101
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Liang Q, Yang S, Mai M, Chen X, Zhu X. Mining phase separation-related diagnostic biomarkers for endometriosis through WGCNA and multiple machine learning techniques: a retrospective and nomogram study. J Assist Reprod Genet 2024; 41:1433-1447. [PMID: 38456992 PMCID: PMC11143086 DOI: 10.1007/s10815-024-03079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the role of phase separation-related genes in the development of endometriosis (EMs) and to identify potential characteristic genes associated with the condition. METHODS We used GEO database data, including 74 non-endometriosis and 74 varying-degree EMs patients. Our approach involved identifying significant gene modules, exploring gene intersections, identifying core genes, and screening for potential EMs biomarkers using weighted gene co-expression network analysis (WGCNA) and various machine learning approaches. We also performed gene set enrichment analysis (GSEA) to understand relevant pathways. This comprehensive approach helps investigate EMs genetics and potential biomarkers. RESULTS Nine genes were identified at the intersection, suggesting their involvement in EMs. GSEA linked DEGs to pathways like complement and coagulation cascades, DNA replication, chemokines, apical plasma membrane processes, and diseases such as Hepatitis B, Human T-cell leukemia virus 1 infection, and COVID-19. Five feature genes (FOS, CFD, CCNA1, CA4, CST1) were selected by machine learning for an effective EMs diagnostic nomogram. GSEA indicated their roles in mismatch repair, cell cycle regulation, complement and coagulation cascades, and IL-17 inflammation. Notable differences in immune cell proportions (CD4 T cells, CD8 T cells, DCs, macrophages) were observed between normal and disease groups, suggesting immune involvement. CONCLUSIONS This study suggests the potential involvement of phase separation-related genes in the pathogenesis of endometriosis (EMs) and identifies promising biomarkers for diagnosis. These findings have implications for further research and the development of new therapeutic strategies for EMs.
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Affiliation(s)
- Qiuyi Liang
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Shengmei Yang
- Obstetrical Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meiyi Mai
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiurong Chen
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China.
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102
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van Haren MHI, Visser BS, Spruijt E. Probing the surface charge of condensates using microelectrophoresis. Nat Commun 2024; 15:3564. [PMID: 38670952 PMCID: PMC11053090 DOI: 10.1038/s41467-024-47885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Biomolecular condensates play an important role in cellular organization. Coacervates are commonly used models that mimic the physicochemical properties of biomolecular condensates. The surface of condensates plays a key role in governing molecular exchange between condensates, accumulation of species at the interface, and the stability of condensates against coalescence. However, most important surface properties, including the surface charge and zeta potential, remain poorly characterized and understood. The zeta potential of coacervates is often measured using laser doppler electrophoresis, which assumes a size-independent electrophoretic mobility. Here, we show that this assumption is incorrect for liquid-like condensates and present an alternative method to study the electrophoretic mobility of coacervates and in vitro condensate models by microelectrophoresis and single-particle tracking. Coacervates have a size-dependent electrophoretic mobility, originating from their fluid nature, from which a well-defined zeta potential is calculated. Interestingly, microelectrophoresis measurements reveal that polylysine chains are enriched at the surface of polylysine/polyaspartic acid complex coacervates, which causes the negatively charged protein ɑ-synuclein to adsorb and accumulate at the interface. Addition of ATP inverts the surface charge, displaces ɑ-synuclein from the surface and may help to suppress its interface-catalyzed aggregation. Together, these findings show how condensate surface charge can be measured and altered, making this microelectrophoresis platform combined with automated single-particle tracking a promising characterization technique for both biomolecular condensates and coacervate protocells.
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Affiliation(s)
- Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6523, AJ, Nijmegen, The Netherlands
| | - Brent S Visser
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6523, AJ, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6523, AJ, Nijmegen, The Netherlands.
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103
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Crawshaw S, Murphy AM, Rowling PJE, Nietlispach D, Itzhaki LS, Carr JP. Investigating the Interactions of the Cucumber Mosaic Virus 2b Protein with the Viral 1a Replicase Component and the Cellular RNA Silencing Factor Argonaute 1. Viruses 2024; 16:676. [PMID: 38793558 PMCID: PMC11125589 DOI: 10.3390/v16050676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
The cucumber mosaic virus (CMV) 2b protein is a suppressor of plant defenses and a pathogenicity determinant. Amongst the 2b protein's host targets is the RNA silencing factor Argonaute 1 (AGO1), which it binds to and inhibits. In Arabidopsis thaliana, if 2b-induced inhibition of AGO1 is too efficient, it induces reinforcement of antiviral silencing by AGO2 and triggers increased resistance against aphids, CMV's insect vectors. These effects would be deleterious to CMV replication and transmission, respectively, but are moderated by the CMV 1a protein, which sequesters sufficient 2b protein molecules into P-bodies to prevent excessive inhibition of AGO1. Mutant 2b protein variants were generated, and red and green fluorescent protein fusions were used to investigate subcellular colocalization with AGO1 and the 1a protein. The effects of mutations on complex formation with the 1a protein and AGO1 were investigated using bimolecular fluorescence complementation and co-immunoprecipitation assays. Although we found that residues 56-60 influenced the 2b protein's interactions with the 1a protein and AGO1, it appears unlikely that any single residue or sequence domain is solely responsible. In silico predictions of intrinsic disorder within the 2b protein secondary structure were supported by circular dichroism (CD) but not by nuclear magnetic resonance (NMR) spectroscopy. Intrinsic disorder provides a plausible model to explain the 2b protein's ability to interact with AGO1, the 1a protein, and other factors. However, the reasons for the conflicting conclusions provided by CD and NMR must first be resolved.
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Affiliation(s)
- Sam Crawshaw
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (S.C.); (A.M.M.)
| | - Alex M. Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (S.C.); (A.M.M.)
| | - Pamela J. E. Rowling
- Department of Pharmacology, University of Cambridge, Tennis Court Rd., Cambridge CB2 1PD, UK; (P.J.E.R.); (L.S.I.)
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Rd., Cambridge CB2 1GA, UK;
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Rd., Cambridge CB2 1PD, UK; (P.J.E.R.); (L.S.I.)
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (S.C.); (A.M.M.)
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104
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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105
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Ibrahim KA, Naidu AS, Miljkovic H, Radenovic A, Yang W. Label-Free Techniques for Probing Biomolecular Condensates. ACS NANO 2024; 18:10738-10757. [PMID: 38609349 DOI: 10.1021/acsnano.4c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.
