201
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Fossat MJ, Pappu RV. q-Canonical Monte Carlo Sampling for Modeling the Linkage between Charge Regulation and Conformational Equilibria of Peptides. J Phys Chem B 2019; 123:6952-6967. [PMID: 31362509 PMCID: PMC10785832 DOI: 10.1021/acs.jpcb.9b05206] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The overall charge content and the patterning of charged residues have a profound impact on the conformational ensembles adopted by intrinsically disordered proteins. These parameters can be altered by charge regulation, which refers to the effects of post-translational modifications, pH-dependent changes to charge, and conformational fluctuations that modify the pKa values of ionizable residues. Although atomistic simulations have played a prominent role in uncovering the major sequence-ensemble relationships of IDPs, most simulations assume fixed charge states for ionizable residues. This may lead to erroneous estimates for conformational equilibria if they are linked to charge regulation. Here, we report the development of a new method we term q-canonical Monte Carlo sampling for modeling the linkage between charge regulation and conformational equilibria. The method, which is designed to be interoperable with the ABSINTH implicit solvation model, operates as follows: For a protein sequence with n ionizable residues, we start with all 2n charge microstates and use a criterion based on model compound pKa values to prune down to a subset of thermodynamically relevant charge microstates. This subset is then grouped into mesostates, where all microstates that belong to a mesostate have the same net charge. Conformational distributions, drawn from a canonical ensemble, are generated for each of the charge microstates that make up a mesostate using a method we designate as proton walk sampling. This method combines Metropolis Monte Carlo sampling in conformational space with an auxiliary Markov process that enables interconversions between charge microstates along a mesostate. Proton walk sampling helps identify the most likely charge microstate per mesostate. We then use thermodynamic integration aided by the multistate Bennett acceptance ratio method to estimate the free energies for converting between mesostates. These free energies are then combined with the per-microstate weights along each mesostate to estimate standard state free energies and pH-dependent free energies for all thermodynamically relevant charge microstates. The results provide quantitative estimates of the probabilities and preferred conformations associated with every thermodynamically accessible charge microstate. We showcase the application of q-canonical sampling using two model systems. The results establish the soundness of the method and the importance of charge regulation in systems characterized by conformational heterogeneity.
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Affiliation(s)
- Martin J. Fossat
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130
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202
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203
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Thoke HS, Bagatolli LA, Olsen LF. Effect of macromolecular crowding on the kinetics of glycolytic enzymes and the behaviour of glycolysis in yeast. Integr Biol (Camb) 2019; 10:587-597. [PMID: 30176029 DOI: 10.1039/c8ib00099a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Water is involved in all aspects of biological activity, both as a solvent and as a reactant. It is hypothesized that intracellular water is in a highly structured state due to the high concentrations of macromolecules in the cell and that this may change the activity of intracellular enzymes due to altered binding affinities and allosteric regulations. Here we first investigate the kinetics of two glycolytic enzymes in artificially crowded aqueous solutions and show that crowding does indeed change their kinetics. Based on our kinetic measurements we propose a new model of oscillating glycolysis that instead of Michaelis-Menten or Monod-Wyman-Changeux kinetics uses the Yang-Ling adsorption isotherm introduced by G. Ling in the frame of the Association-Induction (AI) hypothesis. Using this model, we can reproduce previous experimental observations of the coupling of glycolytic oscillations and intracellular water dynamics, e.g., (i) during the metabolic oscillations, the latter variable oscillates in phase with ATP activity, and (ii) the emergence of glycolytic oscillations largely depends on the extent of intracellular water dipolar relaxation in cells in the resting state. Our results support the view that the extent of intracellular water dipolar relaxation is regulated by the ability of cytoplasmic proteins to polarize intracellular water with the assistance of ATP, as suggested in the AI hypothesis. This hypothesis may be relevant to the interpretation of many other biological oscillators, including cell signalling processes.
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Affiliation(s)
- Henrik S Thoke
- Institute for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK5230 Odense M, Denmark.
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204
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Alexandrov AI, Grosfeld EV, Dergalev AA, Kushnirov VV, Chuprov-Netochin RN, Tyurin-Kuzmin PA, Kireev II, Ter-Avanesyan MD, Leonov SV, Agaphonov MO. Analysis of novel hyperosmotic shock response suggests 'beads in liquid' cytosol structure. Biol Open 2019; 8:bio044529. [PMID: 31285266 PMCID: PMC6679407 DOI: 10.1242/bio.044529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022] Open
Abstract
Proteins can aggregate in response to stresses, including hyperosmotic shock. Formation and disassembly of aggregates is a relatively slow process. We describe a novel instant response of the cell to hyperosmosis, during which chaperones and other proteins form numerous foci with properties uncharacteristic of classical aggregates. These foci appeared/disappeared seconds after shock onset/removal, in close correlation with cell volume changes. Genome-wide and targeted testing revealed chaperones, metabolic enzymes, P-body components and amyloidogenic proteins in the foci. Most of these proteins can form large assemblies and for some, the assembled state was pre-requisite for participation in foci. A genome-wide screen failed to identify genes whose absence prevented foci participation by Hsp70. Shapes of and interconnections between foci, revealed by super-resolution microscopy, indicated that the foci were compressed between other entities. Based on our findings, we suggest a new model of cytosol architecture as a collection of numerous gel-like regions suspended in a liquid network. This network is reduced in volume in response to hyperosmosis and forms small pockets between the gel-like regions.
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Affiliation(s)
- Alexander I Alexandrov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gori 1, bldg 40, Moscow 119234, Russia
| | - Erika V Grosfeld
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
- Chair of Molecular and Cell Biology, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Alexander A Dergalev
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Vitaly V Kushnirov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Roman N Chuprov-Netochin
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Pyotr A Tyurin-Kuzmin
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, M.V. Lomonosov Moscow State University, Lomonosovskiy pr., 27 bldg 1, Moscow 119192, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gori 1, bldg 40, Moscow 119234, Russia
- V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, Moscow 117198, Russia
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Michael D Ter-Avanesyan
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Sergey V Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
- Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya str., 3, Moscow Region, 142290 Puschino, Russia
| | - Michael O Agaphonov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
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205
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Walton ZE, Brooks RC, Dang CV. mTOR Senses Intracellular pH through Lysosome Dispersion from RHEB. Bioessays 2019; 41:e1800265. [PMID: 31157925 PMCID: PMC6730656 DOI: 10.1002/bies.201800265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/18/2019] [Indexed: 02/04/2023]
Abstract
Acidity, generated in hypoxia or hypermetabolic states, perturbs homeostasis and is a feature of solid tumors. That acid peripherally disperses lysosomes is a three-decade-old observation, yet one little understood or appreciated. However, recent work has recognized the inhibitory impact this spatial redistribution has on mechanistic target of rapamycin complex 1 (mTORC1), a key regulator of metabolism. This finding argues for a paradigm shift in localization of mTORC1 activator Ras homolog enriched in brain (RHEB), a conclusion several others have now independently reached. Thus, mTORC1, known to sense amino acids, mitogens, and energy to restrict biosynthesis to times of adequate resources, also senses pH and, via dampened mTOR-governed synthesis of clock proteins, regulates the circadian clock to achieve concerted responses to metabolic stress. While this may allow cancer to endure metabolic deprivation, immune cell mTOR signaling likewise exhibits pH sensitivity, suggesting that suppression of antitumor immune function by solid tumor acidity may additionally fuel cancers, an obstacle potentially reversible through therapeutic pH manipulation.
