratory, Jiaxing, Zhejiang Province, 314002, China.
| | - Xue-Min Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China. .,School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Tao Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China. .,School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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531
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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: 60] [Impact Index Per Article: 20.0] [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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532
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 2021; 12:1936. [PMID: 33782395 PMCID: PMC8007728 DOI: 10.1038/s41467-021-21953-3] [Citation(s) in RCA: 286] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jason A Wagoner
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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533
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Loughlin FE, West DL, Gunzburg MJ, Waris S, Crawford SA, Wilce MCJ, Wilce JA. Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1. Nucleic Acids Res 2021; 49:2403-2417. [PMID: 33621982 PMCID: PMC7969032 DOI: 10.1093/nar/gkab080] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/01/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022] Open
Abstract
TIA-1 is an RNA-binding protein that sequesters target RNA into stress granules under conditions of cellular stress. Promotion of stress granule formation by TIA-1 depends upon self-association of its prion-like domain that facilitates liquid-liquid phase separation and is thought to be enhanced via RNA binding. However, the mechanisms underlying the influence of RNA on TIA-1 self-association have not been previously demonstrated. Here we have investigated the self-associating properties of full-length TIA-1 in the presence of designed and native TIA-1 nucleic acid binding sites in vitro, monitoring phase separation, fibril formation and shape. We show that single stranded RNA and DNA induce liquid-liquid phase separation of TIA-1 in a multisite, sequence-specific manner and also efficiently promote formation of amyloid-like fibrils. Although RNA binding to a single site induces a small conformational change in TIA-1, this alone does not enhance phase separation of TIA-1. Tandem binding sites are required to enhance phase separation of TIA-1 and this is finely tuned by the protein:binding site stoichiometry rather than nucleic acid length. Native tandem TIA-1 binding sites within the 3′ UTR of p53 mRNA also efficiently enhance phase separation of TIA-1 and thus may potentially act as potent nucleation sites for stress granule assembly.
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Affiliation(s)
- Fionna E Loughlin
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Danella L West
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Menachem J Gunzburg
- Monash Institute of Pharmaceutical Sciences, Monash University, Victoria 3052, Australia
| | - Saboora Waris
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simon A Crawford
- Ramaciotti Centre For Cryo Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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534
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Li J, Zhang Y, Chen X, Ma L, Li P, Yu H. Protein phase separation and its role in chromatin organization and diseases. Biomed Pharmacother 2021; 138:111520. [PMID: 33765580 DOI: 10.1016/j.biopha.2021.111520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/04/2021] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
In the physical sciences, solid, liquid, and gas are the most familiar phase states, whose essence is their existence reflecting the different spatial distribution of molecular components. The biological molecules in the living cell also have differences in spatial distribution. The molecules organized in the form of membrane-bound organelles are well recognized. However, the biomolecules organized in membraneless compartments called biomolecular condensates remain elusive. The liquid-liquid phase separation (LLPS), as a new emerging scientific breakthrough, describes the biomolecules assembled in special distribution and appeared as membraneless condensates in the form of a new "phase" compared with the surrounding liquid milieu. LLPS provides an important theoretical basis for explaining the composition of biological molecules and related biological reactions. Mounting evidence has emerged recently that phase-separated condensates participate in various biological activities. This article reviews the occurrence of LLPS and underlying regulatory mechanisms for understanding how multivalent molecules drive phase transitions to form the biomolecular condensates. And, it also summarizes recent major progress in elucidating the roles of LLPS in chromatin organization and provides clues for the development of new innovative therapeutic strategies for related diseases.
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Affiliation(s)
- Jiaqi Li
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Yao Zhang
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Xi Chen
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Lijuan Ma
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haijie Yu
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China.
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535
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Noda NN, Wang Z, Zhang H. Liquid-liquid phase separation in autophagy. J Cell Biol 2021; 219:151909. [PMID: 32603410 PMCID: PMC7401820 DOI: 10.1083/jcb.202004062] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/05/2023] Open
Abstract
Liquid–liquid phase separation (LLPS) compartmentalizes and concentrates biomacromolecules into distinct condensates. Liquid-like condensates can transition into gel and solid states, which are essential for fulfilling their different functions. LLPS plays important roles in multiple steps of autophagy, mediating the assembly of autophagosome formation sites, acting as an unconventional modulator of TORC1-mediated autophagy regulation, and triaging protein cargos for degradation. Gel-like, but not solid, protein condensates can trigger formation of surrounding autophagosomal membranes. Stress and pathological conditions cause aberrant phase separation and transition of condensates, which can evade surveillance by the autophagy machinery. Understanding the mechanisms underlying phase separation and transition will provide potential therapeutic targets for protein aggregation diseases.
