1
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Gil-Garcia M, Benítez-Mateos AI, Papp M, Stoffel F, Morelli C, Normak K, Makasewicz K, Faltova L, Paradisi F, Arosio P. Local environment in biomolecular condensates modulates enzymatic activity across length scales. Nat Commun 2024; 15:3322. [PMID: 38637545 PMCID: PMC11026464 DOI: 10.1038/s41467-024-47435-w] [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: 05/17/2023] [Accepted: 03/28/2024] [Indexed: 04/20/2024] Open
Abstract
The mechanisms that underlie the regulation of enzymatic reactions by biomolecular condensates and how they scale with compartment size remain poorly understood. Here we use intrinsically disordered domains as building blocks to generate programmable enzymatic condensates of NADH-oxidase (NOX) with different sizes spanning from nanometers to microns. These disordered domains, derived from three distinct RNA-binding proteins, each possessing different net charge, result in the formation of condensates characterized by a comparable high local concentration of the enzyme yet within distinct environments. We show that only condensates with the highest recruitment of substrate and cofactor exhibit an increase in enzymatic activity. Notably, we observe an enhancement in enzymatic rate across a wide range of condensate sizes, from nanometers to microns, indicating that emergent properties of condensates can arise within assemblies as small as nanometers. Furthermore, we show a larger rate enhancement in smaller condensates. Our findings demonstrate the ability of condensates to modulate enzymatic reactions by creating distinct effective solvent environments compared to the surrounding solution, with implications for the design of protein-based heterogeneous biocatalysts.
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Affiliation(s)
- Marcos Gil-Garcia
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Florence Stoffel
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Karl Normak
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.
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2
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Morelli C, Faltova L, Capasso Palmiero U, Makasewicz K, Papp M, Jacquat RPB, Pinotsi D, Arosio P. RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates. Nat Chem 2024:10.1038/s41557-024-01467-3. [PMID: 38472406 DOI: 10.1038/s41557-024-01467-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Several RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein-RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid-protein interactions affect the kinetics and molecular pathways of amyloid formation.
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Affiliation(s)
- Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Raphaël P B Jacquat
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zürich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland.
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3
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Linsenmeier M, Faltova L, Morelli C, Capasso Palmiero U, Seiffert C, Küffner AM, Pinotsi D, Zhou J, Mezzenga R, Arosio P. The interface of condensates of the hnRNPA1 low-complexity domain promotes formation of amyloid fibrils. Nat Chem 2023; 15:1340-1349. [PMID: 37749234 PMCID: PMC10533390 DOI: 10.1038/s41557-023-01289-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/05/2023] [Indexed: 09/27/2023]
Abstract
The maturation of liquid-like protein condensates into amyloid fibrils has been associated with several neurodegenerative diseases. However, the molecular mechanisms underlying this liquid-to-solid transition have remained largely unclear. Here we analyse the amyloid formation mediated by condensation of the low-complexity domain of hnRNPA1, a protein involved in amyotrophic lateral sclerosis. We show that phase separation and fibrillization are connected but distinct processes that are modulated by different regions of the protein sequence. By monitoring the spatial and temporal evolution of amyloid formation we demonstrate that the formation of fibrils does not occur homogeneously inside the droplets but is promoted at the interface of the condensates. We further show that coating the interface of the droplets with surfactant molecules inhibits fibril formation. Our results reveal that the interface of biomolecular condensates of hnRNPA1 promotes fibril formation, therefore suggesting interfaces as a potential novel therapeutic target against the formation of aberrant amyloids mediated by condensation.
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Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Chiara Morelli
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Charlotte Seiffert
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Andreas M Küffner
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland
| | - Jiangtao Zhou
- Department for Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Raffaele Mezzenga
- Department for Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Sciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland.
