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Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
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Formicola N, Heim M, Dufourt J, Lancelot AS, Nakamura A, Lagha M, Besse F. Tyramine induces dynamic RNP granule remodeling and translation activation in the Drosophila brain. eLife 2021; 10:65742. [PMID: 33890854 PMCID: PMC8064753 DOI: 10.7554/elife.65742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/04/2021] [Indexed: 02/06/2023] Open
Abstract
Ribonucleoprotein (RNP) granules are dynamic condensates enriched in regulatory RNA binding proteins (RBPs) and RNAs under tight spatiotemporal control. Extensive recent work has investigated the molecular principles underlying RNP granule assembly, unraveling that they form through the self-association of RNP components into dynamic networks of interactions. How endogenous RNP granules respond to external stimuli to regulate RNA fate is still largely unknown. Here, we demonstrate through high-resolution imaging of intact Drosophila brains that Tyramine induces a reversible remodeling of somatic RNP granules characterized by the decondensation of granule-enriched RBPs (e.g. Imp/ZBP1/IGF2BP) and helicases (e.g. Me31B/DDX-6/Rck). Furthermore, our functional analysis reveals that Tyramine signals both through its receptor TyrR and through the calcium-activated kinase CamkII to trigger RNP component decondensation. Finally, we uncover that RNP granule remodeling is accompanied by the rapid and specific translational activation of associated mRNAs. Thus, this work sheds new light on the mechanisms controlling cue-induced rearrangement of physiological RNP condensates.
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Affiliation(s)
- Nadia Formicola
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Marjorie Heim
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Jérémy Dufourt
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, Montpellier, France
| | - Anne-Sophie Lancelot
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, and Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, Montpellier, France
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
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53
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Murakami K, Kajimoto S, Shibata D, Kuroi K, Fujii F, Nakabayashi T. Observation of liquid-liquid phase separation of ataxin-3 and quantitative evaluation of its concentration in a single droplet using Raman microscopy. Chem Sci 2021; 12:7411-7418. [PMID: 34163831 PMCID: PMC8171347 DOI: 10.1039/d0sc06095j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) plays an important role in a variety of biological processes and is also associated with protein aggregation in neurodegenerative diseases. Quantification of LLPS is necessary to elucidate the mechanism of LLPS and the subsequent aggregation process. In this study, we showed that ataxin-3, which is associated with Machado-Joseph disease, exhibits LLPS in an intracellular crowding environment mimicked by biopolymers, and proposed that a single droplet formed in LLPS can be quantified using Raman microscopy in a label-free manner. We succeeded in evaluating the protein concentration and identifying the components present inside and outside a droplet using the O-H stretching band of water as an internal intensity standard. Only water and protein were detected to be present inside droplets with crowding agents remaining outside. The protein concentration in a droplet was dependent on the crowding environment, indicating that the protein concentration and intracellular environment should be considered when investigating LLPS. Raman microscopy has the potential to become a powerful technique for clarifying the chemical nature of LLPS and its relationship with protein aggregation.
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Affiliation(s)
- Kazuki Murakami
- Graduate School of Pharmaceutical Sciences, Tohoku University Aoba-ku Sendai 980-8578 Japan
| | - Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University Aoba-ku Sendai 980-8578 Japan
| | - Daiki Shibata
- Graduate School of Pharmaceutical Sciences, Tohoku University Aoba-ku Sendai 980-8578 Japan
| | - Kunisato Kuroi
- Faculty of Pharmaceutical Sciences, Kobe Gakuin University 1-1-3 Minatojima, Chuo-ku Kobe 650-8586 Japan
| | - Fumihiko Fujii
- Faculty of Pharmaceutical Sciences, Kobe Gakuin University 1-1-3 Minatojima, Chuo-ku Kobe 650-8586 Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University Aoba-ku Sendai 980-8578 Japan
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54
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Azaldegui CA, Vecchiarelli AG, Biteen JS. The emergence of phase separation as an organizing principle in bacteria. Biophys J 2021; 120:1123-1138. [PMID: 33186556 PMCID: PMC8059088 DOI: 10.1016/j.bpj.2020.09.023] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This article assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPS in vivo in bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.