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Affiliation(s)
- Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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536
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Mediani L, Antoniani F, Galli V, Vinet J, Carrà AD, Bigi I, Tripathy V, Tiago T, Cimino M, Leo G, Amen T, Kaganovich D, Cereda C, Pansarasa O, Mandrioli J, Tripathi P, Troost D, Aronica E, Buchner J, Goswami A, Sterneckert J, Alberti S, Carra S. Hsp90-mediated regulation of DYRK3 couples stress granule disassembly and growth via mTORC1 signaling. EMBO Rep 2021; 22:e51740. [PMID: 33738926 PMCID: PMC8097338 DOI: 10.15252/embr.202051740] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/02/2021] [Accepted: 02/19/2021] [Indexed: 12/24/2022] Open
Abstract
Stress granules (SGs) are dynamic condensates associated with protein misfolding diseases. They sequester stalled mRNAs and signaling factors, such as the mTORC1 subunit raptor, suggesting that SGs coordinate cell growth during and after stress. However, the molecular mechanisms linking SG dynamics and signaling remain undefined. We report that the chaperone Hsp90 is required for SG dissolution. Hsp90 binds and stabilizes the dual‐specificity tyrosine‐phosphorylation‐regulated kinase 3 (DYRK3) in the cytosol. Upon Hsp90 inhibition, DYRK3 dissociates from Hsp90 and becomes inactive. Inactive DYRK3 is subjected to two different fates: it either partitions into SGs, where it is protected from irreversible aggregation, or it is degraded. In the presence of Hsp90, DYRK3 is active and promotes SG disassembly, restoring mTORC1 signaling and translation. Thus, Hsp90 links stress adaptation and cell growth by regulating the activity of a key kinase involved in condensate disassembly and translation restoration.
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Affiliation(s)
- Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Francesco Antoniani
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Veronica Galli
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Jonathan Vinet
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy.,Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Arianna Dorotea Carrà
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Ilaria Bigi
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Vadreenath Tripathy
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Dresden, Germany
| | - Tatiana Tiago
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Cimino
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Giuseppina Leo
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Orietta Pansarasa
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Jessica Mandrioli
- Department of Neuroscience, St. Agostino Estense Hospital, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Priyanka Tripathi
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Dirk Troost
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Anand Goswami
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, Modena, Italy
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537
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Protocol for the determination of intracellular phase separation thresholds. STAR Protoc 2021; 2:100308. [PMID: 33554143 PMCID: PMC7856470 DOI: 10.1016/j.xpro.2021.100308] [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] [Indexed: 11/20/2022] Open
Abstract
To date, phase separation studies have largely been limited to in vitro assays using non-native conditions and aggregation-prone recombinant proteins that are often difficult to purify. This protocol describes the determination of relative protein concentration thresholds for phase separation through fluorescent imaging of GFP-tagged proteins in cells. The commercial availability of various plasmids and antibodies, as well as advances in gene editing, allow this procedure to be modified for the study of various phase-separating proteins in their relevant contexts. For complete details on the use and execution of this protocol, please refer to Lee et al. (2020). Determining relative protein concentration thresholds for phase separation in cells Fluorescent imaging and analysis of GFP-tagged proteins at single-cell resolution Immunofluorescent staining and imaging of endogenous proteins Quantification of endogenous protein levels relative to the threshold concentration
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538
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Martin EW, Thomasen FE, Milkovic NM, Cuneo MJ, Grace C, Nourse A, Lindorff-Larsen K, Mittag T. Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation. Nucleic Acids Res 2021; 49:2931-2945. [PMID: 33577679 PMCID: PMC7969017 DOI: 10.1093/nar/gkab063] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 12/29/2020] [Accepted: 01/29/2021] [Indexed: 01/24/2023] Open
Abstract
Liquid-liquid phase separation underlies the membrane-less compartmentalization of cells. Intrinsically disordered low-complexity domains (LCDs) often mediate phase separation, but how their phase behavior is modulated by folded domains is incompletely understood. Here, we interrogate the interplay between folded and disordered domains of the RNA-binding protein hnRNPA1. The LCD of hnRNPA1 is sufficient for mediating phase separation in vitro. However, we show that the folded RRM domains and a folded solubility-tag modify the phase behavior, even in the absence of RNA. Notably, the presence of the folded domains reverses the salt dependence of the driving force for phase separation relative to the LCD alone. Small-angle X-ray scattering experiments and coarse-grained MD simulations show that the LCD interacts transiently with the RRMs and/or the solubility-tag in a salt-sensitive manner, providing a mechanistic explanation for the observed salt-dependent phase separation. These data point to two effects from the folded domains: (i) electrostatically-mediated interactions that compact hnRNPA1 and contribute to phase separation and (ii) increased solubility at higher ionic strengths mediated by the folded domains. The interplay between disordered and folded domains can modify the dependence of phase behavior on solution conditions and can obscure signatures of physicochemical interactions underlying phase separation.