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106
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Dar F, Cohen SR, Mitrea DM, Phillips AH, Nagy G, Leite WC, Stanley CB, Choi JM, Kriwacki RW, Pappu RV. Biomolecular condensates form spatially inhomogeneous network fluids. Nat Commun 2024; 15:3413. [PMID: 38649740 PMCID: PMC11035652 DOI: 10.1038/s41467-024-47602-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.
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Affiliation(s)
- Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Samuel R Cohen
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Diana M Mitrea
- Dewpoint Therapeutics Inc., 451 D Street, Boston, MA, 02210, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gergely Nagy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington C Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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107
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Jung J, Tan C, Sugita Y. GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nat Commun 2024; 15:3370. [PMID: 38643169 PMCID: PMC11032353 DOI: 10.1038/s41467-024-47654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.
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Affiliation(s)
- Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan.
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108
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Bai Y, Ning K. How does severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) achieve immune evasion?: A narrative review. Medicine (Baltimore) 2024; 103:e37780. [PMID: 38640329 PMCID: PMC11030025 DOI: 10.1097/md.0000000000037780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 04/21/2024] Open
Abstract
COVID-19 caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is a highly contagious disease known for its significant lung damage. Although the impact of the COVID-19 pandemic on our daily lives has been limited, the virus has not vanished entirely and continues to undergo mutations. This calls for a concentrated focus on the matter of SARS-CoV-2 immune evasion. Drawing on observations of immune escape mechanisms in other viruses, some scholars have proposed that liquid-liquid phase separation might play a crucial role in SARS-CoV-2's ability to evade the immune system. Within the structure of SARS-CoV-2, the nucleocapsid protein plays a pivotal role in RNA replication and transcription. Concurrently, this protein can engage in phase separation with RNA. A thorough examination of the phase separation related to the nucleocapsid protein may unveil the mechanism by which SARS-CoV-2 accomplishes immune evasion. Moreover, this analysis may provide valuable insights for future development of innovative antiviral drugs or vaccines.
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Affiliation(s)
- Yahu Bai
- Department of Respiratory, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Shandong Institute of Respiratory Diseases, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Kang Ning
- Department of Respiratory, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Shandong Institute of Respiratory Diseases, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
- Department of Respiratory, Occupational Diseases Hospital of Shandong First Medical University, Shandong Province Hospital of Occupational Diseases, Jinan, China
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109
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Song J. Adenosine Triphosphate: The Primordial Molecule That Controls Protein Homeostasis and Shapes the Genome-Proteome Interface. Biomolecules 2024; 14:500. [PMID: 38672516 PMCID: PMC11048592 DOI: 10.3390/biom14040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Adenosine triphosphate (ATP) acts as the universal energy currency that drives various biological processes, while nucleic acids function to store and transmit genetic information for all living organisms. Liquid-liquid phase separation (LLPS) represents the common principle for the formation of membrane-less organelles (MLOs) composed of proteins rich in intrinsically disordered regions (IDRs) and nucleic acids. Currently, while IDRs are well recognized to facilitate LLPS through dynamic and multivalent interactions, the precise mechanisms by which ATP and nucleic acids affect LLPS still remain elusive. This review summarizes recent NMR results on the LLPS of human FUS, TDP-43, and the viral nucleocapsid (N) protein of SARS-CoV-2, as modulated by ATP and nucleic acids, revealing the following: (1) ATP binds to folded domains overlapping with nucleic-acid-binding interfaces; (2) ATP and nucleic acids interplay to biphasically modulate LLPS by competitively binding to overlapping pockets of folded domains and Arg/Lys within IDRs; (3) ATP energy-independently induces protein folding with the highest efficiency known so far. As ATP likely emerged in the prebiotic monomeric world, while LLPS represents a pivotal mechanism to concentrate and compartmentalize rare molecules for forming primordial cells, ATP appears to control protein homeostasis and shape genome-proteome interfaces throughout the evolutionary trajectory, from prebiotic origins to modern cells.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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110
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Mukherjee S, Ramos S, Pezzotti S, Kalarikkal A, Prass TM, Galazzo L, Gendreizig D, Barbosa N, Bordignon E, Havenith M, Schäfer LV. Entropy Tug-of-War Determines Solvent Effects in the Liquid-Liquid Phase Separation of a Globular Protein. J Phys Chem Lett 2024; 15:4047-4055. [PMID: 38580324 PMCID: PMC11033941 DOI: 10.1021/acs.jpclett.3c03421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/15/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Liquid-liquid phase separation (LLPS) plays a key role in the compartmentalization of cells via the formation of biomolecular condensates. Here, we combined atomistic molecular dynamics (MD) simulations and terahertz (THz) spectroscopy to determine the solvent entropy contribution to the formation of condensates of the human eye lens protein γD-Crystallin. The MD simulations reveal an entropy tug-of-war between water molecules that are released from the protein droplets and those that are retained within the condensates, two categories of water molecules that were also assigned spectroscopically. A recently developed THz-calorimetry method enables quantitative comparison of the experimental and computational entropy changes of the released water molecules. The strong correlation mutually validates the two approaches and opens the way to a detailed atomic-level understanding of the different driving forces underlying the LLPS.
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Affiliation(s)
- Saumyak Mukherjee
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Sashary Ramos
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Simone Pezzotti
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Abhishek Kalarikkal
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Tobias M. Prass
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Laura Galazzo
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Dominik Gendreizig
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Natercia Barbosa
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Enrica Bordignon
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Martina Havenith
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Lars V. Schäfer
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
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111
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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] [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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112
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Kang CY, Chang Y, Zieske K. Lipid Membrane Topographies Are Regulators for the Spatial Distribution of Liquid Protein Condensates. NANO LETTERS 2024; 24:4330-4335. [PMID: 38579181 PMCID: PMC11036382 DOI: 10.1021/acs.nanolett.3c04169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/07/2024]
Abstract
Liquid protein condensates play important roles in orchestrating subcellular organization and as biochemical reaction hubs. Recent studies have linked lipid membranes to proteins capable of forming liquid condensates, and shown that biophysical parameters, like protein enrichment and restricted diffusion at membranes, regulate condensate formation and size. However, the impact of membrane topography on liquid condensates remains poorly understood. Here, we devised a cell-free system to reconstitute liquid condensates on lipid membranes with microstructured topographies and demonstrated that lipid membrane topography is a significant biophysical regulator. Using membrane surfaces designed with microwells, we observed ordered condensate patterns. Furthermore, we demonstrate that membrane topographies influence the shape of liquid condensates. Finally, we show that capillary forces, mediated by membrane topographies, lead to the directed fusion of liquid condensates. Our results demonstrate that membrane topography is a potent biophysical regulator for the localization and shape of mesoscale liquid protein condensates.