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Affiliation(s)
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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Alshareedah I, Thurston GM, Banerjee PR. Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates. Biophys J 2021; 120:1161-1169. [PMID: 33453268 PMCID: PMC8059090 DOI: 10.1016/j.bpj.2021.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/27/2020] [Accepted: 01/07/2021] [Indexed: 01/08/2023] Open
Abstract
Living cells organize their internal space into dynamic condensates through liquid-liquid phase separation of multivalent proteins in association with cellular nucleic acids. Here, we study how variations in nucleic acid (NA)-to-protein stoichiometry modulate the condensed phase organization and fluid dynamics in a model system of multicomponent heterotypic condensates. Employing a multiparametric approach comprised of video particle tracking microscopy and optical tweezer-induced droplet fusion, we show that the interfacial tension, but not viscosity, of protein-NA condensates is controlled by the NA/protein ratio across the two-phase regime. In parallel, we utilize fluorescence correlation spectroscopy to quantify protein and NA diffusion in the condensed phase. Fluorescence correlation spectroscopy measurements reveal that the diffusion of the component protein and NA within the condensate core is governed by the viscosity, and hence, also remains insensitive to the changes in NA-to-protein stoichiometry. Collectively, our results provide insights into the regulation of multicomponent heterotypic liquid condensates, reflecting how the bulk mixture composition affects their core versus surface organization and dynamical properties.
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Affiliation(s)
| | - George M Thurston
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York
| | - Priya R Banerjee
- Department of Physics, University at Buffalo SUNY, Buffalo, New York.
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57
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Zeng X, Liu C, Fossat MJ, Ren P, Chilkoti A, Pappu RV. Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures. APL MATERIALS 2021; 9:021119. [PMID: 38362050 PMCID: PMC10868716 DOI: 10.1063/5.0037438] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Many naturally occurring elastomers are intrinsically disordered proteins (IDPs) built up of repeating units and they can demonstrate two types of thermoresponsive phase behavior. Systems characterized by lower critical solution temperatures (LCST) undergo phase separation above the LCST whereas systems characterized by upper critical solution temperatures (UCST) undergo phase separation below the UCST. There is congruence between thermoresponsive coil-globule transitions and phase behavior whereby the theta temperatures above or below which the IDPs transition from coils to globules serve as useful proxies for the LCST / UCST values. This implies that one can design sequences with desired values for the theta temperature with either increasing or decreasing radii of gyration above the theta temperature. Here, we show that the Monte Carlo simulations performed in the so-called intrinsic solvation (IS) limit version of the temperature-dependent the ABSINTH (self-Assembly of Biomolecules Studied by an Implicit, Novel, Tunable Hamiltonian) implicit solvation model, yields a useful heuristic for discriminating between sequences with known LCST versus UCST phase behavior. Accordingly, we use this heuristic in a supervised approach, integrate it with a genetic algorithm, combine this with IS limit simulations, and demonstrate that novel sequences can be designed with LCST phase behavior. These calculations are aided by direct estimates of temperature dependent free energies of solvation for model compounds that are derived using the polarizable AMOEBA (atomic multipole optimized energetics for biomolecular applications) forcefield. To demonstrate the validity of our designs, we calculate coil-globule transition profiles using the full ABSINTH model and combine these with Gaussian Cluster Theory calculations to establish the LCST phase behavior of designed IDPs.