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Affiliation(s)
- Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - F Emil Thomasen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, 2200, Denmark
| | - Nicole M Milkovic
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - Amanda Nourse
- Protein Technologies Center, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, 2200, Denmark
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
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539
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Mateju D, Chao JA. Stress granules: regulators or by-products? FEBS J 2021; 289:363-373. [PMID: 33725420 DOI: 10.1111/febs.15821] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/07/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Cells have to deal with conditions that can cause damage to biomolecules and eventually cell death. To protect against these adverse conditions and promote recovery, cells undergo dramatic changes upon exposure to stress. This involves activation of signaling pathways, cell cycle arrest, translational reprogramming, and reorganization of the cytoplasm. Notably, many stress conditions cause a global inhibition of mRNA translation accompanied by the formation of cytoplasmic condensates called stress granules (SGs), which sequester mRNA together with RNA-binding proteins, translation initiation factors, and other components. SGs are highly conserved in eukaryotes, suggesting that they perform an important function during the stress response. Over the years, many different roles have been assigned to SGs, including translational control, mRNA storage, regulation of mRNA decay, antiviral innate immune response, and modulation of signaling pathways. Most of our understanding, however, has been deduced from correlative data based upon the composition of SGs and only recently have technological innovations allowed hypotheses for SG function to be directly tested. Here, we discuss these challenges and explore the evidence related to the function of SGs.
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Affiliation(s)
- Daniel Mateju
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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540
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Zbinden A, Pérez-Berlanga M, De Rossi P, Polymenidou M. Phase Separation and Neurodegenerative Diseases: A Disturbance in the Force. Dev Cell 2021; 55:45-68. [PMID: 33049211 DOI: 10.1016/j.devcel.2020.09.014] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
Protein aggregation is the main hallmark of neurodegenerative diseases. Many proteins found in pathological inclusions are known to undergo liquid-liquid phase separation, a reversible process of molecular self-assembly. Emerging evidence supports the hypothesis that aberrant phase separation behavior may serve as a trigger of protein aggregation in neurodegeneration, and efforts to understand and control the underlying mechanisms are underway. Here, we review similarities and differences among four main proteins, α-synuclein, FUS, tau, and TDP-43, which are found aggregated in different diseases and were independently shown to phase separate. We discuss future directions in the field that will help shed light on the molecular mechanisms of aggregation and neurodegeneration.
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Affiliation(s)
- Aurélie Zbinden
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Manuela Pérez-Berlanga
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pierre De Rossi
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Magdalini Polymenidou
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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541
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Yi J, Peng J, Yang W, Zhu G, Ren J, Li D, Zheng H. Picornavirus 3C - a protease ensuring virus replication and subverting host responses. J Cell Sci 2021; 134:134/5/jcs253237. [PMID: 33692152 DOI: 10.1242/jcs.253237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The protease 3C is encoded by all known picornaviruses, and the structural features related to its protease and RNA-binding activities are conserved; these contribute to the cleavage of viral polyproteins and the assembly of the viral RNA replication complex during virus replication. Furthermore, 3C performs functions in the host cell through its interaction with host proteins. For instance, 3C has been shown to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and to inactivate key factors in innate immunity signaling pathways, inhibiting the production of interferon and inflammatory cytokines. Importantly, 3C maintains virus infection by subtly subverting host cell death and modifying critical molecules in host organelles. This Review focuses on the molecular mechanisms through which 3C mediates physiological processes involved in virus-host interaction, thus highlighting the picornavirus-mediated pathogenesis caused by 3C.