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Affiliation(s)
- Chae Yeon Kang
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| | - Yoohyun Chang
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| | - Katja Zieske
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
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113
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Shiramasa Y, Yamamoto R, Kashiwagi N, Sasaki F, Imai S, Ike M, Kitazawa S, Kameda T, Kitahara R. An aberrant fused in sarcoma liquid droplet of amyotrophic lateral sclerosis pathological variant, R495X, accelerates liquid-solid phase transition. Sci Rep 2024; 14:8914. [PMID: 38632300 PMCID: PMC11024109 DOI: 10.1038/s41598-024-59604-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
Intracellular aggregation of fused in sarcoma (FUS) is associated with the pathogenesis of familial amyotrophic lateral sclerosis (ALS). Under stress, FUS forms liquid droplets via liquid-liquid phase separation (LLPS). Two types of wild-type FUS LLPS exist in equilibrium: low-pressure LLPS (LP-LLPS) and high-pressure LLPS (HP-LLPS); the former dominates below 2 kbar and the latter over 2 kbar. Although several disease-type FUS variants have been identified, the molecular mechanism underlying accelerated cytoplasmic granule formation in ALS patients remains poorly understood. Herein, we report the reversible formation of the two LLPS states and the irreversible liquid-solid transition, namely droplet aging, of the ALS patient-type FUS variant R495X using fluorescence microscopy and ultraviolet-visible absorption spectroscopy combined with perturbations in pressure and temperature. Liquid-to-solid phase transition was accelerated in the HP-LLPS of R495X than in the wild-type variant; arginine slowed the aging of droplets at atmospheric conditions by inhibiting the formation of HP-LLPS more selectively compared to that of LP-LLPS. Our findings provide new insight into the mechanism by which R495X readily forms cytoplasmic aggregates. Targeting the aberrantly formed liquid droplets (the HP-LLPS state) of proteins with minimal impact on physiological functions could be a novel therapeutic strategy for LLPS-mediated protein diseases.
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Affiliation(s)
- Yutaro Shiramasa
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Ryu Yamamoto
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Norika Kashiwagi
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Fuka Sasaki
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Sawaka Imai
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Mikihito Ike
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ryo Kitahara
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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114
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Song Y. Liquid-liquid phase separation-inspired design of biomaterials. Biomater Sci 2024; 12:1943-1949. [PMID: 38465963 DOI: 10.1039/d3bm02008h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Liquid-liquid phase separation (LLPS) is a crucial biological process that governs biomolecular condensation, assembly, and functionality within phase-separated aqueous environments. This phenomenon serves as a source of inspiration for the creation of artificial designs in both structured and functional biomaterials, presenting novel strategies for manipulating the structures of functional protein aggregates in a wide range of biomedical applications. This mini review summarizes my past research endeavors, offering a panoramic overview of LLPS-inspired biomaterials utilized in the design of structured materials, the development of cell mimetics, and the advancement of intelligent biomaterials.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Metal Matrix Composites, School of Material Science & Engineering, Shanghai Jiao Tong University, China.
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115
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Lee M, Moon HC, Jeong H, Kim DW, Park HY, Shin Y. Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions. Nat Commun 2024; 15:3216. [PMID: 38622120 PMCID: PMC11018775 DOI: 10.1038/s41467-024-47442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Biomolecular condensates, often assembled through phase transition mechanisms, play key roles in organizing diverse cellular activities. The material properties of condensates, ranging from liquid droplets to solid-like glasses or gels, are key features impacting the way resident components associate with one another. However, it remains unclear whether and how different material properties would influence specific cellular functions of condensates. Here, we combine optogenetic control of phase separation with single-molecule mRNA imaging to study relations between phase behaviors and functional performance of condensates. Using light-activated condensation, we show that sequestering target mRNAs into condensates causes translation inhibition. Orthogonal mRNA imaging reveals highly transient nature of interactions between individual mRNAs and condensates. Tuning condensate composition and material property towards more solid-like states leads to stronger translational repression, concomitant with a decrease in molecular mobility. We further demonstrate that β-actin mRNA sequestration in neurons suppresses spine enlargement during chemically induced long-term potentiation. Our work highlights how the material properties of condensates can modulate functions, a mechanism that may play a role in fine-tuning the output of condensate-driven cellular activities.
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Affiliation(s)
- Min Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Hyungseok C Moon
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hyeonjeong Jeong
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, USA
| | - Dong Wook Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea.
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, USA.
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea.
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea.
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116
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Hoang Y, Azaldegui CA, Dow RE, Ghalmi M, Biteen JS, Vecchiarelli AG. An experimental framework to assess biomolecular condensates in bacteria. Nat Commun 2024; 15:3222. [PMID: 38622124 PMCID: PMC11018776 DOI: 10.1038/s41467-024-47330-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
High-resolution imaging of biomolecular condensates in living cells is essential for correlating their properties to those observed through in vitro assays. However, such experiments are limited in bacteria due to resolution limitations. Here we present an experimental framework that probes the formation, reversibility, and dynamics of condensate-forming proteins in Escherichia coli as a means to determine the nature of biomolecular condensates in bacteria. We demonstrate that condensates form after passing a threshold concentration, maintain a soluble fraction, dissolve upon shifts in temperature and concentration, and exhibit dynamics consistent with internal rearrangement and exchange between condensed and soluble fractions. We also discover that an established marker for insoluble protein aggregates, IbpA, has different colocalization patterns with bacterial condensates and aggregates, demonstrating its potential applicability as a reporter to differentiate the two in vivo. Overall, this framework provides a generalizable, accessible, and rigorous set of experiments to probe the nature of biomolecular condensates on the sub-micron scale in bacterial cells.