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Affiliation(s)
| | | | - Chi V. Dang
- Ludwig Institute for Cancer Research, New York, NY 10017
- The Wistar Institute, Philadelphia, PA 19104
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206
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Santarriaga S, Fikejs A, Scaglione J, Scaglione KM. A Heat Shock Protein 48 (HSP48) Biomolecular Condensate Is Induced during Dictyostelium discoideum Development. mSphere 2019; 4:e00314-19. [PMID: 31217303 PMCID: PMC6584373 DOI: 10.1128/msphere.00314-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 11/20/2022] Open
Abstract
The social amoeba Dictyostelium discoideum's proteome contains a vast array of simple sequence repeats, providing a unique model to investigate proteostasis. Upon conditions of cellular stress, D. discoideum undergoes a developmental process, transitioning from a unicellular amoeba to a multicellular fruiting body. Little is known about how proteostasis is maintained during D. discoideum's developmental process. Here, we have identified a novel α-crystallin domain-containing protein, heat shock protein 48 (HSP48), that is upregulated during D. discoideum development. HSP48 functions in part by forming a biomolecular condensate via its highly positively charged intrinsically disordered carboxy terminus. In addition to HSP48, the highly negatively charged primordial chaperone polyphosphate is also upregulated during D. discoideum development, and polyphosphate functions to stabilize HSP48. Upon germination, levels of both HSP48 and polyphosphate dramatically decrease, consistent with a role for HSP48 and polyphosphate during development. Together, our data demonstrate that HSP48 is strongly induced during Dictyostelium discoideum development. We also demonstrate that HSP48 forms a biomolecular condensate and that polyphosphate is necessary to stabilize the HSP48 biomolecular condensate.IMPORTANCE During cellular stress, many microbes undergo a transition to a dormant state. This includes the social amoeba Dictyostelium discoideum that transitions from a unicellular amoeba to a multicellular fruiting body upon starvation. In this work, we identify heat shock protein 48 (HSP48) as a chaperone that is induced during development. We also show that HSP48 forms a biomolecular condensate and is stabilized by polyphosphate. The findings here identify Dictyostelium discoideum as a novel microbe to investigate protein quality control pathways during the transition to dormancy.
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Affiliation(s)
| | - Alicia Fikejs
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jamie Scaglione
- Department of Computational and Physical Sciences, Carroll University, Waukesha, Wisconsin, USA
| | - K Matthew Scaglione
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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207
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Abstract
Cells under stress must adjust their physiology, metabolism, and architecture to adapt to the new conditions. Most importantly, they must down-regulate general gene expression, but at the same time induce synthesis of stress-protective factors, such as molecular chaperones. Here, we investigate how the process of phase separation is used by cells to ensure adaptation to stress. We summarize recent findings and propose that the solubility of important translation factors is specifically affected by changes in physical-chemical parameters such temperature or pH and modulated by intrinsically disordered prion-like domains. These stress-triggered changes in protein solubility induce phase separation into condensates that regulate the activity of the translation factors and promote cellular fitness. Prion-like domains play important roles in this process as environmentally regulated stress sensors and modifier sequences that determine protein solubility and phase behavior. We propose that protein phase separation is an evolutionary conserved feature of proteins that cells harness to regulate adaptive stress responses and ensure survival in extreme environmental conditions.
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Affiliation(s)
- Titus M Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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208
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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209
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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210
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Shchepachev V, Bresson S, Spanos C, Petfalski E, Fischer L, Rappsilber J, Tollervey D. Defining the RNA interactome by total RNA-associated protein purification. Mol Syst Biol 2019; 15:e8689. [PMID: 30962360 PMCID: PMC6452921 DOI: 10.15252/msb.20188689] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
The RNA binding proteome (RBPome) was previously investigated using UV crosslinking and purification of poly(A)-associated proteins. However, most cellular transcripts are not polyadenylated. We therefore developed total RNA-associated protein purification (TRAPP) based on 254 nm UV crosslinking and purification of all RNA-protein complexes using silica beads. In a variant approach (PAR-TRAPP), RNAs were labelled with 4-thiouracil prior to 350 nm crosslinking. PAR-TRAPP in yeast identified hundreds of RNA binding proteins, strongly enriched for canonical RBPs. In comparison, TRAPP identified many more proteins not expected to bind RNA, and this correlated strongly with protein abundance. Comparing TRAPP in yeast and E. coli showed apparent conservation of RNA binding by metabolic enzymes. Illustrating the value of total RBP purification, we discovered that the glycolytic enzyme enolase interacts with tRNAs. Exploiting PAR-TRAPP to determine the effects of brief exposure to weak acid stress revealed specific changes in late 60S ribosome biogenesis. Furthermore, we identified the precise sites of crosslinking for hundreds of RNA-peptide conjugates, using iTRAPP, providing insights into potential regulation. We conclude that TRAPP is a widely applicable tool for RBPome characterization.
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Affiliation(s)
- Vadim Shchepachev
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Stefan Bresson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Lutz Fischer
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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211
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Ahmed WW, Fodor É, Almonacid M, Bussonnier M, Verlhac MH, Gov N, Visco P, van Wijland F, Betz T. Active Mechanics Reveal Molecular-Scale Force Kinetics in Living Oocytes. Biophys J 2019; 114:1667-1679. [PMID: 29642036 PMCID: PMC5954280 DOI: 10.1016/j.bpj.2018.02.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 11/27/2022] Open
Abstract
Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and facilitate enhanced motion. The kinetics of molecular motors have been precisely characterized in vitro by single molecule approaches, but their in vivo behavior remains elusive. Here, we study the active diffusion of vesicles in mouse oocytes, where this process plays a key role in nuclear positioning during development, and combine an experimental and theoretical framework to extract molecular-scale force kinetics (force, power stroke, and velocity) of the in vivo active process. Assuming a single dominant process, we find that the nonequilibrium activity induces rapid kicks of duration τ ∼ 300 μs resulting in an average force of F ∼ 0.4 pN on vesicles in in vivo oocytes, remarkably similar to the kinetics of in vitro myosin-V. Our results reveal that measuring in vivo active fluctuations allows extraction of the molecular-scale activity in agreement with single-molecule studies and demonstrates a mesoscopic framework to access force kinetics.
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Affiliation(s)
- Wylie W Ahmed
- Department of Physics, California State University, Fullerton, California; Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Paris, France; Sorbonne Universités, UPMC Université Paris 06, Paris, France.
| | - Étienne Fodor
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom; Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, Paris, France
| | - Maria Almonacid
- CIRB, Collège de France, and CNRS-UMR7241 and INSERM-U1050, Équipe Labellisée Fondation pour la Recherche Médicale, Paris, France
| | - Matthias Bussonnier
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Paris, France; Sorbonne Universités, UPMC Université Paris 06, Paris, France
| | - Marie-Hélène Verlhac
- CIRB, Collège de France, and CNRS-UMR7241 and INSERM-U1050, Équipe Labellisée Fondation pour la Recherche Médicale, Paris, France
| | - Nir Gov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Paolo Visco
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, Paris, France
| | - Frédéric van Wijland
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, Paris, France
| | - Timo Betz
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Paris, France; Sorbonne Universités, UPMC Université Paris 06, Paris, France; Institute of Cell Biology, Center for Molecular Biology of Inflammation, Cells-in-Motion Cluster of Excellence, Münster University, Münster, Germany
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212
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Verdile V, De Paola E, Paronetto MP. Aberrant Phase Transitions: Side Effects and Novel Therapeutic Strategies in Human Disease. Front Genet 2019; 10:173. [PMID: 30967892 PMCID: PMC6440380 DOI: 10.3389/fgene.2019.00173] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
Phase separation is a physiological process occurring spontaneously when single-phase molecular complexes separate in two phases, a concentrated phase and a more diluted one. Eukaryotic cells employ phase transition strategies to promote the formation of intracellular territories not delimited by membranes with increased local RNA concentration, such as nucleolus, paraspeckles, P granules, Cajal bodies, P-bodies, and stress granules. These organelles contain both proteins and coding and non-coding RNAs and play important roles in different steps of the regulation of gene expression and in cellular signaling. Recently, it has been shown that most human RNA-binding proteins (RBPs) contain at least one low-complexity domain, called prion-like domain (PrLD), because proteins harboring them display aggregation properties like prion proteins. PrLDs support RBP function and contribute to liquid–liquid phase transitions that drive ribonucleoprotein granule assembly, but also render RBPs prone to misfolding by promoting the formation of pathological aggregates that lead to toxicity in specific cell types. Protein–protein and protein-RNA interactions within the separated phase can enhance the transition of RBPs into solid aberrant aggregates, thus causing diseases. In this review, we highlight the role of phase transition in human disease such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and in cancer. Moreover, we discuss novel therapeutic strategies focused to control phase transitions by preventing the conversion into aberrant aggregates. In this regard, the stimulation of chaperone machinery to disassemble membrane-less organelles, the induction of pathways that could inhibit aberrant phase separation, and the development of antisense oligonucleotides (ASOs) to knockdown RNAs could be evaluated as novel therapeutic strategies for the treatment of those human diseases characterized by aberrant phase transition aggregates.