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Affiliation(s)
- Jiamin Yi
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Jiangling Peng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Wenping Yang
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Guoqiang Zhu
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Jingjing Ren
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
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542
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Tolay N, Buchberger A. Comparative profiling of stress granule clearance reveals differential contributions of the ubiquitin system. Life Sci Alliance 2021; 4:4/5/e202000927. [PMID: 33687997 PMCID: PMC8008963 DOI: 10.26508/lsa.202000927] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 01/09/2023] Open
Abstract
This study shows that ubiquitin conjugates associate with various types of stress granules and that an active ubiquitin system is required for the efficient clearance of some types of stress granules. Stress granules (SGs) are cytoplasmic condensates containing untranslated mRNP complexes. They are induced by various proteotoxic conditions such as heat, oxidative, and osmotic stress. SGs are believed to protect mRNPs from degradation and to enable cells to rapidly resume translation when stress conditions subside. SG dynamics are controlled by various posttranslational modifications, but the role of the ubiquitin system has remained controversial. Here, we present a comparative analysis addressing the involvement of the ubiquitin system in SG clearance. Using high-resolution immunofluorescence microscopy, we found that ubiquitin associated to varying extent with SGs induced by heat, arsenite, H2O2, sorbitol, or combined puromycin and Hsp70 inhibitor treatment. SG-associated ubiquitin species included K48- and K63-linked conjugates, whereas free ubiquitin was not significantly enriched. Inhibition of the ubiquitin activating enzyme, deubiquitylating enzymes, the 26S proteasome and p97/VCP impaired the clearance of arsenite- and heat-induced SGs, whereas SGs induced by other stress conditions were little affected. Our data underline the differential involvement of the ubiquitin system in SG clearance, a process important to prevent the formation of disease-linked aberrant SGs.
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Affiliation(s)
- Nazife Tolay
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander Buchberger
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
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543
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Ruff KM, Dar F, Pappu RV. Ligand effects on phase separation of multivalent macromolecules. Proc Natl Acad Sci U S A 2021; 118:e2017184118. [PMID: 33653957 PMCID: PMC7958451 DOI: 10.1073/pnas.2017184118] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/30/2020] [Indexed: 01/23/2023] Open
Abstract
Biomolecular condensates enable spatial and temporal control over cellular processes by concentrating biomolecules into nonstoichiometric assemblies. Many condensates form via reversible phase transitions of condensate-specific multivalent macromolecules known as scaffolds. Phase transitions of scaffolds can be regulated by changing the concentrations of ligands, which are defined as nonscaffold molecules that bind to specific sites on scaffolds. Here, we use theory and computation to uncover rules that underlie ligand-mediated control over scaffold phase behavior. We use the stickers-and-spacers model wherein reversible noncovalent cross-links among stickers drive phase transitions of scaffolds, and spacers modulate the driving forces for phase transitions. We find that the modulatory effects of ligands are governed by the valence of ligands, whether they bind directly to stickers versus spacers, and the relative affinities of ligand-scaffold versus scaffold-scaffold interactions. In general, all ligands have a diluting effect on the concentration of scaffolds within condensates. Whereas monovalent ligands destabilize condensates, multivalent ligands can stabilize condensates by binding directly to spacers or destabilize condensates by binding directly to stickers. Bipartite ligands that bind to stickers and spacers can alter the structural organization of scaffold molecules within condensates even when they have a null effect on condensate stability. Our work highlights the importance of measuring dilute phase concentrations of scaffolds as a function of ligand concentration in cells. This can reveal whether ligands modulate scaffold phase behavior by enabling or suppressing phase separation at endogenous levels, thereby regulating the formation and dissolution of condensates in vivo.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130;
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Furqan Dar
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130;
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
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544
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Abstract