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Affiliation(s)
- Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Rachel E Dow
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Julie S Biteen
- Doctoral Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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117
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Chen D, Shi C, Xu W, Rong Q, Wu Q. Regulation of phase separation and antiviral activity of Cactin by glycolytic enzyme PGK via phosphorylation in Drosophila. mBio 2024; 15:e0137823. [PMID: 38446061 PMCID: PMC11005415 DOI: 10.1128/mbio.01378-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) plays a crucial role in various biological processes in eukaryotic organisms, including immune responses in mammals. However, the specific function of LLPS in immune responses in Drosophila melanogaster remains poorly understood. Cactin, a highly conserved protein in eukaryotes, is involved in a non-canonical signaling pathway associated with Nuclear factor-κB (NF-κB)-related pathways in Drosophila. In this study, we investigated the role of Cactin in LLPS and its implications for immune response modulation. We discovered that Cactin undergoes LLPS, forming droplet-like particles, primarily mediated by its intrinsically disordered region (IDR). Utilizing immunoprecipitation and mass spectrometry analysis, we identified two phosphorylation sites at serine residues 99 and 104 within the IDR1 domain of Cactin. Co-immunoprecipitation and mass spectrometry further revealed phosphoglycerate kinase (PGK) as a Cactin-interacting protein responsible for regulating its phosphorylation. Phosphorylation of Cactin by PGK induced a transition from stable aggregates to dynamic liquid droplets, enhancing its ability to interact with other components in the cellular environment. Overexpression of PGK inhibited Drosophila C virus (DCV) replication, while PGK knockdown increased replication. DCV infection also increased Cactin phosphorylation. We also found that phosphorylation enhances the antiviral ability of Cactin by promoting liquid-phase droplet formation. These findings demonstrate the role of Cactin-phase separation in regulating DCV replication and highlight the modulation of its antiviral function through phosphorylation, providing insights into the interplay between LLPS and antiviral defense mechanisms. IMPORTANCE Liquid-liquid phase separation (LLPS) plays an integral role in various biological processes in eukaryotic organisms. Although several studies have highlighted its crucial role in modulating immune responses in mammals, its function in immune responses in Drosophila melanogaster remains poorly understood. Our study investigated the role of Cactin in LLPS and its implications for immune response modulation. We identified that phosphoglycerate kinase (PGK), an essential enzyme in the glycolytic pathway, phosphorylates Cactin, facilitating its transition from a relatively stable aggregated state to a more dynamic liquid droplet phase during the phase separation process. This transformation allows Cactin to rapidly interact with other cellular components, enhancing its antiviral properties and ultimately inhibiting virus replication. These findings expand our understanding of the role of LLPS in the antiviral defense mechanism, shedding light on the intricate mechanisms underlying immune responses in D. melanogaster.
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Affiliation(s)
- Dongchao Chen
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
| | - Chang Shi
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
| | - Wen Xu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiqi Rong
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingfa Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Precision Pharmaceutical Preparations and Clinical Pharmacy, Hefei, Anhui, China
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118
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Wilcox K, Yamagami KR, Roopnarine BK, Linscott A, Morozova S. Effect of Polymer Gel Elasticity on Complex Coacervate Phase Behavior. ACS POLYMERS AU 2024; 4:109-119. [PMID: 38618006 PMCID: PMC11010254 DOI: 10.1021/acspolymersau.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 04/16/2024]
Abstract
Gels are key materials in biological systems such as tissues and may control biocondensate formation and structure. To further understand the effects of elastic environments on biomacromolecular assembly, we have investigated the phase behavior and radii of complex coacervate droplets in polyacrylamide (PAM) networks as a function of gel modulus. Poly-l-lysine (PLL) and sodium hyaluronate (HA) complex coacervate phases were prepared in PAM gels with moduli varying from 0.035 to 15.0 kPa. The size of the complex coacervate droplets is reported from bright-field microscopy and confocal fluorescence microscopy. Overall, the complex coacervate droplet volume decreases inversely with the modulus. Fluorescence microscopy is also used to determine the phase behavior and concentration of fluorescently tagged HA in the complex coacervate phases as a function of ionic strength (100-270 mM). We find that the critical ionic strength and complex coacervate stability are nonmonotonic as a function of the network modulus and that the local gel concentration can be used to control phase behavior and complex coacervate droplet size scale. By understanding how elastic environments influence simple electrostatic assembly, we can further understand how biomacromolecules exist in complex, crowded, and elastic cellular environments.
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Affiliation(s)
- Kathryn
G. Wilcox
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Kai R. Yamagami
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Brittany K. Roopnarine
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Adam Linscott
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Svetlana Morozova
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
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119
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Zhang Q, Lin Z, Du X, Zhou Z. Liquid-Liquid Phase Separation within Dense-Core Vesicles in Sympathetic Adrenal Chromaffin Cells. Neurosci Bull 2024:10.1007/s12264-024-01201-6. [PMID: 38589711 DOI: 10.1007/s12264-024-01201-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/02/2024] [Indexed: 04/10/2024] Open
Affiliation(s)
- Quanfeng Zhang
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Beijing, 100871, China.
| | - Zhaohan Lin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Beijing, 100871, China
| | - Xinyu Du
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Beijing, 100871, China
| | - Zhuan Zhou
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China.
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
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120
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Sun X, Zhou Y, Wang Z, Peng M, Wei X, Xie Y, Wen C, Liu J, Ye M. Biomolecular Condensates Decipher Molecular Codes of Cell Fate: From Biophysical Fundamentals to Therapeutic Practices. Int J Mol Sci 2024; 25:4127. [PMID: 38612940 PMCID: PMC11012904 DOI: 10.3390/ijms25074127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Cell fate is precisely modulated by complex but well-tuned molecular signaling networks, whose spatial and temporal dysregulation commonly leads to hazardous diseases. Biomolecular condensates (BCs), as a newly emerging type of biophysical assemblies, decipher the molecular codes bridging molecular behaviors, signaling axes, and clinical prognosis. Particularly, physical traits of BCs play an important role; however, a panoramic view from this perspective toward clinical practices remains lacking. In this review, we describe the most typical five physical traits of BCs, and comprehensively summarize their roles in molecular signaling axes and corresponding major determinants. Moreover, establishing the recent observed contribution of condensate physics on clinical therapeutics, we illustrate next-generation medical strategies by targeting condensate physics. Finally, the challenges and opportunities for future medical development along with the rapid scientific and technological advances are highlighted.