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4
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Küffner AM, Linsenmeier M, Grigolato F, Prodan M, Zuccarini R, Capasso Palmiero U, Faltova L, Arosio P. Sequestration within biomolecular condensates inhibits Aβ-42 amyloid formation. Chem Sci 2021; 12:4373-4382. [PMID: 34163700 PMCID: PMC8179469 DOI: 10.1039/d0sc04395h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Biomolecular condensates are emerging as an efficient strategy developed by cells to control biochemical reactions in space and time by locally modifying composition and environment. Yet, local increase in protein concentration within these compartments could promote aberrant aggregation events, including the nucleation and growth of amyloid fibrils. Understanding protein stability within the crowded and heterogeneous environment of biological condensates is therefore crucial, not only when the aggregation-prone protein is the scaffold element of the condensates but also when proteins are recruited as client molecules within the compartments. Here, we investigate the partitioning and aggregation kinetics of the amyloidogenic peptide Abeta42 (Aβ-42), the peptide strongly associated with Alzheimer's disease, recruited into condensates based on low complexity domains (LCDs) derived from the DEAD-box proteins Laf1, Dbp1 and Ddx4, which are associated with biological membraneless organelles. We show that interactions between Aβ-42 and the scaffold proteins promote sequestration and local increase of the peptide concentration within the condensates. Yet, heterotypic interactions within the condensates inhibit the formation of amyloid fibrils. These results demonstrate that biomolecular condensates could sequester aggregation-prone proteins and prevent aberrant aggregation events, despite the local increase in their concentration. Biomolecular condensates could therefore work not only as hot-spots of protein aggregation but also as protective reservoirs, since the heterogenous composition of the condensates could prevent the formation of ordered fibrillar aggregates. Biomolecular condensates sequester an aggregation-prone peptide and prevent its aggregation, showing that heterotypic interactions within the condensates can prevent the formation of amyloid fibrils, despite the local increase in concentration.![]()
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Affiliation(s)
- Andreas M Küffner
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Marc Prodan
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Remo Zuccarini
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich Zurich 8093 Switzerland
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5
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Poghosyan E, Iacovache I, Faltova L, Leitner A, Yang P, Diener DR, Aebersold R, Zuber B, Ishikawa T. The structure and symmetry of the radial spoke protein complex in Chlamydomonas flagella. J Cell Sci 2020; 133:jcs245233. [PMID: 32694165 DOI: 10.1242/jcs.245233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022] Open
Abstract
The radial spoke is a key element in a transducer apparatus controlling the motility of eukaryotic cilia. The transduction biomechanics is a long-standing question in cilia biology. The radial spoke has three regions - a spoke head, a bifurcated neck and a stalk. Although the neck and the stalk are asymmetric, twofold symmetry of the head has remained controversial. In this work we used single particle cryo-electron microscopy (cryo-EM) analysis to generate a 3D structure of the whole radial spoke at unprecedented resolution. We show the head region at 15 Å (1.5 nm) resolution and confirm twofold symmetry. Using distance constraints generated by cross-linking mass spectrometry, we locate two components, RSP2 and RSP4, at the head and neck regions. Our biophysical analysis of isolated RSP4, RSP9, and RSP10 affirmed their oligomeric state. Our results enable us to redefine the boundaries of the regions and propose a model of organization of the radial spoke component proteins.