Biomolecular condensates enable spatial and temporal control over cellular processes by concentrating biomolecules into nonstoichiometric assemblies. Many condensates form via reversible phase transitions of condensate-specific multivalent macromolecules known as scaffolds. Phase transitions of scaffolds can be regulated by changing the concentrations of ligands, which are defined as nonscaffold molecules that bind to specific sites on scaffolds. Here, we use theory and computation to uncover rules that underlie ligand-mediated control over scaffold phase behavior. We use the stickers-and-spacers model wherein reversible noncovalent cross-links among stickers drive phase transitions of scaffolds, and spacers modulate the driving forces for phase transitions. We find that the modulatory effects of ligands are governed by the valence of ligands, whether they bind directly to stickers versus spacers, and the relative affinities of ligand-scaffold versus scaffold-scaffold interactions. In general, all ligands have a diluting effect on the concentration of scaffolds within condensates. Whereas monovalent ligands destabilize condensates, multivalent ligands can stabilize condensates by binding directly to spacers or destabilize condensates by binding directly to stickers. Bipartite ligands that bind to stickers and spacers can alter the structural organization of scaffold molecules within condensates even when they have a null effect on condensate stability. Our work highlights the importance of measuring dilute phase concentrations of scaffolds as a function of ligand concentration in cells. This can reveal whether ligands modulate scaffold phase behavior by enabling or suppressing phase separation at endogenous levels, thereby regulating the formation and dissolution of condensates in vivo.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130;
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Furqan Dar
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130;
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
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545
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Kim W, Kim DY, Lee KH. RNA-Binding Proteins and the Complex Pathophysiology of ALS. Int J Mol Sci 2021; 22:ijms22052598. [PMID: 33807542 PMCID: PMC7961459 DOI: 10.3390/ijms22052598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have identified disease-causing mutations and accelerated the unveiling of complex molecular pathogenic mechanisms, which may be important for understanding the disease and developing therapeutic strategies. Many disease-related genes encode RNA-binding proteins, and most of the disease-causing RNA or proteins encoded by these genes form aggregates and disrupt cellular function related to RNA metabolism. Disease-related RNA or proteins interact or sequester other RNA-binding proteins. Eventually, many disease-causing mutations lead to the dysregulation of nucleocytoplasmic shuttling, the dysfunction of stress granules, and the altered dynamic function of the nucleolus as well as other membrane-less organelles. As RNA-binding proteins are usually components of several RNA-binding protein complexes that have other roles, the dysregulation of RNA-binding proteins tends to cause diverse forms of cellular dysfunction. Therefore, understanding the role of RNA-binding proteins will help elucidate the complex pathophysiology of ALS. Here, we summarize the current knowledge regarding the function of disease-associated RNA-binding proteins and their role in the dysfunction of membrane-less organelles.
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Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
| | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
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546
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Esposito M, Fang C, Cook KC, Park N, Wei Y, Spadazzi C, Bracha D, Gunaratna RT, Laevsky G, DeCoste CJ, Slabodkin H, Brangwynne CP, Cristea IM, Kang Y. TGF-β-induced DACT1 biomolecular condensates repress Wnt signalling to promote bone metastasis. Nat Cell Biol 2021; 23:257-267. [PMID: 33723425 PMCID: PMC7970447 DOI: 10.1038/s41556-021-00641-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/26/2021] [Indexed: 02/07/2023]
Abstract
The complexity of intracellular signalling requires both a diversity of molecular players and the sequestration of activity to unique compartments within the cell. Recent findings on the role of liquid-liquid phase separation provide a distinct mechanism for the spatial segregation of proteins to regulate signalling pathway crosstalk. Here, we discover that DACT1 is induced by TGFβ and forms protein condensates in the cytoplasm to repress Wnt signalling. These condensates do not localize to any known organelles but, rather, exist as phase-separated proteinaceous cytoplasmic bodies. The deletion of intrinsically disordered domains within the DACT1 protein eliminates its ability to both form protein condensates and suppress Wnt signalling. Isolation and mass spectrometry analysis of these particles revealed a complex of protein machinery that sequesters casein kinase 2-a Wnt pathway activator. We further demonstrate that DACT1 condensates are maintained in vivo and that DACT1 is critical to breast and prostate cancer bone metastasis.
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Affiliation(s)
- Mark Esposito
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Cao Fang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Katelyn C Cook
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nana Park
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yong Wei
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Chiara Spadazzi
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Dan Bracha
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Ramesh T Gunaratna
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Gary Laevsky
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Hannah Slabodkin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA.
- Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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547
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Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T. Self-assembly of multi-component mitochondrial nucleoids via phase separation. EMBO J 2021; 40:e107165. [PMID: 33619770 DOI: 10.15252/embj.2020107165] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 01/19/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondria contain an autonomous and spatially segregated genome. The organizational unit of their genome is the nucleoid, which consists of mitochondrial DNA (mtDNA) and associated architectural proteins. Here, we show that phase separation is the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid). The major mtDNA-binding protein TFAM spontaneously phase separates in vitro via weak, multivalent interactions into droplets with slow internal dynamics. TFAM and mtDNA form heterogenous, viscoelastic structures in vitro, which recapitulate the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to various forms of cellular stress, as evidenced by the enlarged and transcriptionally active nucleoids in mitochondria from patients with the premature aging disorder Hutchinson-Gilford Progeria Syndrome (HGPS). Our results point to phase separation as an evolutionarily conserved mechanism of genome organization.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, NIH, Bethesda, MD, USA.,National Institute of General Medical Sciences, NIH, Bethesda, MD, USA
| | | | - Jane Tian
- National Institute on Aging, NIH, Baltimore, MD, USA
| | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
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548
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The Paradoxes of Viral mRNA Translation during Mammalian Orthoreovirus Infection. Viruses 2021; 13:v13020275. [PMID: 33670092 PMCID: PMC7916891 DOI: 10.3390/v13020275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
De novo viral protein synthesis following entry into host cells is essential for viral replication. As a consequence, viruses have evolved mechanisms to engage the host translational machinery while at the same time avoiding or counteracting host defenses that act to repress translation. Mammalian orthoreoviruses are dsRNA-containing viruses whose mRNAs were used as models for early investigations into the mechanisms that underpin the recognition and engagement of eukaryotic mRNAs by host cell ribosomes. However, there remain many unanswered questions and paradoxes regarding translation of reoviral mRNAs in the context of infection. This review summarizes the current state of knowledge about reovirus translation, identifies key unanswered questions, and proposes possible pathways toward a better understanding of reovirus translation.
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549
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Boija A, Klein IA, Young RA. Biomolecular Condensates and Cancer. Cancer Cell 2021; 39:174-192. [PMID: 33417833 PMCID: PMC8721577 DOI: 10.1016/j.ccell.2020.12.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
Malignant transformation is characterized by dysregulation of diverse cellular processes that have been the subject of detailed genetic, biochemical, and structural studies, but only recently has evidence emerged that many of these processes occur in the context of biomolecular condensates. Condensates are membrane-less bodies, often formed by liquid-liquid phase separation, that compartmentalize protein and RNA molecules with related functions. New insights from condensate studies portend a profound transformation in our understanding of cellular dysregulation in cancer. Here we summarize key features of biomolecular condensates, note where they have been implicated-or will likely be implicated-in oncogenesis, describe evidence that the pharmacodynamics of cancer therapeutics can be greatly influenced by condensates, and discuss some of the questions that must be addressed to further advance our understanding and treatment of cancer.
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Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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550
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Prentzell MT, Rehbein U, Cadena Sandoval M, De Meulemeester AS, Baumeister R, Brohée L, Berdel B, Bockwoldt M, Carroll B, Chowdhury SR, von Deimling A, Demetriades C, Figlia G, de Araujo MEG, Heberle AM, Heiland I, Holzwarth B, Huber LA, Jaworski J, Kedra M, Kern K, Kopach A, Korolchuk VI, van 't Land-Kuper I, Macias M, Nellist M, Palm W, Pusch S, Ramos Pittol JM, Reil M, Reintjes A, Reuter F, Sampson JR, Scheldeman C, Siekierska A, Stefan E, Teleman AA, Thomas LE, Torres-Quesada O, Trump S, West HD, de Witte P, Woltering S, Yordanov TE, Zmorzynska J, Opitz CA, Thedieck K. G3BPs tether the TSC complex to lysosomes and suppress mTORC1 signaling. Cell 2021; 184:655-674.e27. [PMID: 33497611 PMCID: PMC7868890 DOI: 10.1016/j.cell.2020.12.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022]
Abstract
Ras GTPase-activating protein-binding proteins 1 and 2 (G3BP1 and G3BP2, respectively) are widely recognized as core components of stress granules (SGs). We report that G3BPs reside at the cytoplasmic surface of lysosomes. They act in a non-redundant manner to anchor the tuberous sclerosis complex (TSC) protein complex to lysosomes and suppress activation of the metabolic master regulator mechanistic target of rapamycin complex 1 (mTORC1) by amino acids and insulin. Like the TSC complex, G3BP1 deficiency elicits phenotypes related to mTORC1 hyperactivity. In the context of tumors, low G3BP1 levels enhance mTORC1-driven breast cancer cell motility and correlate with adverse outcomes in patients. Furthermore, G3bp1 inhibition in zebrafish disturbs neuronal development and function, leading to white matter heterotopia and neuronal hyperactivity. Thus, G3BPs are not only core components of SGs but also a key element of lysosomal TSC-mTORC1 signaling.