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Affiliation(s)
- Xing Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Yangyang Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Zhiyan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Menglan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Xianhua Wei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Yifang Xie
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Chengcai Wen
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
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121
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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122
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Borne V, Weiss M. Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos. Biophys J 2024:S0006-3495(24)00243-1. [PMID: 38576160 DOI: 10.1016/j.bpj.2024.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024] Open
Abstract
Early embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell-division timing and the subsequent mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo without breaking its eggshell. Compressing embryos to about two-thirds of their unperturbed diameter only resulted in markedly slower cell divisions. In contrast, compressing embryos to half of their native diameter frequently resulted in a loss of cytokinesis, yielding a non-natural syncytium that still allowed for multiple divisions of nuclei. Although the orientation of mitotic axes was strongly altered in the syncytium, key features of division timing and spatial arrangement of nuclei remained surprisingly similar to those of unperturbed embryos in the first few division cycles. This suggests that few, very robust mechanisms provide a basic and resilient program for safeguarding the early embryogenesis of C. elegans.
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Affiliation(s)
- Vincent Borne
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, Bayreuth, Germany.
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123
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Su J, Xu X, Cseke LJ, Whittier S, Zhou R, Zhang Z, Dietz Z, Singh K, Yang B, Chen SY, Picking W, Zou X, Gassmann W. Cell-specific polymerization-driven biomolecular condensate formation fine-tunes root tissue morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587845. [PMID: 38617336 PMCID: PMC11014531 DOI: 10.1101/2024.04.02.587845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Formation of biomolecular condensates can be driven by weak multivalent interactions and emergent polymerization. However, the mechanism of polymerization-mediated condensate formation is less studied. We found lateral root cap cell (LRC)-specific SUPPRESSOR OF RPS4-RLD1 (SRFR1) condensates fine-tune primary root development. Polymerization of the SRFR1 N-terminal domain is required for both LRC condensate formation and optimal root growth. Surprisingly, the first intrinsically disordered region (IDR1) of SRFR1 can be functionally substituted by a specific group of intrinsically disordered proteins known as dehydrins. This finding facilitated the identification of functional segments in the IDR1 of SRFR1, a generalizable strategy to decode unknown IDRs. With this functional information we further improved root growth by modifying the SRFR1 condensation module, providing a strategy to improve plant growth and resilience.
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124
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Wilhelm KB, Vissa A, Groves JT. Differential Roles of Kinetic On- and Off-Rates in T-Cell Receptor Signal Integration Revealed with a Modified Fab'-DNA Ligand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587588. [PMID: 38617215 PMCID: PMC11014569 DOI: 10.1101/2024.04.01.587588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly-binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide-MHC (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab'-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rate of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells (LAT), which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from synthetic ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.
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Affiliation(s)
- Kiera B Wilhelm
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| | - Anand Vissa
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| | - Jay T Groves
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
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125
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Wu ZP, Bloom KS, Forest MG, Cao XZ. Transient crosslinking controls the condensate formation pathway within chromatin networks. Phys Rev E 2024; 109:L042401. [PMID: 38755828 PMCID: PMC11137846 DOI: 10.1103/physreve.109.l042401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
The network structure of densely packed chromatin within the nucleus of eukaryotic cells acts in concert with nonequilibrium processes. Using statistical physics simulations, we explore the control provided by transient crosslinking of the chromatin network by structural-maintenance-of-chromosome (SMC) proteins over (i) the physical properties of the chromatin network and (ii) condensate formation of embedded molecular species. We find that the density and lifetime of transient SMC crosslinks regulate structural relaxation modes and tune the sol-vs-gel state of the chromatin network, which imparts control over the kinetic pathway to condensate formation. Specifically, lower density, shorter-lived crosslinks induce sollike networks and a droplet-fusion pathway, whereas higher density, longer-lived crosslinks induce gellike networks and an Ostwald-ripening pathway.
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Affiliation(s)
- Zong-Pei Wu
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - M. Gregory Forest
- Departments of Mathematics, Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xue-Zheng Cao
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
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126
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Hernandez-Candia CN, Brady BR, Harrison E, Tucker CL. A platform to induce and mature biomolecular condensates using chemicals and light. Nat Chem Biol 2024; 20:452-462. [PMID: 38191942 PMCID: PMC10978248 DOI: 10.1038/s41589-023-01520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Biomolecular condensates are membraneless compartments that impart spatial and temporal organization to cells. Condensates can undergo maturation, transitioning from dynamic liquid-like states into solid-like states associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Huntington's disease. Despite their important roles, many aspects of condensate biology remain incompletely understood, requiring tools for acutely manipulating condensate-relevant processes within cells. Here we used the BCL6 BTB domain and its ligands BI-3802 and BI-3812 to create a chemical genetic platform, BTBolig, allowing inducible condensate formation and dissolution. We also developed optogenetic and chemical methods for controlled induction of condensate maturation, where we surprisingly observed recruitment of chaperones into the condensate core and formation of dynamic biphasic condensates. Our work provides insights into the interaction of condensates with proteostasis pathways and introduces a suite of chemical-genetic approaches to probe the role of biomolecular condensates in health and disease.
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Affiliation(s)
| | - Brian R Brady
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Evan Harrison
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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127
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Meier SM, Steinmetz MO, Barral Y. Microtubule specialization by +TIP networks: from mechanisms to functional implications. Trends Biochem Sci 2024; 49:318-332. [PMID: 38350804 DOI: 10.1016/j.tibs.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
To fulfill their actual cellular role, individual microtubules become functionally specialized through a broad range of mechanisms. The 'search and capture' model posits that microtubule dynamics and functions are specified by cellular targets that they capture (i.e., a posteriori), independently of the microtubule-organizing center (MTOC) they emerge from. However, work in budding yeast indicates that MTOCs may impart a functional identity to the microtubules they nucleate, a priori. Key effectors in this process are microtubule plus-end tracking proteins (+TIPs), which track microtubule tips to regulate their dynamics and facilitate their targeted interactions. In this review, we discuss potential mechanisms of a priori microtubule specialization, focusing on recent findings indicating that +TIP networks may undergo liquid biomolecular condensation in different cell types.
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Affiliation(s)
- Sandro M Meier
- Institute of Biochemistry, Department of Biology, and Bringing Materials to Life Initiative, ETH Zürich, Switzerland; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland; Bringing Materials to Life Initiative, ETH Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland; University of Basel, Biozentrum, CH-4056 Basel, Switzerland.
