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Orti F, Fernández ML, Marino‐Buslje C. MLOsMetaDB, a meta-database to centralize the information on liquid-liquid phase separation proteins and membraneless organelles. Protein Sci 2024; 33:e4858. [PMID: 38063081 PMCID: PMC10751725 DOI: 10.1002/pro.4858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/29/2023] [Accepted: 12/03/2023] [Indexed: 12/28/2023]
Abstract
Over the past few years, there has been a focus on proteins that create separate liquid phases in the intracellular liquid environment, known as membraneless organelles (MLOs). These organelles allow for the spatiotemporal associations of macromolecules that dynamically exchange within the cellular milieu. They provide a form of compartmentalization crucial for organizing key functions in many cells. Metabolic processes and signaling pathways in both the cytoplasm and nucleus are among the functions performed by MLOs, which are facilitated by diverse combinations of proteins and nucleic acids. However, disruptions in these liquid-liquid phase separation processes (LLPS) may lead to several diseases, such as neurodegenerative disorders and cancer, among others. To foster the study of this process and MLO function, we present MLOsMetaDB (http://mlos.leloir.org.ar), a comprehensive resource of information on MLO- and LLPS-related proteins. Our database integrates and centralizes available information for every protein involved in MLOs, which is otherwise disseminated across a plethora of different databases. Our manuscript outlines the development and features of MLOsMetaDB, which provides an interactive and user-friendly environment with modern biological visualizations and easy and quick access to proteins based on LLPS role, MLO location, and organisms. In addition, it offers an advanced search for making complex queries to generate customized information. Furthermore, MLOsMetaDB provides evolutionary information by collecting the orthologs of every protein in the same database. Overall, MLOsMetaDB is a valuable resource as a starting point for researchers studying the many processes driven by LLPS proteins and membraneless organelles.
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Affiliation(s)
| | - María Laura Fernández
- Instituto de física interdisciplinaria y aplicada (IFNIA)Universidad de Buenos AiresArgentina
- Dto. de Física. Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresArgentina
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Roy S, Guljamow A, Dittmann E. Impact of temperature on the temporal dynamics of microcystin in Microcystis aeruginosa PCC7806. Front Microbiol 2023; 14:1200816. [PMID: 37720143 PMCID: PMC10500830 DOI: 10.3389/fmicb.2023.1200816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Cyanobacterial blooms pose a serious threat to water quality and human health due to the production of the potent hepatotoxin microcystin. In microcystin-producing strains of the widespread genus Microcystis, the toxin is largely constitutively produced, but there are fluctuations between the cellular and extracellular pool and between free microcystin and protein-bound microcystin. Here we addressed the question of how different temperatures affect the growth and temporal dynamics of secondary metabolite production in the strain Microcystis aeruginosa PCC7806 and its microcystin-deficient ΔmcyB mutant. While the wild-type strain showed pronounced growth advantages at 20°C, 30°C, and 35°C, respectively, the ΔmcyB mutant was superior at 25°C. We further show that short-term incubations at 25°C-35°C result in lower amounts of freely soluble microcystin than incubations at 20°C and that microcystin congener ratios differ at the different temperatures. Subsequent assessment of the protein-bound microcystin pool by dot blot analysis and subcellular localization of microcystin using immunofluorescence microscopy showed re-localization of microcystin into the protein-bound pool combined with an enhanced condensation at the cytoplasmic membrane at temperatures above 25°C. This temperature threshold also applies to the condensate formation of the carbon-fixing enzyme RubisCO thereby likely contributing to reciprocal growth advantages of wild type and ΔmcyB mutant at 20°C and 25°C. We discuss these findings in the context of the environmental success of Microcystis at higher temperatures.
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Affiliation(s)
| | | | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Pesce G, Gondelaud F, Ptchelkine D, Nilsson JF, Bignon C, Cartalas J, Fourquet P, Longhi S. Experimental Evidence of Intrinsic Disorder and Amyloid Formation by the Henipavirus W Proteins. Int J Mol Sci 2022; 23:ijms23020923. [PMID: 35055108 PMCID: PMC8780864 DOI: 10.3390/ijms23020923] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Henipaviruses are severe human pathogens within the Paramyxoviridae family. Beyond the P protein, the Henipavirus P gene also encodes the V and W proteins which share with P their N-terminal, intrinsically disordered domain (NTD) and possess a unique C-terminal domain. Henipavirus W proteins antagonize interferon (IFN) signaling through NTD-mediated binding to STAT1 and STAT4, and prevent type I IFN expression and production of chemokines. Structural and molecular information on Henipavirus W proteins is lacking. By combining various bioinformatic approaches, we herein show that the Henipaviruses W proteins are predicted to be prevalently disordered and yet to contain short order-prone segments. Using limited proteolysis, differential scanning fluorimetry, analytical size exclusion chromatography, far-UV circular dichroism and small-angle X-ray scattering, we experimentally confirmed their overall disordered nature. In addition, using Congo red and Thioflavin T binding assays and negative-staining transmission electron microscopy, we show that the W proteins phase separate to form amyloid-like fibrils. The present study provides an additional example, among the few reported so far, of a viral protein forming amyloid-like fibrils, therefore significantly contributing to enlarge our currently limited knowledge of viral amyloids. In light of the critical role of the Henipavirus W proteins in evading the host innate immune response and of the functional role of phase separation in biology, these studies provide a conceptual asset to further investigate the functional impact of the phase separation abilities of the W proteins.
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Affiliation(s)
- Giulia Pesce
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Frank Gondelaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Denis Ptchelkine
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Juliet F. Nilsson
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Christophe Bignon
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Jérémy Cartalas
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Patrick Fourquet
- INSERM, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS), Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille University, 27 Bvd Leï Roure, CS 30059, 13273 Marseille, France;
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
- Correspondence:
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Grosch M, Ittermann S, Shaposhnikov D, Drukker M. Chromatin-Associated Membraneless Organelles in Regulation of Cellular Differentiation. Stem Cell Reports 2020; 15:1220-1232. [PMID: 33217325 PMCID: PMC7724471 DOI: 10.1016/j.stemcr.2020.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-free intracellular biocondensates are enclosures of proteins and nucleic acids that form by phase separation. Extensive ensembles of nuclear "membraneless organelles" indicate their involvement in genome regulation. Indeed, nuclear bodies have been linked to regulation of gene expression by formation of condensates made of chromatin and RNA processing factors. Important questions pertain to the involvement of membraneless organelles in determining cell identity through their cell-type-specific composition and function. Paraspeckles provide a prism to these questions because they exhibit striking cell-type-specific patterns and since they are crucial in embryogenesis. Here, we outline known interactions between paraspeckles and chromatin, and postulate how such interactions may be important in regulation of cell fate transitions. Moreover, we propose long non-coding RNAs (lncRNAs) as candidates for similar regulation because many form foci that resemble biocondensates and exhibit dynamic patterns during differentiation. Finally, we outline approaches that could ascertain how chromatin-associated membraneless organelles regulate cellular differentiation.
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Affiliation(s)
- Markus Grosch
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Sebastian Ittermann
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, Einsteinweg 55, 2333 CC RA Leiden, The Netherlands.
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