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Affiliation(s)
- Emiliya Poghosyan
- Paul Scherrer Institute, Department of Biology and Chemistry, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
- ETH Zurich, Department of Biology, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Ioan Iacovache
- University of Bern, Institute of Anatomy, Baltzerstrasse 2, 3012 Bern, Switzerland
| | - Lenka Faltova
- Paul Scherrer Institute, Department of Biology and Chemistry, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Alexander Leitner
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Dennis R Diener
- Paul Scherrer Institute, Department of Biology and Chemistry, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Ruedi Aebersold
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- University of Zurich, Faculty of Science, Rämistrasse 71, 8006 Zürich, Switzerland
| | - Benoit Zuber
- University of Bern, Institute of Anatomy, Baltzerstrasse 2, 3012 Bern, Switzerland
| | - Takashi Ishikawa
- Paul Scherrer Institute, Department of Biology and Chemistry, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
- ETH Zurich, Department of Biology, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
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6
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Küffner AM, Prodan M, Zuccarini R, Capasso Palmiero U, Faltova L, Arosio P. Acceleration of an Enzymatic Reaction in Liquid Phase Separated Compartments Based on Intrinsically Disordered Protein Domains. ChemSystemsChem 2020. [DOI: 10.1002/syst.202000027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas M. Küffner
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Marc Prodan
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Remo Zuccarini
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
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7
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Küffner AM, Prodan M, Zuccarini R, Capasso Palmiero U, Faltova L, Arosio P. Front Cover: Acceleration of an Enzymatic Reaction in Liquid Phase Separated Compartments Based on Intrinsically Disordered Protein Domains (ChemSystemsChem 4/2020). ChemSystemsChem 2020. [DOI: 10.1002/syst.202000028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andreas M. Küffner
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Marc Prodan
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Remo Zuccarini
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
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8
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Capasso Palmiero U, Küffner AM, Krumeich F, Faltova L, Arosio P. Inside Cover: Adaptive Chemoenzymatic Microreactors Composed of Inorganic Nanoparticles and Bioinspired Intrinsically Disordered Proteins (Angew. Chem. Int. Ed. 21/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202005761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Umberto Capasso Palmiero
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Andreas M. Küffner
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Frank Krumeich
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
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9
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Capasso Palmiero U, Küffner AM, Krumeich F, Faltova L, Arosio P. Innentitelbild: Adaptive Chemoenzymatic Microreactors Composed of Inorganic Nanoparticles and Bioinspired Intrinsically Disordered Proteins (Angew. Chem. 21/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Umberto Capasso Palmiero
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Andreas M. Küffner
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Frank Krumeich
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
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10
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Capasso Palmiero U, Küffner AM, Krumeich F, Faltova L, Arosio P. Adaptive Chemoenzymatic Microreactors Composed of Inorganic Nanoparticles and Bioinspired Intrinsically Disordered Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Umberto Capasso Palmiero
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Andreas M. Küffner
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Frank Krumeich
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
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11
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Fiedler T, Fabrice TN, Studer V, Vinet A, Faltova L, Kammerer RA, Steinmetz MO, Sharpe T, Pieters J. Homodimerization of coronin A through the C-terminal coiled-coil domain is essential for multicellular differentiation of Dictyostelium discoideum. FEBS Lett 2020; 594:2116-2127. [PMID: 32298460 DOI: 10.1002/1873-3468.13787] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 11/09/2022]
Abstract
Coronin proteins are widely expressed among eukaryotic organisms. Most coronins consist of a WD-repeat domain followed by a C-terminal coiled coil. Dictyostelium discoideum expresses a single short coronin coronin A, which has been implicated in both actin modulation and multicellular differentiation. Whether coronin A's coiled coil is important for functionality, as well as the oligomeric state of coronin A is not known. Here, we show that the coiled-coil domain in Dictyostelium coronin A functions in homodimerization, is dispensable for coronin A stability and localization but essential for multicellular differentiation. These results allow a better understanding of the role for the coiled-coil domain of coronin A in oligomerization and demonstrate that its presence is essential for multicellular differentiation.