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Affiliation(s)
- Veronica Verdile
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
| | - Elisa De Paola
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
| | - Maria Paola Paronetto
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
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213
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Yoo H, Triandafillou C, Drummond DA. Cellular sensing by phase separation: Using the process, not just the products. J Biol Chem 2019; 294:7151-7159. [PMID: 30877200 DOI: 10.1074/jbc.tm118.001191] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Phase separation creates two distinct liquid phases from a single mixed liquid phase, like oil droplets separating from water. Considerable attention has focused on how the products of phase separation-the resulting condensates-might act as biological compartments, bioreactors, filters, and membraneless organelles in cells. Here, we expand this perspective, reviewing recent results showing how cells instead use the process of phase separation to sense intracellular and extracellular changes. We review case studies in phase separation-based sensing and discuss key features, such as extraordinary sensitivity, which make the process of phase separation ideally suited to meet a range of sensory challenges cells encounter.
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Affiliation(s)
- Haneul Yoo
- From the Department of Biochemistry and Molecular Biology
| | | | - D Allan Drummond
- From the Department of Biochemistry and Molecular Biology, .,Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
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214
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Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM. Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP. Nat Commun 2019; 10:1155. [PMID: 30858367 PMCID: PMC6411743 DOI: 10.1038/s41467-019-09107-y] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/22/2019] [Indexed: 02/03/2023] Open
Abstract
Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was recently discovered to function as a biological hydrotrope. Here, we use mass spectrometry to interrogate ATP-mediated regulation of protein thermal stability and protein solubility on a proteome-wide scale. Thermal proteome profiling reveals high affinity interactions of ATP as a substrate and as an allosteric modulator that has widespread influence on protein complexes and their stability. Further, we develop a strategy for proteome-wide solubility profiling, and discover ATP-dependent solubilization of at least 25% of the insoluble proteome. ATP increases the solubility of positively charged, intrinsically disordered proteins, and their susceptibility for solubilization varies depending on their localization to different membrane-less organelles. Moreover, a few proteins, exhibit an ATP-dependent decrease in solubility, likely reflecting polymer formation. Our data provides a proteome-wide, quantitative insight into how ATP influences protein structure and solubility across the spectrum of physiologically relevant concentrations. ATP can function as a biological hydrotrope, but its global effects on protein solubility have not yet been characterized. Here, the authors quantify the effect of ATP on the thermal stability and solubility of the cellular proteome, providing insights into protein solubility regulation by ATP.
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Affiliation(s)
- Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120, Heidelberg, Germany
| | - Thilo Werner
- Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Ina Günthner
- Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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215
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Khan T, Kandola TS, Wu J, Venkatesan S, Ketter E, Lange JJ, Rodríguez Gama A, Box A, Unruh JR, Cook M, Halfmann R. Quantifying Nucleation In Vivo Reveals the Physical Basis of Prion-like Phase Behavior. Mol Cell 2019; 71:155-168.e7. [PMID: 29979963 PMCID: PMC6086602 DOI: 10.1016/j.molcel.2018.06.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/26/2018] [Accepted: 06/07/2018] [Indexed: 01/29/2023]
Abstract
Protein self-assemblies modulate protein activities over biological timescales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these timescales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed distributed amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a protein's self-assembly as a function of cellular concentration. We show that kinetic barriers limit the nucleation of ordered self-assemblies and that the persistence of the barriers with respect to concentration relates to structure. Supersaturation resulting from sequence-encoded nucleation barriers gave rise to prion behavior and enabled a prion-forming protein, Sup35 PrD, to partition into dynamic intracellular condensates or to form toxic aggregates. Our results suggest that nucleation barriers govern cytoplasmic inheritance, subcellular organization, and proteotoxicity.
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Affiliation(s)
- Tarique Khan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tejbir S Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- 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
| | | | - Ellen Ketter
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- 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.
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216
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Begarani F, D'Autilia F, Signore G, Del Grosso A, Cecchini M, Gratton E, Beltram F, Cardarelli F. Capturing Metabolism-Dependent Solvent Dynamics in the Lumen of a Trafficking Lysosome. ACS NANO 2019; 13:1670-1682. [PMID: 30649861 DOI: 10.1021/acsnano.8b07682] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The eukaryotic cell compartmentalizes into spatially confined, membrane-enclosed, intracellular structures ( e. g., organelles, endosomes, and vesicles). Here, peculiar physicochemical properties of the local environment occur and participate in the regulation of ongoing molecular processes. In spite of the huge amount of available environmental probes, experiments on subcellular structures are severely challenged by their three-dimensional (3D) movement. This bottleneck is tackled here by focusing an excitation light beam in a periodic orbit around the structure of interest. The recorded signal is used as feedback to localize the structure position at high temporal resolution: microseconds along the orbit, milliseconds between orbits. The lysosome is selected as the intracellular target, together with 6-acetyl-2-dimethylaminonaphthalene (ACDAN) as probe of the physicochemical properties of the intralysosomal environment. Generalized polarization (GP) analysis of ACDAN emission is used to get a quantitative view on intralysosomal solvent dipolar relaxation. Thus, raster image correlation spectroscopy (RICS) analysis reveals that the ACDAN GP signal is fluctuating in the micro-to-millisecond time range during natural organelle 3D trafficking. We show that ACDAN GP fluctuations are characteristic of lysosomes in living cells, are selectively abolished by lysosomal basification, and depend on metabolic energy in the form of ATP. We argue that intralysosomal ACDAN GP fluctuates according to the ongoing organelle metabolism. Indeed, we report alterations in amplitude and timing of GP fluctuations in a cellular model of lysosomal storage disorder (LSD). The strategy proposed provides insight into the elusive local environment of a trafficking lysosome and supports similar molecular investigations at the subcellular level.
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Affiliation(s)
- Filippo Begarani
- Laboratorio NEST, Scuola Normale Superiore , Pisa 56127 , Italy
- Center for Nanotechnology Innovation@NEST (CNI@NEST) , Pisa 56127 , Italy
| | | | | | - Ambra Del Grosso
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore , Pisa 56127 , Italy
| | - Marco Cecchini
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore , Pisa 56127 , Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697-2715 , United States
| | - Fabio Beltram
- Laboratorio NEST, Scuola Normale Superiore , Pisa 56127 , Italy
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217
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Fregin B, Czerwinski F, Biedenweg D, Girardo S, Gross S, Aurich K, Otto O. High-throughput single-cell rheology in complex samples by dynamic real-time deformability cytometry. Nat Commun 2019; 10:415. [PMID: 30679420 PMCID: PMC6346011 DOI: 10.1038/s41467-019-08370-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 01/08/2019] [Indexed: 11/25/2022] Open
Abstract
In life sciences, the material properties of suspended cells have attained significance close to that of fluorescent markers but with the advantage of label-free and unbiased sample characterization. Until recently, cell rheological measurements were either limited by acquisition throughput, excessive post processing, or low-throughput real-time analysis. Real-time deformability cytometry expanded the application of mechanical cell assays to fast on-the-fly phenotyping of large sample sizes, but has been restricted to single material parameters as the Young's modulus. Here, we introduce dynamic real-time deformability cytometry for comprehensive cell rheological measurements at up to 100 cells per second. Utilizing Fourier decomposition, our microfluidic method is able to disentangle cell response to complex hydrodynamic stress distributions and to determine viscoelastic parameters independent of cell shape. We demonstrate the application of our technology for peripheral blood cells in whole blood samples including the discrimination of B- and CD4+ T-lymphocytes by cell rheological properties.
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Affiliation(s)
- Bob Fregin
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Fabian Czerwinski
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Doreen Biedenweg
- Universitätsmedizin Greifswald, Fleischmannstr. 8, 17489, Greifswald, Germany
| | - Salvatore Girardo
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - Stefan Gross
- Universitätsmedizin Greifswald, Fleischmannstr. 8, 17489, Greifswald, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Konstanze Aurich
- Universitätsmedizin Greifswald, Fleischmannstr. 8, 17489, Greifswald, Germany
| | - Oliver Otto
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany.
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany.