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, and Bringing Materials to Life Initiative, ETH Zürich, Switzerland; Bringing Materials to Life Initiative, ETH Zürich, Switzerland.
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128
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Ryu K, Park G, Cho WK. Emerging insights into transcriptional condensates. Exp Mol Med 2024; 56:820-826. [PMID: 38658705 PMCID: PMC11059374 DOI: 10.1038/s12276-024-01228-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Eukaryotic transcription, a fundamental process that governs cell-specific gene expression, has long been the subject of extensive investigations in the fields of molecular biology, biochemistry, and structural biology. Recent advances in microscopy techniques have led to a fascinating concept known as "transcriptional condensates." These dynamic assemblies are the result of a phenomenon called liquid‒liquid phase separation, which is driven by multivalent interactions between the constituent proteins in cells. The essential proteins associated with transcription are concentrated in transcriptional condensates. Recent studies have shed light on the temporal dynamics of transcriptional condensates and their potential role in enhancing the efficiency of transcription. In this article, we explore the properties of transcriptional condensates, investigate how they evolve over time, and evaluate the significant impact they have on the process of transcription. Furthermore, we highlight innovative techniques that allow us to manipulate these condensates, thus demonstrating their responsiveness to cellular signals and their connection to transcriptional bursting. As our understanding of transcriptional condensates continues to grow, they are poised to revolutionize our understanding of eukaryotic gene regulation.
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Affiliation(s)
- Kwangmin Ryu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Gunhee Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Won-Ki Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
- KAIST Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
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129
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Guo D, Xiong Y, Fu B, Sha Z, Li B, Wu H. Liquid-Liquid phase separation in bacteria. Microbiol Res 2024; 281:127627. [PMID: 38262205 DOI: 10.1016/j.micres.2024.127627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Cells are the essential building blocks of living organisms, responsible for carrying out various biochemical reactions and performing specific functions. In eukaryotic cells, numerous membrane organelles have evolved to facilitate these processes by providing specific spatial locations. In recent years, it has also been discovered that membraneless organelles play a crucial role in the subcellular organization of bacteria, which are single-celled prokaryotic microorganisms characterized by their simple structure and small size. These membraneless organelles in bacteria have been found to undergo Liquid-Liquid phase separation (LLPS), a molecular mechanism that allows for their assembly. Through extensive research, the occurrence of LLPS and its role in the spatial organization of bacteria have been better understood. Various biomacromolecules have been identified to exhibit LLPS properties in different bacterial species. LLPS which is introduced into synthetic biology applies to bacteria has important implications, and three recent research reports have shed light on its potential applications in this field. Overall, this review investigates the molecular mechanisms of LLPS occurrence and its significance in bacteria while also considering the future prospects of implementing LLPS in synthetic biology.
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Affiliation(s)
- Dong Guo
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhou Sha
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Bohao Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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130
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Ye S, Latham AP, Tang Y, Hsiung CH, Chen J, Luo F, Liu Y, Zhang B, Zhang X. Micropolarity governs the structural organization of biomolecular condensates. Nat Chem Biol 2024; 20:443-451. [PMID: 37973891 PMCID: PMC10978266 DOI: 10.1038/s41589-023-01477-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023]
Abstract
Membraneless organelles within cells have unique microenvironments that play a critical role in their functions. However, how microenvironments of biomolecular condensates affect their structure and function remains unknown. In this study, we investigated the micropolarity and microviscosity of model biomolecular condensates by fluorescence lifetime imaging coupling with environmentally sensitive fluorophores. Using both in vitro and in cellulo systems, we demonstrated that sufficient micropolarity difference is key to forming multilayered condensates, where the shells present more polar microenvironments than the cores. Furthermore, micropolarity changes were shown to be accompanied by conversions of the layered structures. Decreased micropolarities of the granular components, accompanied by the increased micropolarities of the dense fibrillar components, result in the relocation of different nucleolus subcompartments in transcription-stalled conditions. Our results demonstrate the central role of the previously overlooked micropolarity in the regulation of structures and functions of membraneless organelles.
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Affiliation(s)
- Songtao Ye
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Yuqi Tang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chia-Heng Hsiung
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Junlin Chen
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Feng Luo
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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131
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Valyaeva AA, Sheval EV. Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:688-700. [PMID: 38831505 DOI: 10.1134/s0006297924040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 06/05/2024]
Abstract
Eukaryotic cells are characterized by a high degree of compartmentalization of their internal contents, which ensures precise and controlled regulation of intracellular processes. During many processes, including different stages of transcription, dynamic membraneless compartments termed biomolecular condensates are formed. Transcription condensates contain various transcription factors and RNA polymerase and are formed by high- and low-specificity interactions between the proteins, DNA, and nearby RNA. This review discusses recent data demonstrating important role of nonspecific multivalent protein-protein and RNA-protein interactions in organization and regulation of transcription.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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132
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Zhang Q, Ye H, Liu C, Zhou H, He M, Liang X, Zhou Y, Wang K, Qin Y, Li Z, Chen M. PABP-driven secondary condensed phase within RSV inclusion bodies activates viral mRNAs for ribosomal recruitment. Virol Sin 2024; 39:235-250. [PMID: 38072230 PMCID: PMC11074649 DOI: 10.1016/j.virs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024] Open
Abstract
Inclusion bodies (IBs) of respiratory syncytial virus (RSV) are formed by liquid-liquid phase separation (LLPS) and contain internal structures termed "IB-associated granules" (IBAGs), where anti-termination factor M2-1 and viral mRNAs are concentrated. However, the mechanism of IBAG formation and the physiological function of IBAGs are unclear. Here, we found that the internal structures of RSV IBs are actual M2-1-free viral messenger ribonucleoprotein (mRNP) condensates formed by secondary LLPS. Mechanistically, the RSV nucleoprotein (N) and M2-1 interact with and recruit PABP to IBs, promoting PABP to bind viral mRNAs transcribed in IBs by RNA-recognition motif and drive secondary phase separation. Furthermore, PABP-eIF4G1 interaction regulates viral mRNP condensate composition, thereby recruiting specific translation initiation factors (eIF4G1, eIF4E, eIF4A, eIF4B and eIF4H) into the secondary condensed phase to activate viral mRNAs for ribosomal recruitment. Our study proposes a novel LLPS-regulated translation mechanism during viral infection and a novel antiviral strategy via targeting on secondary condensed phase.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanzhe Ye
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Cong Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haiwu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mingbin He
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaodong Liang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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133
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Liang P, Wu Y, Zheng S, Zhang J, Yang S, Wang J, Ma S, Zhang M, Gu Z, Liu Q, Jiang W, Xing Q, Wang B. Paxillin phase separation promotes focal adhesion assembly and integrin signaling. J Cell Biol 2024; 223:e202209027. [PMID: 38466167 PMCID: PMC10926639 DOI: 10.1083/jcb.202209027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/04/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2024] Open
Abstract
Focal adhesions (FAs) are transmembrane protein assemblies mediating cell-matrix connection. Although protein liquid-liquid phase separation (LLPS) has been tied to the organization and dynamics of FAs, the underlying mechanisms remain unclear. Here, we experimentally tune the LLPS of PXN/Paxillin, an essential scaffold protein of FAs, by utilizing a light-inducible Cry2 system in different cell types. In addition to nucleating FA components, light-triggered PXN LLPS potently activates integrin signaling and subsequently accelerates cell spreading. In contrast to the homotypic interaction-driven LLPS of PXN in vitro, PXN condensates in cells are associated with the plasma membrane and modulated by actomyosin contraction and client proteins of FAs. Interestingly, non-specific weak intermolecular interactions synergize with specific molecular interactions to mediate the multicomponent condensation of PXN and are efficient in promoting FA assembly and integrin signaling. Thus, our data establish an active role of the PXN phase transition into a condensed membrane-associated compartment in promoting the assembly/maturation of FAs.