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Affiliation(s)
| | | | - Vera Studer
- Biozentrum, University of Basel, Switzerland
| | | | - Lenka Faltova
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Michel O Steinmetz
- Biozentrum, University of Basel, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
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12
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Capasso Palmiero U, Küffner AM, Krumeich F, Faltova L, Arosio P. Adaptive Chemoenzymatic Microreactors Composed of Inorganic Nanoparticles and Bioinspired Intrinsically Disordered Proteins. Angew Chem Int Ed Engl 2020; 59:8138-8142. [DOI: 10.1002/anie.202000835] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/28/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Umberto Capasso Palmiero
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Andreas M. Küffner
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Frank Krumeich
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied BiosciencesInstitute for Chemical and BioengineeringETH Zurich 8093 Zurich Switzerland
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13
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Küffner AM, Prodan M, Zuccarini R, Capasso Palmiero U, Faltova L, Arosio P. Acceleration of an Enzymatic Reaction in Liquid Phase Separated Compartments Based on Intrinsically Disordered Protein Domains. ChemSystemsChem 2020. [DOI: 10.1002/syst.202000001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andreas M. Küffner
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Marc Prodan
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Remo Zuccarini
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
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14
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Faltova L, Jiang K, Frey D, Wu Y, Capitani G, Prota AE, Akhmanova A, Steinmetz MO, Kammerer RA. Crystal Structure of a Heterotetrameric Katanin p60:p80 Complex. Structure 2019; 27:1375-1383.e3. [PMID: 31353241 DOI: 10.1016/j.str.2019.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 05/27/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
Katanin is a microtubule-severing enzyme that is crucial for many cellular processes. Katanin consists of two subunits, p60 and p80, that form a stable complex. The interaction between subunits is mediated by the p60 N-terminal microtubule-interacting and -trafficking domain (p60-MIT) and the p80 C-terminal domain (p80-CTD). Here, we performed a biophysical characterization of the mouse p60-MIT:p80-CTD heterodimer and show that this complex can assemble into heterotetramers. We identified two mutations that enhance heterotetramer formation and determined the X-ray crystal structure of this mutant complex. The structure revealed a domain-swapped heterotetramer consisting of two p60-MIT:p80-CTD heterodimers. Structure-based sequence alignments suggest that heterotetramerization of katanin might be a common feature of various species. Furthermore, we show that enhanced heterotetramerization of katanin impairs its microtubule end-binding properties and increases the enzyme's microtubule lattice binding and severing activities. Therefore, our findings suggest the existence of different katanin oligomers that possess distinct functional properties.
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Affiliation(s)
- Lenka Faltova
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Kai Jiang
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430071, China; Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Daniel Frey
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Yufan Wu
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland; Biozentrum, University of Basel, 4056 Basel, Switzerland.
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland.
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15
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Linsenmeier M, Küffner A, Faltova L, Hondele M, Weis K, Arosio P. Protein Phase Transition: From Biology Towards New Protein Materials. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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16
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Chalupska D, Różycki B, Humpolickova J, Faltova L, Klima M, Boura E. Phosphatidylinositol 4-kinase IIIβ (PI4KB) forms highly flexible heterocomplexes that include ACBD3, 14-3-3, and Rab11 proteins. Sci Rep 2019; 9:567. [PMID: 30679637 PMCID: PMC6345845 DOI: 10.1038/s41598-018-37158-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIβ (PI4KB) is a key enzyme of the Golgi system because it produces its lipid hallmark - the phosphatidylinositol 4-phosphate (PI4P). It is recruited to Golgi by the Golgi resident ACBD3 protein, regulated by 14-3-3 proteins and it also serves as an adaptor because it recruits the small GTPase Rab11. Here, we analyzed the protein complexes formed by PI4KB in vitro using small angle x-ray scattering (SAXS) and we discovered that these protein complexes are highly flexible. The 14-3-3:PI4KB:Rab11 protein complex has 2:1:1 stoichiometry and its different conformations are rather compact, however, the ACBD3:PI4KB protein complex has both, very compact and very extended conformations. Furthermore, in vitro reconstitution revealed that the membrane is necessary for the formation of ACBD3:PI4KB:Rab11 protein complex at physiological (nanomolar) concentrations.
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Affiliation(s)
- Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Lenka Faltova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen, PSI, Switzerland
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic.