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218
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Midtvedt D, Olsén E, Höök F, Jeffries GDM. Label-free spatio-temporal monitoring of cytosolic mass, osmolarity, and volume in living cells. Nat Commun 2019; 10:340. [PMID: 30664642 PMCID: PMC6341078 DOI: 10.1038/s41467-018-08207-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023] Open
Abstract
Microorganisms adapt their biophysical properties in response to changes in their local environment. However, quantifying these changes at the single-cell level has only recently become possible, largely relying on fluorescent labeling strategies. In this work, we utilize yeast (Saccharomyces cerevisiae) to demonstrate label-free quantification of changes in both intracellular osmolarity and macromolecular concentration in response to changes in the local environment. By combining a digital holographic microscope with a millifluidic chip, the temporal response of cellular water flux was successfully isolated from the rate of production of higher molecular weight compounds, in addition to identifying the produced compounds in terms of the product of their refractive index increment [Formula: see text] and molar mass. The ability to identify, quantify and temporally resolve multiple biophysical processes in living cells at the single cell level offers a crucial complement to label-based strategies, suggesting broad applicability in studies of a wide-range of cellular processes.
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Affiliation(s)
- Daniel Midtvedt
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Erik Olsén
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Höök
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Gavin D M Jeffries
- Department of Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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219
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Zhang J, Wang Y, Zheng Z, Sun X, Chen T, Li C, Zhang X, Guo J. Intracellular ion and protein nanoparticle-induced osmotic pressure modify astrocyte swelling and brain edema in response to glutamate stimuli. Redox Biol 2019; 21:101112. [PMID: 30685709 PMCID: PMC6351271 DOI: 10.1016/j.redox.2019.101112] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/02/2019] [Accepted: 01/14/2019] [Indexed: 12/28/2022] Open
Abstract
Intracellular tension activity plays a crucial role in cytotoxic brain edema and astrocyte swelling. Here, a few genetically encoded FRET-based tension probes were designed to detect cytoskeletal structural tension optically, including their magnitude and vectors. The astrocyte swelling resulted in GFAP tension increment, which is associated with the antagonistic effect of inward microfilaments (MFs) and microtubules (MTs) forces. In glutamate-induced astrocyte swelling, GFAP tension rise resulted from outward ion and protein nanoparticle-induced osmotic pressure (PN-OP) increases, where PN-OP could be elicited by MF and MT depolymerization, protein nanoparticle production, and activation of cofilin and stathmin-1. Attenuation of both ion osmotic pressure and PN-OP by drug combinations, together with free-radical scavenger, relieved cerebral edema in vivo. The study suggests that intracellular osmotic pressure (especially PN-OP) has a pivotal role in glutamate-induced astrocyte swelling and brain edema. Recovery of cytoplasmic potential is a promising target to develop new drugs and cure brain edema.
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Affiliation(s)
- JiaRui Zhang
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - YuXuan Wang
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - ZiHui Zheng
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - XiaoHe Sun
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - TingTing Chen
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - Chen Li
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - XiaoLong Zhang
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - Jun Guo
- State Key Laboratory Cultivation Base For TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, PR China; Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, PR China.
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220
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Liu M, Heimlicher MB, Bächler M, Ibeneche-Nnewihe CC, Florin EL, Brunner D, Hoenger A. Glucose starvation triggers filamentous septin assemblies in an S. pombe septin-2 deletion mutant. Biol Open 2019; 8:8/1/bio037622. [PMID: 30602528 PMCID: PMC6361201 DOI: 10.1242/bio.037622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Using correlative light and electron microscopy (CLEM), we studied the intracellular organization by of glucose-starved fission yeast cells (Schizosaccharomyces pombe) with regards to the localization of septin proteins throughout the cytoplasm. Thereby, we found that for cells carrying a deletion of the gene encoding septin-2 (spn2Δ), starvation causes a GFP-tagged version of septin-3 (spn3-GFP) and family members, to assemble into a single, prominent filamentous structure. It was previously shown that during exponential growth, spn2Δ cells form septin-3 polymers. However, the polymers we observed during exponential growth are different from the spn3p-GFP structure we observed in starved cells. Using CLEM, in combination with anti-GFP immunolabeling on plastic-sections, we could assign spn3p-GFP to the filaments we have found in EM pictures. Besides septin-3, these filamentous assemblies most likely also contain septin-1 as an RFP-tagged version of this protein forms a very similar structure in starved spn2Δ cells. Our data correlate phase-contrast and fluorescence microscopy with electron micrographs of plastic-embedded cells, and further on with detailed views of tomographic 3D reconstructions. Cryo-electron microscopy of spn2Δ cells in vitrified sections revealed a very distinct overall morphology of the spn3p-GFP assembly. The fine-structured, regular density pattern suggests the presence of assembled septin-3 filaments that are clearly different from F-actin bundles. Furthermore, we found that starvation causes substantial mitochondria fission, together with massive decoration of their outer membrane by ribosomes.
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Affiliation(s)
- Minghua Liu
- University of Colorado at Boulder, Department of Molecular, Cellular and Developmental Biology, UCB-0347, Boulder, CO 80309, USA
| | - Maria B Heimlicher
- University of Zürich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mirjam Bächler
- University of Zürich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Chieze C Ibeneche-Nnewihe
- University of Texas at Austin, Center for Nonlinear Dynamics and Department of Physics, Austin, TX 78712, USA
| | - Ernst-Ludwig Florin
- University of Texas at Austin, Center for Nonlinear Dynamics and Department of Physics, Austin, TX 78712, USA
| | - Damian Brunner
- University of Zürich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Hoenger
- University of Colorado at Boulder, Department of Molecular, Cellular and Developmental Biology, UCB-0347, Boulder, CO 80309, USA
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221
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Sagot I, Laporte D. The cell biology of quiescent yeast – a diversity of individual scenarios. J Cell Sci 2019; 132:132/1/jcs213025. [DOI: 10.1242/jcs.213025] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
ABSTRACT
Most cells, from unicellular to complex organisms, spend part of their life in quiescence, a temporary non-proliferating state. Although central for a variety of essential processes including tissue homeostasis, development and aging, quiescence is poorly understood. In fact, quiescence encompasses various cellular situations depending on the cell type and the environmental niche. Quiescent cell properties also evolve with time, adding another layer of complexity. Studying quiescence is, above all, limited by the fact that a quiescent cell can be recognized as such only after having proved that it is capable of re-proliferating. Recent cellular biology studies in yeast have reported the relocalization of hundreds of proteins and the reorganization of several cellular machineries upon proliferation cessation. These works have revealed that quiescent cells can display various properties, shedding light on a plethora of individual behaviors. The deciphering of the molecular mechanisms beyond these reorganizations, together with the understanding of their cellular functions, have begun to provide insights into the physiology of quiescent cells. In this Review, we discuss recent findings and emerging concepts in Saccharomyces cerevisiae quiescent cell biology.
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Affiliation(s)
- Isabelle Sagot
- Centre National de la Recherche Scientifique, Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, UMR5095-33077 Bordeaux cedex, France
| | - Damien Laporte
- Centre National de la Recherche Scientifique, Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, UMR5095-33077 Bordeaux cedex, France
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222
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Wang M, Bokros M, Theodoridis PR, Lee S. Nucleolar Sequestration: Remodeling Nucleoli Into Amyloid Bodies. Front Genet 2019; 10:1179. [PMID: 31824572 PMCID: PMC6881480 DOI: 10.3389/fgene.2019.01179] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/24/2019] [Indexed: 01/14/2023] Open
Abstract
This year marks the 20th anniversary of the discovery that the nucleolus can temporarily immobilize proteins, a process known as nucleolar sequestration. This review reflects on the progress made to understand the physiological roles of nucleolar sequestration and the mechanisms involved in the immobilization of proteins. We discuss how protein immobilization can occur through a highly choreographed amyloidogenic program that converts the nucleolus into a large fibrous organelle with amyloid-like characteristics called the amyloid body (A-body). We propose a working model of A-body biogenesis that includes a role for low-complexity ribosomal intergenic spacer RNA (rIGSRNA) and a discrete peptide sequence, the amyloid-converting motif (ACM), found in many proteins that undergo immobilization. Amyloid bodies provide a unique model to study the multistep assembly of a membraneless compartment and may provide alternative insights into the pathological amyloidogenesis involved in neurological disorders.
