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Sternke-Hoffmann R, Sun X, Menzel A, Pinto MDS, Venclovaitė U, Wördehoff M, Hoyer W, Zheng W, Luo J. Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions. bioRxiv 2024:2024.03.01.582895. [PMID: 38464093 PMCID: PMC10925286 DOI: 10.1101/2024.03.01.582895] [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] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The coacervation and structural rearrangement of the protein alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson's disease. While aggregation is recognized as the key element of amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work showed that factors promoting or inhibiting amyloid formation have similar effects on phase separation. Here, we provide a detailed scanning of a wide range of parameters including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and phase separation. The influence of salt on aggregation under crowded conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, we find a monotonic salt dependence of phase separation due to the intermolecular interaction. Furthermore, we observe the time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving the aggregates through a variety of heterotypic interactions, thus preventing αSyn from its dynamically arrested state.
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Affiliation(s)
- Rebecca Sternke-Hoffmann
- Department of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Xun Sun
- Department of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Andreas Menzel
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Miriam Dos Santos Pinto
- Department of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Urtė Venclovaitė
- Department of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Michael Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, United States
| | - Jinghui Luo
- Department of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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2
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Sementa D, Dave D, Fisher RS, Wang T, Elbaum-Garfinkle S, Ulijn RV. Sequence-Tunable Phase Behavior and Intrinsic Fluorescence in Dynamically Interacting Peptides. Angew Chem Int Ed Engl 2023; 62:e202311479. [PMID: 37934145 DOI: 10.1002/anie.202311479] [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: 08/09/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/08/2023]
Abstract
A conceptual framework towards understanding biological condensed phases is emerging, derived from biological, biomimetic, and synthetic sequences. However, de novo peptide condensate design remains a challenge due to an incomplete understanding of the structural and interactive complexity. We designed peptide modules based on a simple repeat motif composed of tripeptide spacers (GSG, SGS, GLG) interspersed with adhesive amino acids (R/H and Y). We show, using sequence editing and a combination of computation and experiment, that n→π* interactions in GLG backbones are a dominant factor in providing sufficient backbone structure, which in turn regulates the water interface, collectively promoting liquid droplet formation. Moreover, these R(GLG)Y and H(GLG)Y condensates unexpectedly display sequence-dependent emission that is a consequence of their non-covalent network interactions, and readily observable by confocal microscopy.
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Affiliation(s)
- Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Dhwanit Dave
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York (CUNY), 695 Park Avenue, New York, NY 10065, USA
| | - Rachel S Fisher
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Tong Wang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Shana Elbaum-Garfinkle
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York (CUNY), 695 Park Avenue, New York, NY 10065, USA
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3
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Sahgal A, Uversky V, Davé V. Microproteins transitioning into a new Phase: Defining the undefined. Methods 2023; 220:38-54. [PMID: 37890707 DOI: 10.1016/j.ymeth.2023.10.009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.
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Affiliation(s)
- Aayushi Sahgal
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vrushank Davé
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Pathology and Cell Biology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States.
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4
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Li Q, Song Q, Guo W, Cao Y, Cui X, Chen D, Shum HC. Synthetic Membraneless Droplets for Synaptic-Like Clustering of Lipid Vesicles. Angew Chem Int Ed Engl 2023; 62:e202313096. [PMID: 37728515 DOI: 10.1002/anie.202313096] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
In eukaryotic cells, the membraneless organelles (MLOs) formed via liquid-liquid phase separation (LLPS) are found to interact intimately with membranous organelles (MOs). One major mode is the clustering of MOs by MLOs, such as the formation of clusters of synaptic vesicles at nerve terminals mediated by the synapsin-rich MLOs. Aqueous droplets, including complex coacervates and aqueous two-phase systems, have been plausible MLO-mimics to emulate or elucidate biological processes. However, neither of them can cluster lipid vesicles (LVs) like MLOs. In this work, we develop a synthetic droplet assembled from a combination of two different interactions underlying the formation of these two droplets, namely, associative and segregative interactions, which we call segregative-associative (SA) droplets. The SA droplets cluster and disperse LVs recapitulating the key functional features of synapsin condensates, which can be attributed to the weak electrostatic interaction environment provided by SA droplets. This work suggests LLPS with combined segregative and associative interactions as a possible route for synaptic clustering of lipid vesicles and highlights SA droplets as plausible MLO-mimics and models for studying and mimicking related cellular dynamics.