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17
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Faltova L, Küffner AM, Hondele M, Weis K, Arosio P. Multifunctional Protein Materials and Microreactors using Low Complexity Domains as Molecular Adhesives. ACS Nano 2018; 12:9991-9999. [PMID: 30216718 DOI: 10.1021/acsnano.8b04304] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recent findings indicate that a class of disordered amino acid sequences promotes functional phase transition of biomolecules in nature. Such sequences consist of low complexity domains (LCDs) that are rich in specific amino acids. In this work, we exploit these sequences by conjugating them to soluble globular domains to develop molecular adhesives that enable sensitive, controlled self-assembly of these proteins into supramolecular architectures. In particular, we used the enzyme adenylate kinase and the green fluorescent protein as soluble domains, and we show that the addition of low complexity regions induces the formation of protein particles via a multistep process. This multistep pathway involves an initial liquid-liquid phase transition, which creates protein-rich droplets that mature into protein aggregates over time. These protein aggregates consist of permeable structures that maintain activity and release active soluble proteins. We show that the LCDs dictate specific noncovalent intermolecular interactions and phase properties that are largely independent of the given globular domain. We further demonstrate that this feature, together with the dynamic state of the initial dense liquid phase, allows one to directly assemble different globular domains within the same architecture, thereby enabling the generation of both static multifunctional biomaterials and dynamic microscale bioreactors.
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18
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Grignaschi E, Cereghetti G, Grigolato F, Kopp MRG, Caimi S, Faltova L, Saad S, Peter M, Arosio P. A hydrophobic low-complexity region regulates aggregation of the yeast pyruvate kinase Cdc19 into amyloid-like aggregates in vitro. J Biol Chem 2018; 293:11424-11432. [PMID: 29853641 DOI: 10.1074/jbc.ra117.001628] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/15/2018] [Indexed: 11/06/2022] Open
Abstract
Cells form stress granules (SGs) upon stress stimuli to protect sensitive proteins and RNA from degradation. In the yeast Saccharomyces cerevisiae, specific stresses such as nutrient starvation and heat-shock trigger recruitment of the yeast pyruvate kinase Cdc19 into SGs. This RNA-binding protein was shown to form amyloid-like aggregates that are physiologically reversible and essential for cell cycle restart after stress. Cellular Cdc19 exists in an equilibrium between a homotetramer and monomer state. Here, we show that Cdc19 aggregation in vitro is governed by protein quaternary structure, and we investigate the physical-chemical basis of Cdc19's assembly properties. Equilibrium shift toward the monomer state exposes a hydrophobic low-complexity region (LCR), which is prone to induce intermolecular interactions with surrounding proteins. We further demonstrate that hydrophobic/hydrophilic interfaces can trigger Cdc19 aggregation in vitro Moreover, we performed in vitro biophysical analyses to compare Cdc19 aggregates with fibrils produced by two known dysfunctional amyloidogenic peptides. We show that the Cdc19 aggregates share several structural features with pathological amyloids formed by human insulin and the Alzheimer's disease-associated Aβ42 peptide, particularly secondary β-sheet structure, thermodynamic stability, and staining by the thioflavin T dye. However, Cdc19 aggregates could not seed aggregation. These results indicate that Cdc19 adopts an amyloid-like structure in vitro that is regulated by the exposure of a hydrophobic LCR in its monomeric form. Together, our results highlight striking structural similarities between functional and dysfunctional amyloids and reveal the crucial role of hydrophobic/hydrophilic interfaces in regulating Cdc19 aggregation.
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Affiliation(s)
- Erica Grignaschi
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Gea Cereghetti
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Stefano Caimi
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Shady Saad
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland.
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19
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Jiang K, Faltova L, Hua S, Capitani G, Prota AE, Landgraf C, Volkmer R, Kammerer RA, Steinmetz MO, Akhmanova A. Structural Basis of Formation of the Microtubule Minus-End-Regulating CAMSAP-Katanin Complex. Structure 2018; 26:375-382.e4. [DOI: 10.1016/j.str.2017.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/28/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022]
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