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Affiliation(s)
- Miling Wang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Michael Bokros
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Phaedra Rebecca Theodoridis
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
- Department of Urology, Miller School of Medicine, University of Miami, FL, United States
- *Correspondence: Stephen Lee,
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223
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Kieliszek M, Błażejak S, Bzducha-Wróbel A, Kot AM. Effect of Selenium on Lipid and Amino Acid Metabolism in Yeast Cells. Biol Trace Elem Res 2019; 187:316-327. [PMID: 29675568 PMCID: PMC6315055 DOI: 10.1007/s12011-018-1342-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/09/2018] [Indexed: 12/27/2022]
Abstract
This article discusses the effect of selenium in aqueous solutions on aspects of lipid and amino acid metabolism in the cell biomass of Saccharomyces cerevisiae MYA-2200 and Candida utilis ATCC 9950 yeasts. The yeast biomass was obtained by using waste products (potato wastewater and glycerol). Selenium, at a dose of 20 mg/L of aqueous solution, affected the differentiation of cellular morphology. Yeast enriched with selenium was characterized by a large functional diversity in terms of protein and amino acid content. The protein content in the biomass of S. cerevisiae enriched with selenium (42.6%) decreased slightly as compared to that in the control sample without additional selenium supplementation (48.4%). Moreover, yeasts of both strains enriched with selenium contained a large amount of glutamic acid, aspartic acid, lysine, and leucine. Analysis of fatty acid profiles in S. cerevisiae yeast supplemented with selenium showed an increase in the unsaturated fatty acid content (e.g., C18:1). The presence of margaric acid (C17:0) and hexadecanoic acid (C17:1) was found in the C. utilis biomass enriched with selenium, in contrast to that of S. cerevisiae. These results indicate that selenium may induce lipid peroxidation, which consequently affects the loss of integrity of the cytoplasmic membrane. Yeast enriched with selenium with optimal amino acid and lipid composition can be used to prepare a novel formula of dietary supplements, which can be applied directly to various diets for both humans and animals.
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Affiliation(s)
- Marek Kieliszek
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland.
| | - Stanisław Błażejak
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland
| | - Anna Bzducha-Wróbel
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland
| | - Anna M Kot
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland
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224
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Pillai M, Jha SK. The Folding and Aggregation Energy Landscapes of Tethered RRM Domains of Human TDP-43 Are Coupled via a Metastable Molten Globule-like Oligomer. Biochemistry 2018; 58:608-620. [DOI: 10.1021/acs.biochem.8b01013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Meenakshi Pillai
- Physical and Materials Chemistry Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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225
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Pu Y, Li Y, Jin X, Tian T, Ma Q, Zhao Z, Lin SY, Chen Z, Li B, Yao G, Leake MC, Lo CJ, Bai F. ATP-Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic Tolerance. Mol Cell 2018; 73:143-156.e4. [PMID: 30472191 DOI: 10.1016/j.molcel.2018.10.022] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 09/07/2018] [Accepted: 10/15/2018] [Indexed: 01/06/2023]
Abstract
Cell dormancy is a widespread mechanism used by bacteria to evade environmental threats, including antibiotics. Here we monitored bacterial antibiotic tolerance and regrowth at the single-cell level and found that each individual survival cell shows different "dormancy depth," which in return regulates the lag time for cell resuscitation after removal of antibiotic. We further established that protein aggresome-a collection of endogenous protein aggregates-is an important indicator of bacterial dormancy depth, whose formation is promoted by decreased cellular ATP level. For cells to leave the dormant state and resuscitate, clearance of protein aggresome and recovery of proteostasis are required. We revealed that the ability to recruit functional DnaK-ClpB machineries, which facilitate protein disaggregation in an ATP-dependent manner, determines the lag time for bacterial regrowth. Better understanding of the key factors regulating bacterial regrowth after surviving antibiotic attack could lead to new therapeutic strategies for combating bacterial antibiotic tolerance.
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Affiliation(s)
- Yingying Pu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingxing Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Jin
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Tian Tian
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Qi Ma
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Ziyi Zhao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Ssu-Yuan Lin
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhong-Li, Taoyuan 32001, Republic of China
| | - Zhanghua Chen
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Binghui Li
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, Beijing 100069, China
| | - Guang Yao
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Mark C Leake
- Department of Physics, University of York, York YO10, UK; Department of Biology, University of York, York YO10, UK
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhong-Li, Taoyuan 32001, Republic of China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.
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226
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Schavemaker PE, Boersma AJ, Poolman B. How Important Is Protein Diffusion in Prokaryotes? Front Mol Biosci 2018; 5:93. [PMID: 30483513 PMCID: PMC6243074 DOI: 10.3389/fmolb.2018.00093] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/22/2018] [Indexed: 12/31/2022] Open
Abstract
That diffusion is important for the proper functioning of cells is without question. The extent to which the diffusion coefficient is important is explored here for prokaryotic cells. We discuss the principles of diffusion focusing on diffusion-limited reactions, summarize the known values for diffusion coefficients in prokaryotes and in in vitro model systems, and explain a number of cases where diffusion coefficients are either limiting for reaction rates or necessary for the existence of phenomena. We suggest a number of areas that need further study including expanding the range of organism growth temperatures, direct measurements of diffusion limitation, expanding the range of cell sizes, diffusion limitation for membrane proteins, and taking into account cellular context when assessing the possibility of diffusion limitation.
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Affiliation(s)
- Paul E Schavemaker
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
| | - Arnold J Boersma
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
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227
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Ditlev JA, Case LB, Rosen MK. Who's In and Who's Out-Compositional Control of Biomolecular Condensates. J Mol Biol 2018; 430:4666-4684. [PMID: 30099028 PMCID: PMC6204295 DOI: 10.1016/j.jmb.2018.08.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.
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Affiliation(s)
- Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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228
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Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers. J Mol Biol 2018; 430:4619-4635. [DOI: 10.1016/j.jmb.2018.06.031] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022]
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229
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Abstract
There is growing interest in the topic of intracellular phase transitions that lead to the formation of biologically regulated biomolecular condensates. These condensates are membraneless bodies formed by phase separation of key protein and nucleic acid molecules from the cytoplasmic or nucleoplasmic milieus. The drivers of phase separation are referred to as scaffolds whereas molecules that preferentially partition into condensates formed by scaffolds are known as clients. Recent advances have shown that it is possible to generate physical and functional facsimiles of many biomolecular condensates in vitro. This is achieved by titrating the concentration of key scaffold proteins and solution parameters such as salt concentration, pH, or temperature. The ability to reproduce phase separation in vitro allows one to compare the relationships between information encoded in the sequences of scaffold proteins and the driving forces for phase separation. Many scaffold proteins include intrinsically disordered regions whereas others are entirely disordered. Our focus is on comparative assessments of phase separation for different scaffold proteins, specifically intrinsically disordered linear multivalent proteins. We highlight the importance of coexistence curves known as binodals for quantifying phase behavior and comparing driving forces for sequence-specific phase separation. We describe the information accessible from full binodals and highlight different methods for-and challenges associated with-mapping binodals. In essence, we provide a wish list for in vitro characterization of phase separation of intrinsically disordered proteins. Fulfillment of this wish list through key advances in experiment, computation, and theory should bring us closer to being able to predict in vitro phase behavior for scaffold proteins and connect this to the functions and features of biomolecular condensates.
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Affiliation(s)
- Ammon E Posey
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, United States.
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230
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Yu S, Sheats J, Cicuta P, Sclavi B, Cosentino Lagomarsino M, Dorfman KD. Subdiffusion of loci and cytoplasmic particles are different in compressed Escherichia coli cells. Commun Biol 2018; 1:176. [PMID: 30374466 PMCID: PMC6200837 DOI: 10.1038/s42003-018-0185-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. Although recent work has addressed the role of non-equilibrium sources of activity and crowding, the consequences of mechanical perturbations are relatively less explored. Here we use a microfabricated valve system to track both fluorescently labeled chromosomal loci and cytoplasmic particles in Escherichia coli cells shortly after applying a compressive force, observing the response on time scales that are too sudden to allow for biochemical response from the cell. Cytoplasmic diffusion slows markedly on compression but the exponent governing the growth of the ensemble-averaged mean-squared displacement of cytoplasmic particles is unaffected. In contrast, the corresponding exponent for DNA loci changes significantly. These results suggest that DNA elasticity and nucleoid organization play a more important role in loci subdiffusion than cytoplasmic viscoelasticity under such short time scales.
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Affiliation(s)
- Shi Yu
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA
- School of Chemical Engineering and Technology, China University of Mining & Technology, Xuzhou, 221116, China
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA
| | - Pietro Cicuta
- Cavendish Laboratory, Cambridge University, Cambridge, UK
| | - Bianca Sclavi
- LBPA, UMR 8113 du CNRS, École Normale Supérieure Paris-Saclay, Cachan, France
| | - Marco Cosentino Lagomarsino
- Génophysique/Genomic Physics Group, UMR 7238 CNRS Génomique des Microorganismes, Université Pierre et Marie Curie, 4, Place Jussieu, 75005, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie, 4 Place Jussieu, Paris, France
- IFOM Institute for Molecular Oncology, Milan, Italy
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA.