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Affiliation(s)
- Qingchuan Li
- School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, P.R.China
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
| | - Qingchun Song
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Wei Guo
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
| | - Yang Cao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xinyu Cui
- Department of Public Health, Mudanjiang Medical University, Mudanjiang, 157000, P. R. China
| | - Dairong Chen
- School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, P.R.China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
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5
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Liu W, Samanta A, Deng J, Akintayo CO, Walther A. Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets. Angew Chem Int Ed Engl 2022; 61:e202208951. [PMID: 36112754 PMCID: PMC9828218 DOI: 10.1002/anie.202208951] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Liquid-liquid phase separation provides a versatile approach to fabricating cell-mimicking coacervates. Recently, it was discovered that phase separation of single-stranded DNA (ssDNA) allows for forming protocells and microgels in multicomponent systems. However, the mechanism of the ssDNA phase separation is not comprehensively understood. Here, we present mechanistic insights into the metal-dependent phase separation of ssDNA and leverage this understanding for a straightforward formation of all-DNA droplets. Two phase separation temperatures are found that correspond to the formation of primary nuclei and a growth process. Ca2+ allows for irreversible, whereas Mg2+ leads to reversible phase separation. Capitalizing on these differences makes it possible to control the information transfer of one-component DNA droplets and two-component core-shell protocells. This study introduces new kinetic traps of phase separating ssDNA that lead to new phenomena in cell-mimicking systems.
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Affiliation(s)
- Wei Liu
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Avik Samanta
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Jie Deng
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany,Present address: Department of Cancer BiologyDana-Farber Cancer Institute and Wyss Institute for Biologically Inspired EngineeringHarvard Medical SchoolBostonMA 02115USA
| | - Cecilia Oluwadunsin Akintayo
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany,Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany,Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
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6
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Yu J, Qi D, Mäkilä E, Lassila L, Papageorgiou AC, Peurla M, Rosenholm JM, Zhao Z, Vallittu P, Jalkanen S, Jia C, Li J. Small-Molecule-based Supramolecular Plastics Mediated by Liquid-Liquid Phase Separation. Angew Chem Int Ed Engl 2022; 61:e202204611. [PMID: 35929612 PMCID: PMC9804437 DOI: 10.1002/anie.202204611] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 01/05/2023]
Abstract
Plastics are one of the most widely used polymeric materials. However, they are often undegradable and non-recyclable due to the very stable covalent bonds of macromolecules, causing environmental pollution and health problems. Here, we report that liquid-liquid phase separation (LLPS) could drive the formation of robust, stable, and sustainable plastics using small molecules. The LLPS process could sequester and concentrate solutes, strengthen the non-covalent association between molecules and produce a bulk material whose property was highly related to the encapsulated water amounts. It was a robust plastic with a remarkable Young's modulus of 139.5 MPa when the water content was low while became adhesive and could instantly self-heal with more absorbed water. Finally, responsiveness enabled the material to be highly recyclable. This work allowed us to understand the LLPS at the molecular level and demonstrated that LLPS is a promising approach to exploring eco-friendly supramolecular plastics that are potential substitutes for conventional polymers.