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Affiliation(s)
- Peigang Liang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchen Wu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanyuan Zheng
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiaqi Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuo Yang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinfang Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Suibin Ma
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mengjun Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhuang Gu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingfeng Liu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenxue Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qiong Xing
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
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134
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Furuki T, Nobeyama T, Suetaka S, Matsui R, Fukuoka T, Arai M, Shiraki K. Reentrant condensation of a multicomponent cola/milk system induced by polyphosphate. Food Chem X 2024; 21:101165. [PMID: 38328695 PMCID: PMC10847600 DOI: 10.1016/j.fochx.2024.101165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
Reentrant condensation (RC) is a protein behavior in which the protein solution shifts between the one- and two-phase state more than twice by increasing a single parameter. Although RC would be a candidate mechanism for the physicochemical design of food additives, no realistic model has been established under diverse contaminants like food materials. Here, we found that a mixture of cola and milk yielded RC. At pH 3.2-3.6, cola induced milk condensation at 30-40%, while lower or higher concentrations of cola did not. Furthermore, we reduced this cola/milk system to two pure components, casein in milk and polyphosphate (polyP) in cola, and investigated the characteristics of casein concentration and zeta potential. This was the first experimental demonstration of RC occurrence in a multicomponent system. The well-characterized cola/milk system would explore both the universal nature of proteins and the industrial application of RC.
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Affiliation(s)
- Tomohiro Furuki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Ishikawa Prefectural Nanao High School, E-1-1 Nishi-fujihashi, Nanao, Ishikawa 926-0817, Japan
| | - Tomohiro Nobeyama
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Shunji Suetaka
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Ryokei Matsui
- Ishikawa Prefectural Nanao High School, E-1-1 Nishi-fujihashi, Nanao, Ishikawa 926-0817, Japan
| | - Tatsuhiko Fukuoka
- Ishikawa Prefectural Nanao High School, E-1-1 Nishi-fujihashi, Nanao, Ishikawa 926-0817, Japan
| | - Munehito Arai
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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135
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Ma M, Duan Y, Peng C, Wu Y, Zhang X, Chang B, Wang F, Yang H, Zheng R, Cheng H, Cheng Y, He Y, Huang J, Lei J, Ma H, Li L, Wang J, Huang X, Tang F, Liu J, Li J, Ying R, Wang P, Sha W, Gao Y, Wang L, Ge B. Mycobacterium tuberculosis inhibits METTL14-mediated m 6A methylation of Nox2 mRNA and suppresses anti-TB immunity. Cell Discov 2024; 10:36. [PMID: 38548762 PMCID: PMC10978938 DOI: 10.1038/s41421-024-00653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/29/2024] [Indexed: 04/01/2024] Open
Abstract
Internal N6-methyladenosine (m6A) modifications are among the most abundant modifications of messenger RNA, playing a critical role in diverse biological and pathological processes. However, the functional role and regulatory mechanism of m6A modifications in the immune response to Mycobacterium tuberculosis infection remains unknown. Here, we report that methyltransferase-like 14 (METTL14)-dependent m6A methylation of NAPDH oxidase 2 (Nox2) mRNA was crucial for the host immune defense against M. tuberculosis infection and that M. tuberculosis-secreted antigen EsxB (Rv3874) inhibited METTL14-dependent m6A methylation of Nox2 mRNA. Mechanistically, EsxB interacted with p38 MAP kinase and disrupted the association of TAB1 with p38, thus inhibiting the TAB1-mediated autophosphorylation of p38. Interaction of EsxB with p38 also impeded the binding of p38 with METTL14, thereby inhibiting the p38-mediated phosphorylation of METTL14 at Thr72. Inhibition of p38 by EsxB restrained liquid-liquid phase separation (LLPS) of METTL14 and its subsequent interaction with METTL3, preventing the m6A modification of Nox2 mRNA and its association with the m6A-binding protein IGF2BP1 to destabilize Nox2 mRNA, reduce ROS levels, and increase intracellular survival of M. tuberculosis. Moreover, deletion or mutation of the phosphorylation site on METTL14 impaired the inhibition of ROS level by EsxB and increased bacterial burden or histological damage in the lungs during infection in mice. These findings identify a previously unknown mechanism that M. tuberculosis employs to suppress host immunity, providing insights that may empower the development of effective immunomodulators that target M. tuberculosis.
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Affiliation(s)
- Mingtong Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yongjia Duan
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Cheng Peng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - You Wu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinning Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Boran Chang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Hongyu Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yuanna Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yifan He
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jingping Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jinming Lei
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hanyu Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Liru Li
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Fen Tang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ruoyan Ying
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Wang
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Lin Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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137
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Sun J, Qu J, Zhao C, Zhang X, Liu X, Wang J, Wei C, Liu X, Wang M, Zeng P, Tang X, Ling X, Qing L, Jiang S, Chen J, Chen TSR, Kuang Y, Gao J, Zeng X, Huang D, Yuan Y, Fan L, Yu H, Ding J. Precise prediction of phase-separation key residues by machine learning. Nat Commun 2024; 15:2662. [PMID: 38531854 DOI: 10.1038/s41467-024-46901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.