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231
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Laporte D, Gouleme L, Jimenez L, Khemiri I, Sagot I. Mitochondria reorganization upon proliferation arrest predicts individual yeast cell fate. eLife 2018; 7:35685. [PMID: 30299253 PMCID: PMC6177259 DOI: 10.7554/elife.35685] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Most cells spend the majority of their life in a non-proliferating state. When proliferation cessation is irreversible, cells are senescent. By contrast, if the arrest is only temporary, cells are defined as quiescent. These cellular states are hardly distinguishable without triggering proliferation resumption, hampering thus the study of quiescent cells properties. Here we show that quiescent and senescent yeast cells are recognizable based on their mitochondrial network morphology. Indeed, while quiescent yeast cells display numerous small vesicular mitochondria, senescent cells exhibit few globular mitochondria. This allowed us to reconsider at the individual-cell level, properties previously attributed to quiescent cells using population-based approaches. We demonstrate that cell’s propensity to enter quiescence is not influenced by replicative age, volume or density. Overall, our findings reveal that quiescent cells are not all identical but that their ability to survive is significantly improved when they exhibit the specific reorganization of several cellular machineries.
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Affiliation(s)
- Damien Laporte
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Laëtitia Gouleme
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Laure Jimenez
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Ines Khemiri
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Isabelle Sagot
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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232
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Syga Ł, Spakman D, Punter CM, Poolman B. Method for immobilization of living and synthetic cells for high-resolution imaging and single-particle tracking. Sci Rep 2018; 8:13789. [PMID: 30213985 PMCID: PMC6137044 DOI: 10.1038/s41598-018-32166-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/16/2018] [Indexed: 12/15/2022] Open
Abstract
Super-resolution imaging and single-particle tracking require cells to be immobile as any movement reduces the resolution of the measurements. Here, we present a method based on APTES-glutaraldehyde coating of glass surfaces to immobilize cells without compromising their growth. Our method of immobilization is compatible with Saccharomyces cerevisiae, Escherichia coli, and synthetic cells (here, giant-unilamellar vesicles). The method introduces minimal background fluorescence and is suitable for imaging of single particles at high resolution. With S. cerevisiae we benchmarked the method against the commonly used concanavalin A approach. We show by total internal reflection fluorescence microscopy that modifying surfaces with ConA introduces artifacts close to the glass surface, which are not present when immobilizing with the APTES-glutaraldehyde method. We demonstrate validity of the method by measuring the diffusion of membrane proteins in yeast with single-particle tracking and of lipids in giant-unilamellar vesicles with fluorescence recovery after photobleaching. Importantly, the physical properties and shape of the fragile GUVs are not affected upon binding to APTES-glutaraldehyde coated glass. The APTES-glutaraldehyde is a generic method of immobilization that should work with any cell or synthetic system that has primary amines on the surface.
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Affiliation(s)
- Łukasz Syga
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dian Spakman
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Christiaan M Punter
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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233
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Ribeiro S, Ebbinghaus S, Marcos JC. Protein folding and quinary interactions: creating cellular organisation through functional disorder. FEBS Lett 2018; 592:3040-3053. [DOI: 10.1002/1873-3468.13211] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/16/2018] [Accepted: 07/29/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Sara Ribeiro
- Centre of Chemistry University of Minho Braga Portugal
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry Technical University Braunschweig Germany
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234
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Analysis of eIF2B bodies and their relationships with stress granules and P-bodies. Sci Rep 2018; 8:12264. [PMID: 30115954 PMCID: PMC6095920 DOI: 10.1038/s41598-018-30805-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/06/2018] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic cells respond to stress and changes in the environment in part by repressing translation and forming cytoplasmic assemblies called stress granules and P-bodies, which harbor non-translating mRNAs and proteins. A third, but poorly understood, assembly called the eIF2B body can form and contains the eIF2B complex, an essential guanine exchange factor for the translation initiation factor eIF2. Hypomorphic EIF2B alleles can lead to Vanishing White Matter Disease (VWMD), a leukodystrophy that causes progressive white matter loss. An unexplored question is how eIF2B body formation is controlled and whether VWMD alleles in EIF2B alter the formation of eIF2B bodies, stress granules, or P-bodies. To examine these issues, we assessed eIF2B body, stress granule, and P-body induction in wild-type yeast cells and cells carrying VWMD alleles in the EIF2B2 (GCD7) and EIF2B5 (GCD6) subunits of eIF2B. We demonstrate eIF2B bodies are rapidly and reversibly formed independently of stress granules during acute glucose deprivation. VWMD mutations had diverse effects on stress-induced assemblies with some alleles altering eIF2B bodies, and others leading to increased P-body formation. Moreover, some VWMD-causing mutations in GCD7 caused hyper-sensitivity to chronic GCN2 activation, consistent with VWMD mutations causing hyper-sensitivity to eIF2α phosphorylation and thereby impacting VWMD pathogenesis.
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235
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Cholesterol modulates acetylcholine receptor diffusion by tuning confinement sojourns and nanocluster stability. Sci Rep 2018; 8:11974. [PMID: 30097590 PMCID: PMC6086833 DOI: 10.1038/s41598-018-30384-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/20/2018] [Indexed: 11/08/2022] Open
Abstract
Translational motion of neurotransmitter receptors is key for determining receptor number at the synapse and hence, synaptic efficacy. We combine live-cell STORM superresolution microscopy of nicotinic acetylcholine receptor (nAChR) with single-particle tracking, mean-squared displacement (MSD), turning angle, ergodicity, and clustering analyses to characterize the lateral motion of individual molecules and their collective behaviour. nAChR diffusion is highly heterogeneous: subdiffusive, Brownian and, less frequently, superdiffusive. At the single-track level, free walks are transiently interrupted by ms-long confinement sojourns occurring in nanodomains of ~36 nm radius. Cholesterol modulates the time and the area spent in confinement. Turning angle analysis reveals anticorrelated steps with time-lag dependence, in good agreement with the permeable fence model. At the ensemble level, nanocluster assembly occurs in second-long bursts separated by periods of cluster disassembly. Thus, millisecond-long confinement sojourns and second-long reversible nanoclustering with similar cholesterol sensitivities affect all trajectories; the proportion of the two regimes determines the resulting macroscopic motional mode and breadth of heterogeneity in the ensemble population.
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236
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Cereghetti G, Saad S, Dechant R, Peter M. Reversible, functional amyloids: towards an understanding of their regulation in yeast and humans. Cell Cycle 2018; 17:1545-1558. [PMID: 29963943 DOI: 10.1080/15384101.2018.1480220] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein aggregates, and in particular amyloids, are generally considered to be inherently irreversible aberrant clumps, and are often associated with pathologies, such as Alzheimer's disease, Parkinson's disease, or systemic amyloidosis. However, recent evidence demonstrates that some aggregates are not only fully reversible, but also perform essential physiological functions. Despite these new findings, very little is known about how these functional protein aggregates are regulated in a physiological context. Here, we take the yeast pyruvate kinase Cdc19 as an example of a protein forming functional, reversible, solid, amyloid-like aggregates in response to stress conditions. Cdc19 aggregation is regulated via an aggregation-prone low complexity region (LCR). In favorable growth conditions, this LCR is prevented from aggregating by phosphorylation or oligomerization, while upon glucose starvation it becomes exposed and allows aggregation. We suggest that LCR phosphorylation, oligomerization or partner-binding may be general and widespread mechanisms regulating LCR-mediated reversible protein aggregation. Moreover, we show that, as predicted by computational tools, Cdc19 forms amyloid-like aggregates in vitro. Interestingly, we also observe striking similarities between Cdc19 and its mammalian counterpart, PKM2. Indeed, also PKM2 harbors a LCR and contains several peptides with high amyloidogenic propensity, which coincide with known phosphorylation sites. Thus, we speculate that the formation of reversible, amyloid-like aggregates may be a general physiological mechanism for cells to adapt to stress conditions, and that the underlying regulatory mechanisms may be conserved from yeast to humans.