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Affiliation(s)
- Jingjing Yu
- MediCity Research LaboratoryUniversity of TurkuTykistökatu 620520TurkuFinland
| | - Dawei Qi
- MediCity Research LaboratoryUniversity of TurkuTykistökatu 620520TurkuFinland
| | - Ermei Mäkilä
- Laboratory of Industrial PhysicsDepartment of Physics and AstronomyInstitute of DentistryUniversity of Turku20014TurkuFinland
| | - Lippo Lassila
- Department of Biomaterials Science and Turku Clinical Biomaterials Centre, TCBCUniversity of Turku20014TurkuFinland
| | - Anastassios C. Papageorgiou
- Turku Bioscience CentreUniversity of Turku20521TurkuFinland,Turku Bioscience CentreÅbo Akademi University20521TurkuFinland
| | - Markus Peurla
- Institute of Biomedicine and FICAN West Cancer Research LaboratoriesUniversity of Turku20014TurkuFinland
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences LaboratoryFaculty of Science and EngineeringÅbo Akademi UniversityTykistökatu 620520TurkuFinland
| | - Zhao Zhao
- MediCity Research LaboratoryUniversity of TurkuTykistökatu 620520TurkuFinland
| | - Pekka Vallittu
- Department of Biomaterials Science and Turku Clinical Biomaterials Centre, TCBCUniversity of Turku20014TurkuFinland,City of Turku Welfare DivisionPuolalankatu 520101TurkuFinland
| | - Sirpa Jalkanen
- MediCity Research LaboratoryUniversity of TurkuTykistökatu 620520TurkuFinland
| | - Chunman Jia
- Hainan Provincial Key Laboratory of Fine ChemSchool of Chemical Engineering and TechnologyHainan University570228HaikouChina,One Health InstituteHainan University570228HaikouChina
| | - Jianwei Li
- MediCity Research LaboratoryUniversity of TurkuTykistökatu 620520TurkuFinland,Hainan Provincial Key Laboratory of Fine ChemSchool of Chemical Engineering and TechnologyHainan University570228HaikouChina,One Health InstituteHainan University570228HaikouChina
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7
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Jonchhe S, Pan W, Pokhrel P, Mao H. Small Molecules Modulate Liquid-to-Solid Transitions in Phase-Separated Tau Condensates. Angew Chem Int Ed Engl 2022; 61:e202113156. [PMID: 35320624 PMCID: PMC9156559 DOI: 10.1002/anie.202113156] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 09/28/2021] [Indexed: 11/08/2022]
Abstract
In Tau protein condensates formed by the Liquid-Liquid Phase Separation (LLPS) process, liquid-to-solid transitions lead to the formation of fibrils implicated in Alzheimer's disease. Here, by tracking two contacting Tau-rich droplets using a simple and nonintrusive video microscopy, we found that the halftime of the liquid-to-solid transition in the Tau condensate is affected by the Hofmeister series according to the solvation energy of anions. After dissecting functional groups of physiologically relevant small molecules using a multivariate approach, we found that charged groups facilitate the liquid-to-solid transition in a manner similar to the Hofmeister effect, whereas hydrophobic alkyl chains and aromatic rings inhibit the transition. Our results not only elucidate the driving force of the liquid-to-solid transition in Tau condensates, but also provide guidelines to design small molecules to modulate this important transition for many biological functions for the first time.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Wei Pan
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Advanced Materials and Liquid Crystal Institute, Department of Biomedical Sciences, Kent State University, Kent, OH 44242, USA
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Abstract
In nature, simple organisms evolved mechanisms to form intricate biosilica nanostructures, far exceeding current synthetic manufacturing. Based on the properties of extracted biomacromolecules, polycation–polyanion pairs were suggested as moderators of biosilica formation. However, the chemical principles of this polymer‐induced silicification remain unclear. Here, we used a biomimetic polycation–polyanion system to study polymer‐induced silicification. We demonstrate that it is the polymer phase separation process, rather than silica–polymer interactions, which controls silica precipitation. Since ionic strength controls this electrostatic phase separation, it can be used to tune the morphology and structure of the precipitates. In situ cryo electron microscopy highlights the pivotal role of the hydrated polymer condensates in this process. These results pave the road for developing nanoscale morphologies of bioinspired silica based on the chemistry of liquid‐liquid phase separation.
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Affiliation(s)
- Hang Zhai
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tatyana Bendikov
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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