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Affiliation(s)
- Mirja Tamara Prentzell
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands; Department of Bioinformatics and Molecular Genetics (Faculty of Biology), University of Freiburg, Freiburg 79104, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg 79104, Germany
| | - Ulrike Rehbein
- Department of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands; Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg 26129, Germany; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Marti Cadena Sandoval
- Department of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Ann-Sofie De Meulemeester
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Leuven BE-3000, Belgium
| | - Ralf Baumeister
- Department of Bioinformatics and Molecular Genetics (Faculty of Biology), University of Freiburg, Freiburg 79104, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg 79104, Germany; Signalling Research Centres BIOSS and CIBSS & ZBMZ Center for Biochemistry and Molecular Cell Research (Faculty of Medicine), University of Freiburg, Freiburg 79104, Germany
| | - Laura Brohée
- Cell Growth Control in Health and Age-Related Disease Group, Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne 50931, Germany
| | - Bianca Berdel
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Mathias Bockwoldt
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Bernadette Carroll
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Suvagata Roy Chowdhury
- Cell Signaling and Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Andreas von Deimling
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of Neuropathology, Institute of Pathology, Heidelberg University, Heidelberg 69120, Germany
| | - Constantinos Demetriades
- Cell Growth Control in Health and Age-Related Disease Group, Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne 50931, Germany; CECAD Cluster of Excellence, University of Cologne, Cologne 50931, Germany
| | - Gianluca Figlia
- Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Heidelberg University, Heidelberg 69120, Germany
| | | | - Alexander M Heberle
- Department of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Birgit Holzwarth
- Department of Bioinformatics and Molecular Genetics (Faculty of Biology), University of Freiburg, Freiburg 79104, Germany
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria; Austrian Drug Screening Institute (ADSI), Innsbruck 6020, Austria
| | - Jacek Jaworski
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Magdalena Kedra
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Katharina Kern
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Andrii Kopach
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Viktor I Korolchuk
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ineke van 't Land-Kuper
- Department of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands; Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg 26129, Germany
| | - Matylda Macias
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Wilhelm Palm
- Cell Signaling and Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Stefan Pusch
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of Neuropathology, Institute of Pathology, Heidelberg University, Heidelberg 69120, Germany
| | - Jose Miguel Ramos Pittol
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Michèle Reil
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Anja Reintjes
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Friederike Reuter
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University Medical School, Cardiff CF14 4AY, UK
| | - Chloë Scheldeman
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Leuven BE-3000, Belgium; Neurogenetics Research Group, VUB, Brussels 1090, Belgium
| | - Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Leuven BE-3000, Belgium
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Aurelio A Teleman
- Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Heidelberg University, Heidelberg 69120, Germany
| | - Laura E Thomas
- Institute of Life Science, Swansea University, Swansea SA2 8PP, UK
| | - Omar Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Saskia Trump
- Molecular Epidemiology Unit, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin 13353, Germany
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University Medical School, Cardiff CF14 4AY, UK
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Leuven BE-3000, Belgium
| | - Sandra Woltering
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Teodor E Yordanov
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria; Division of Cell and Developmental Biology, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
| | - Justyna Zmorzynska
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Christiane A Opitz
- Brain Cancer Metabolism Group, German Consortium of Translational Cancer Research (DKTK) & German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of Neurology, University Hospital Heidelberg and National Center for Tumor Diseases, Heidelberg 69120, Germany.
| | - Kathrin Thedieck
- Department of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands; Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg 26129, Germany; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria.
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