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Affiliation(s)
- Gea Cereghetti
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland.,b Life Science Zürich , Molecular Life Sciences , Zürich , Switzerland
| | - Shady Saad
- c Department of Chemical and Systems Biology , Stanford University , Stanford, CA , USA
| | - Reinhard Dechant
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
| | - Matthias Peter
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
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237
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Govers SK, Mortier J, Adam A, Aertsen A. Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells. PLoS Biol 2018; 16:e2003853. [PMID: 30153247 PMCID: PMC6112618 DOI: 10.1371/journal.pbio.2003853] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 07/20/2018] [Indexed: 12/17/2022] Open
Abstract
Protein misfolding and aggregation are typically perceived as inevitable and detrimental processes tied to a stress- or age-associated decline in cellular proteostasis. A careful reassessment of this paradigm in the E. coli model bacterium revealed that the emergence of intracellular protein aggregates (PAs) was not related to cellular aging but closely linked to sublethal proteotoxic stresses such as exposure to heat, peroxide, and the antibiotic streptomycin. After removal of the proteotoxic stress and resumption of cellular proliferation, the polarly deposited PA was subjected to limited disaggregation and therefore became asymmetrically inherited for a large number of generations. Many generations after the original PA-inducing stress, the cells inheriting this ancestral PA displayed a significantly increased heat resistance compared to their isogenic, PA-free siblings. This PA-mediated inheritance of heat resistance could be reproduced with a conditionally expressed, intracellular PA consisting of an inert, aggregation-prone mutant protein, validating the role of PAs in increasing resistance and indicating that the resistance-conferring mechanism does not depend on the origin of the PA. Moreover, PAs were found to confer robustness to other proteotoxic stresses, as imposed by reactive oxygen species or streptomycin exposure, suggesting a broad protective effect. Our findings therefore reveal the potential of intracellular PAs to serve as long-term epigenetically inheritable and functional memory elements, physically referring to a previous cellular insult that occurred many generations ago and meanwhile improving robustness to a subsequent proteotoxic stress. The latter is presumably accomplished through the PA-mediated asymmetric inheritance of protein quality control components leading to their specific enrichment in PA-bearing cells.
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Affiliation(s)
- Sander K. Govers
- KU Leuven, Department of Microbial and Molecular Systems, Leuven, Belgium
| | - Julien Mortier
- KU Leuven, Department of Microbial and Molecular Systems, Leuven, Belgium
| | - Antoine Adam
- KU Leuven, Department of Computer Science, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Leuven, Belgium
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238
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Urbanska M, Rosendahl P, Kräter M, Guck J. High-throughput single-cell mechanical phenotyping with real-time deformability cytometry. Methods Cell Biol 2018; 147:175-198. [PMID: 30165957 DOI: 10.1016/bs.mcb.2018.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mechanical properties of cells can serve as a label-free marker of cell state and function and their alterations have been implicated in processes such as cancer metastasis, leukocyte activation, or stem cell differentiation. Over recent years, new techniques for single-cell mechanical characterization at high throughput have been developed to accelerate discovery in the field of mechanical phenotyping. One such technique is real-time deformability cytometry (RT-DC), a robust technology based on microfluidics that performs continuous mechanical characterization of cells in a contactless manner at rates of up to 1000 cells per second. This tremendous throughput allows for comparison of large sample numbers and precise characterization of heterogeneous cell populations. Additionally, parameters acquired in RT-DC measurements can be used to determine the apparent Young's modulus of individual cells. In this chapter, we present practical aspects important for the implementation of the RT-DC methodology, including a description of the setup, operation principles, and experimental protocols. In the latter, we describe a variety of preparation procedures for samples originating from different sources including 2D and 3D cell cultures as well as blood and tissue-derived primary cells, and discuss obstacles that may arise during their measurements. Finally, we provide insights into standard data analysis procedures and discuss the method's performance in light of other available techniques.
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Affiliation(s)
- Marta Urbanska
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Philipp Rosendahl
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Martin Kräter
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Jochen Guck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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239
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Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018. [PMID: 29937223 DOI: 10.1016/j.cell.2018.1005.1042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
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Affiliation(s)
- M Delarue
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - S Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - I V Surovtsev
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA
| | - S Pinglay
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - K J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - M Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J I Gutierrez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - D Sang
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G Poterewicz
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - J K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA
| | - J M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - C Jacobs-Wagner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06511, USA
| | - B D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - L J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA.
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240
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Herbig M, Mietke A, Müller P, Otto O. Statistics for real-time deformability cytometry: Clustering, dimensionality reduction, and significance testing. BIOMICROFLUIDICS 2018; 12:042214. [PMID: 29937952 PMCID: PMC5999349 DOI: 10.1063/1.5027197] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Real-time deformability (RT-DC) is a method for high-throughput mechanical and morphological phenotyping of cells in suspension. While analysis rates exceeding 1000 cells per second allow for a label-free characterization of complex biological samples, e.g., whole blood, data evaluation has so far been limited to a few geometrical and material parameters such as cell size, deformation, and elastic Young's modulus. But as a microscopy-based technology, RT-DC actually generates and yields multidimensional datasets that require automated and unbiased tools to obtain morphological and rheological cell information. Here, we present a statistical framework to shed light on this complex parameter space and to extract quantitative results under various experimental conditions. As model systems, we apply cell lines as well as primary cells and highlight more than 11 parameters that can be obtained from RT-DC data. These parameters are used to identify sub-populations in heterogeneous samples using Gaussian mixture models, to perform a dimensionality reduction using principal component analysis, and to quantify the statistical significance applying linear mixed models to datasets of multiple replicates.
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Affiliation(s)
- M. Herbig
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | | | - P. Müller
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - O. Otto
- Author to whom the correspondence should be addressed:
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241
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Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018; 174:338-349.e20. [PMID: 29937223 PMCID: PMC10080728 DOI: 10.1016/j.cell.2018.05.042] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022]
Abstract
Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
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Affiliation(s)
- M Delarue
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - S Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - I V Surovtsev
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA
| | - S Pinglay
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - K J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - M Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J I Gutierrez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - D Sang
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G Poterewicz
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - J K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA
| | - J M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - C Jacobs-Wagner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06511, USA
| | - B D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - L J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA.
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242
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Franzmann TM, Alberti S. Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior. J Biol Chem 2018; 294:7128-7136. [PMID: 29921587 DOI: 10.1074/jbc.tm118.001190] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many proteins, such as RNA-binding proteins, have complex folding landscapes. How cells maintain the solubility and folding state of such proteins, particularly under stress conditions, is largely unknown. Here, we argue that prion-like low-complexity regions (LCRs) are key regulators of protein solubility and folding. We discuss emerging evidence that prion-like LCRs are not, as commonly thought, autonomous aggregation modules that adopt amyloid-like conformations, but protein-specific sequences with chaperone-like functions. On the basis of recent findings, we propose that prion-like LCRs have evolved to regulate protein phase behavior and to protect proteins against proteotoxic damage.
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Affiliation(s)
- Titus M Franzmann
- From the Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Simon Alberti
- From the Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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243
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Kroschwald S, Munder MC, Maharana S, Franzmann TM, Richter D, Ruer M, Hyman AA, Alberti S. Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery. Cell Rep 2018; 23:3327-3339. [DOI: 10.1016/j.celrep.2018.05.041] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/10/2018] [Accepted: 05/14/2018] [Indexed: 01/23/2023] Open
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244
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Carpenter K, Bell RB, Yunus J, Amon A, Berchowitz LE. Phosphorylation-Mediated Clearance of Amyloid-like Assemblies in Meiosis. Dev Cell 2018; 45:392-405.e6. [PMID: 29738715 DOI: 10.1016/j.devcel.2018.04.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 10/17/2022]
Abstract
Amyloids are fibrous protein assemblies that are often described as irreversible and intrinsically pathogenic. However, yeast cells employ amyloid-like assemblies of the RNA-binding protein Rim4 to control translation during meiosis. Here, we show that multi-site phosphorylation of Rim4 is critical for its regulated disassembly and degradation and that failure to clear Rim4 assemblies interferes with meiotic progression. Furthermore, we identify the protein kinase Ime2 to bring about Rim4 clearance via phosphorylation of Rim4's intrinsically disordered region. Rim4 phosphorylation leads to reversal of its amyloid-like properties and degradation by the proteasome. Our data support a model in which a threshold amount of phosphorylation, rather than modification of critical residues, is required for Rim4 clearance. Our results further demonstrate that at least some amyloid-like assemblies are not as irreversible as previously thought. We propose that the natural pathways by which cells process these structures could be deployed to act on disease-related amyloids.