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Affiliation(s)
- Xiangze Zeng
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Martin J. Fossat
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
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Vladimirova O, De Leo A, Deng Z, Wiedmer A, Hayden J, Lieberman PM. Phase separation and DAXX redistribution contribute to LANA nuclear body and KSHV genome dynamics during latency and reactivation. PLoS Pathog 2021; 17:e1009231. [PMID: 33471863 PMCID: PMC7943007 DOI: 10.1371/journal.ppat.1009231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/09/2021] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) can drive formation of diverse and essential macromolecular structures, including those specified by viruses. Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) genomes associate with the viral encoded Latency-Associated Nuclear Antigen (LANA) to form stable nuclear bodies (NBs) during latent infection. Here, we show that LANA-NB formation and KSHV genome conformation involves LLPS. Using LLPS disrupting solvents, we show that LANA-NBs are partially disrupted, while DAXX and PML foci are highly resistant. LLPS disruption altered the LANA-dependent KSHV chromosome conformation but did not stimulate lytic reactivation. We found that LANA-NBs undergo major morphological transformation during KSHV lytic reactivation to form LANA-associated replication compartments encompassing KSHV DNA. DAXX colocalizes with the LANA-NBs during latency but is evicted from the LANA-associated lytic replication compartments. These findings indicate the LANA-NBs are dynamic super-molecular nuclear structures that partly depend on LLPS and undergo morphological transitions corresponding to the different modes of viral replication. During latent infection, gamma-herpesvirus genomes are maintained as extrachromosomal circular DNA, referred to as episomes, by dedicated viral-encoded episome maintenance proteins. KSHV-encoded LANA maintains viral episomes through binding as an oligomeric protein to repetitive DNA elements in the viral terminal repeats (TRs). Viral episomes can be visualized as LANA-associated nuclear bodies (LANA-NBs). Here, we show that LANA-NBs utilize mechanisms of self-assembly through liquid-liquid phase separation (LLPS) to build dynamic structures that change during cell cycle and viral life cycle. We find that DAXX is a component of the latent phase LANA-NBs, but is evicted during the transition to lytic replication where LANA remains associated with KSHV DNA to form a ring-like replication compartment.
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Affiliation(s)
| | - Alessandra De Leo
- Department of Immunology, H. Lee Moffit Cancer and Research Center, Tampa Florida, United States of America
| | - Zhong Deng
- The Wistar Institute, Philadelphia, United States of America
| | - Andreas Wiedmer
- The Wistar Institute, Philadelphia, United States of America
| | - James Hayden
- The Wistar Institute, Philadelphia, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, United States of America
- * E-mail:
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59
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Erlendsson S, Teilum K. Binding Revisited-Avidity in Cellular Function and Signaling. Front Mol Biosci 2021; 7:615565. [PMID: 33521057 PMCID: PMC7841115 DOI: 10.3389/fmolb.2020.615565] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
When characterizing biomolecular interactions, avidity, is an umbrella term used to describe the accumulated strength of multiple specific and unspecific interactions between two or more interaction partners. In contrast to the affinity, which is often sufficient to describe monovalent interactions in solution and where the binding strength can be accurately determined by considering only the relationship between the microscopic association and dissociation rates, the avidity is a phenomenological macroscopic parameter linked to several microscopic events. Avidity also covers potential effects of reduced dimensionality and/or hindered diffusion observed at or near surfaces e.g., at the cell membrane. Avidity is often used to describe the discrepancy or the "extra on top" when cellular interactions display binding that are several orders of magnitude stronger than those estimated in vitro. Here we review the principles and theoretical frameworks governing avidity in biological systems and the methods for predicting and simulating avidity. While the avidity and effects thereof are well-understood for extracellular biomolecular interactions, we present here examples of, and discuss how, avidity and the underlying kinetics influences intracellular signaling processes.
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Affiliation(s)
- Simon Erlendsson
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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60
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Biedzinski S, Parmar B, Weber SC. Beyond Equilibrium Phase Diagrams: Enzymatic Activity Shakes Up Bacterial Condensates. Mol Cell 2020; 79:205-206. [PMID: 32679075 DOI: 10.1016/j.molcel.2020.06.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Phase separation is a thermodynamic process, but cells are inherently out of equilibrium. Guilhas et al. (2020) identify an active process through which an ATP-dependent motor controls the number and position of biomolecular condensates in bacteria.
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Affiliation(s)
- Stefan Biedzinski
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Baljyot Parmar
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Stephanie C Weber
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada; Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada.
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