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Affiliation(s)
- Kayla Carpenter
- Department of Genetics and Development, Columbia University Medical Center, 701 W. 168th Street, Hammer Health Sciences Building, Room 1520, New York, NY 10032, USA
| | - Rachel Brietta Bell
- Department of Genetics and Development, Columbia University Medical Center, 701 W. 168th Street, Hammer Health Sciences Building, Room 1520, New York, NY 10032, USA
| | - Julius Yunus
- Department of Genetics and Development, Columbia University Medical Center, 701 W. 168th Street, Hammer Health Sciences Building, Room 1520, New York, NY 10032, USA
| | - Angelika Amon
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Edwin Berchowitz
- Department of Genetics and Development, Columbia University Medical Center, 701 W. 168th Street, Hammer Health Sciences Building, Room 1520, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY, USA.
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245
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Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA. Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping. Cell Rep 2018; 20:2735-2748. [PMID: 28903051 DOI: 10.1016/j.celrep.2017.08.074] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/21/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022] Open
Abstract
A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis.
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Affiliation(s)
- Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ashwani Kumar
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhna Phanse
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yoshito Kakihara
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | | | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Jamie Snider
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Wen Wang
- Department of Computer Science & Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA; Program in Bioinformatics and Computational Biology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Edgar Erik Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Chad L Myers
- Department of Computer Science & Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA; Program in Bioinformatics and Computational Biology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Igor Stagljar
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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246
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Alberti S, Carra S. Quality Control of Membraneless Organelles. J Mol Biol 2018; 430:4711-4729. [PMID: 29758260 DOI: 10.1016/j.jmb.2018.05.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
The formation of membraneless organelles (MLOs) by phase separation has emerged as a new way of organizing the cytoplasm and nucleoplasm of cells. Examples of MLOs forming via phase separation are nucleoli in the nucleus and stress granules in the cytoplasm. The main components of these MLOs are macromolecules such as RNAs and proteins. In order to assemble by phase separation, these proteins and RNAs have to undergo many cooperative interactions. These cooperative interactions are supported by specific molecular features within phase-separating proteins, such as multivalency and the presence of disordered domains that promote weak and transient interactions. However, these features also predispose phase-separating proteins to aberrant behavior. Indeed, evidence is emerging for a strong link between phase-separating proteins, MLOs, and age-related diseases. In this review, we discuss recent progress in understanding the formation, properties, and functions of MLOs. We pay special attention to the emerging link between MLOs and age-related diseases, and we explain how changes in the composition and physical properties of MLOs promote their conversion into an aberrant state. Furthermore, we discuss the key role of the protein quality control machinery in regulating the properties and functions of MLOs and thus in preventing age-related diseases.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Science, University of Modena and Reggio Emilia, Center for Neuroscience and Neurotechnology, 41125 Modena, Italy.
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247
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Zhou HX, Nguemaha V, Mazarakos K, Qin S. Why Do Disordered and Structured Proteins Behave Differently in Phase Separation? Trends Biochem Sci 2018; 43:499-516. [PMID: 29716768 DOI: 10.1016/j.tibs.2018.03.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 11/26/2022]
Abstract
Intracellular membraneless organelles and their myriad cellular functions have garnered tremendous recent interest. It is becoming well accepted that they form via liquid-liquid phase separation (LLPS) of protein mixtures (often including RNA), where the organelles correspond to a protein-rich droplet phase coexisting with a protein-poor bulk phase. The major protein components contain disordered regions and often also RNA-binding domains, and the disordered fragments on their own easily undergo LLPS. By contrast, LLPS for structured proteins has been observed infrequently. The contrasting phase behaviors can be explained by modeling disordered and structured proteins, respectively, as polymers and colloids. These physical models also provide a better understanding of the regulation of droplet formation by cellular signals and its dysregulation leading to diseases.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
| | - Valery Nguemaha
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Konstantinos Mazarakos
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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248
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van Leeuwen W, van der Krift F, Rabouille C. Modulation of the secretory pathway by amino-acid starvation. J Cell Biol 2018; 217:2261-2271. [PMID: 29669743 PMCID: PMC6028531 DOI: 10.1083/jcb.201802003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
As a major anabolic pathway, the secretory pathway needs to adapt to the demands of the surrounding environment and responds to different exogenous signals and stimuli. In this context, the transport in the early secretory pathway from the endoplasmic reticulum (ER) to the Golgi apparatus appears particularly regulated. For instance, protein export from the ER is critically stimulated by growth factors. Conversely, nutrient starvation also modulates functions of the early secretory pathway in multiple ways. In this review, we focus on amino-acid starvation and how the function of the early secretory pathway is redirected to fuel autophagy, how the ER exit sites are remodeled into novel cytoprotective stress assemblies, and how secretion is modulated in vivo in starving organisms. With the increasingly exciting knowledge on mechanistic target of rapamycin complex 1 (mTORC1), the major nutrient sensor, it is also a good moment to establish how the modulation of the secretory pathway by amino-acid restriction intersects with this major signaling hub.
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Affiliation(s)
- Wessel van Leeuwen
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Felix van der Krift
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands .,Department of Cell Biology, University Medical Center Groningen, Groningen, Netherlands
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249
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Marshall RS, Vierstra RD. Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation. eLife 2018; 7:34532. [PMID: 29624167 PMCID: PMC5947986 DOI: 10.7554/elife.34532] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/05/2018] [Indexed: 12/14/2022] Open
Abstract
26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required for granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability. Proteins perform many jobs within an organism, including providing structure and support, and protecting against infection. The levels of the many proteins in a cell need to be carefully controlled so that the correct amounts are present at the right place and time to perform these tasks. This control can be achieved by balancing the production of new proteins with the break down (or degradation) of proteins that are no longer required or become dysfunctional. Most cells have two pathways for degrading proteins. One pathway breaks down individual proteins specifically marked for elimination; this causes them to be recognized by a structure called the proteasome, which chops proteins into smaller pieces. Larger protein assemblies – including the proteasome itself – are to big for the proteasome and thus need to be degraded by another pathway called autophagy. This process engulfs and delivers parts of a cell to a membrane-bound compartment called the vacuole, which ‘digests’ and recycles these larger constituents. Proteasomes are degraded by autophagy when they are not working correctly and when nitrogen (a crucial nutrient) is in short supply. However, proteasomes are not degraded when cells lack carbon, even though this starvation is known to activate autophagy in the same way that an absence of nitrogen does. So how do proteasomes escape degradation when cells are starved for carbon? Marshall and Vierstra now show that upon carbon starvation, proteasomes rapidly exit the cell nucleus and cluster together in the main part of the cell (termed the cytosol). These clusters are known as proteasome storage granules (PSGs). In fungi and plants, mutations or conditions inside the cell that make it difficult for PSGs to assemble cause proteasomes to instead be broken down in the vacuole when carbon availability is low. Clustering into PSGs therefore protects proteasomes from autophagy. This clustering appears advantageous to cells; yeast cells that could form PSGs were better able to start growing again when their nutrient supply improved. Protein clustering (also known as aggregation) is an important strategy that cells use to survive stressful conditions. However, it can also be harmful when proteins aggregate inappropriately, such as occurs in Alzheimer’s disease. Researchers may be able to use PSG assembly as a convenient model to study the causes and consequences of protein aggregation; this knowledge could ultimately be applied to improve human health and crop productivity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, United States
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250
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Abstract
Non-Gaussian diffusion is commonly considered as a result of fluctuating diffusivity, which is correlated in time or in space or both. In this work, we investigate the non-Gaussian diffusion in static disordered media via a quenched trap model, where the diffusivity is spatially correlated. Several unique effects due to quenched disorder are reported. We analytically estimate the diffusion coefficient D_{dis} and its fluctuation over samples of finite size. We show a mechanism of population splitting in the non-Gaussian diffusion. It results in a sharp peak in the distribution of displacement P(x,t) around x=0, that has frequently been observed in experiments. We examine the fidelity of the coarse-grained diffusion map, which is reconstructed from particle trajectories. Finally, we propose a procedure to estimate the correlation length in static disordered environments, where the information stored in the sample-to-sample fluctuation has been utilized.
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Affiliation(s)
- Liang Luo
- Department of Physics, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Applied Physics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Yi
- Department of Physics, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Applied Physics, Huazhong Agricultural University, Wuhan 430070, China
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