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Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiale Qu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cai Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyao Zhang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mulan Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoru Ling
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiahao Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tara S R Chen
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yalan Kuang
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Jinhang Gao
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Dongfeng Huang
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Junjun Ding
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
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138
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Jia L, Gao S, Qiao Y. Optical Control over Liquid–Liquid Phase Separation. SMALL METHODS 2024:e2301724. [PMID: 38530063 DOI: 10.1002/smtd.202301724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/12/2024] [Indexed: 03/27/2024]
Abstract
Liquid-liquid phase separation (LLPS) is responsible for the emergence of intracellular membrane-less organelles and the development of coacervate protocells. Benefitting from the advantages of simplicity, precision, programmability, and noninvasiveness, light has become an effective tool to regulate the assembly dynamics of LLPS, and mediate various biochemical processes associated with LLPS. In this review, recent advances in optically controlling membrane-less organelles within living organisms are summarized, thereby modulating a series of biological processes including irreversible protein aggregation pathologies, transcription activation, metabolic flux, genomic rearrangements, and enzymatic reactions. Among these, the intracellular systems (i.e., optoDroplet, Corelet, PixELL, CasDrop, and other optogenetic systems) that enable the photo-mediated control over biomolecular condensation are highlighted. The design of photoactive complex coacervate protocells in laboratory settings by utilizing photochromic molecules such as azobenzene and diarylethene is further discussed. This review is expected to provide in-depth insights into phase separation-associated biochemical processes, bio-metabolism, and diseases.
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Affiliation(s)
- Liyan Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Gao
- Department of Orthopedic, Peking University Third Hospital, Beijing, 100191, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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139
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Meng L, Mao S, Lin J. Heterogeneous elasticity drives ripening and controls bursting kinetics of transcriptional condensates. Proc Natl Acad Sci U S A 2024; 121:e2316610121. [PMID: 38489385 PMCID: PMC10962985 DOI: 10.1073/pnas.2316610121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/10/2024] [Indexed: 03/17/2024] Open
Abstract
Many biomolecular condensates, including transcriptional condensates, are formed in elastic mediums. In this work, we study the nonequilibrium condensate dynamics in a chromatin-like environment modeled as a heterogeneous elastic medium. We demonstrate that the ripening process in such an elastic medium exhibits a temporal power-law scaling of the average condensate radius, depending on the local stiffness distribution and different from Ostwald ripening. Moreover, we incorporate an active process to model the dissolution of transcriptional condensates upon RNA accumulation. Intriguingly, three types of kinetics of condensate growth emerge, corresponding to constitutively expressed, transcriptional-bursting, and silenced genes. Furthermore, the simulated burst frequency decreases exponentially with the local stiffness, through which we infer a lognormal distribution of local stiffness in living cells using the transcriptome-wide distribution of burst frequency. Under the inferred stiffness distribution, the simulated distributions of bursting kinetic parameters agree reasonably well with the experimental data. Our findings reveal the interplay between biomolecular condensates and elastic mediums, yielding far-reaching implications for gene expression.
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Affiliation(s)
- Lingyu Meng
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Sheng Mao
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing100871, China
| | - Jie Lin
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
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140
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Binti S, Linder AG, Edeen PT, Fay DS. A conserved protein tyrosine phosphatase, PTPN-22, functions in diverse developmental processes in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584557. [PMID: 38559252 PMCID: PMC10980042 DOI: 10.1101/2024.03.12.584557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein tyrosine phosphatases non-receptor type (PTPNs) have been studied extensively in the context of the adaptive immune system; however, their roles beyond immunoregulation are less well explored. Here we identify novel functions for the conserved C. elegans phosphatase PTPN-22, establishing its role in nematode molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppressed molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases NEKL-2 (human NEK8/NEK9) and NEKL-3 (human NEK6/NEK7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22, we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22. Consistent with this interaction, loss of DNBP-1 also suppressed nekl-associated molting defects. Genetic analysis, co-localization studies, and proximity labeling revealed roles for PTPN-22 in several epidermal adhesion complexes, including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one-third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, these studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - Adison G Linder
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - Philip T Edeen
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
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141
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Fisher AG. Cell and developmental biology: grand challenges. Front Cell Dev Biol 2024; 12:1377073. [PMID: 38559812 PMCID: PMC10978741 DOI: 10.3389/fcell.2024.1377073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Amanda G. Fisher
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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142
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Lujan P, Garcia-Cabau C, Wakana Y, Vera Lillo J, Rodilla-Ramírez C, Sugiura H, Malhotra V, Salvatella X, Garcia-Parajo MF, Campelo F. Sorting of secretory proteins at the trans-Golgi network by human TGN46. eLife 2024; 12:RP91708. [PMID: 38466628 DOI: 10.7554/elife.91708] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Secretory proteins are sorted at the trans-Golgi network (TGN) for export into specific transport carriers. However, the molecular players involved in this fundamental process remain largely elusive. Here, we identified the human transmembrane protein TGN46 as a receptor for the export of secretory cargo protein PAUF in CARTS - a class of protein kinase D-dependent TGN-to-plasma membrane carriers. We show that TGN46 is necessary for cargo sorting and loading into nascent carriers at the TGN. By combining quantitative fluorescence microscopy and mutagenesis approaches, we further discovered that the lumenal domain of TGN46 encodes for its cargo sorting function. In summary, our results define a cellular function of TGN46 in sorting secretory proteins for export from the TGN.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yuichi Wakana
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Javier Vera Lillo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carmen Rodilla-Ramírez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hideaki Sugiura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vivek Malhotra
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
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143
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Hou S, Hu J, Yu Z, Li D, Liu C, Zhang Y. Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions. Nat Commun 2024; 15:2147. [PMID: 38459060 PMCID: PMC10923898 DOI: 10.1038/s41467-024-46445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
The burgeoning comprehension of protein phase separation (PS) has ushered in a wealth of bioinformatics tools for the prediction of phase-separating proteins (PSPs). These tools often skew towards PSPs with a high content of intrinsically disordered regions (IDRs), thus frequently undervaluing potential PSPs without IDRs. Nonetheless, PS is not only steered by IDRs but also by the structured modular domains and interactions that aren't necessarily reflected in amino acid sequences. In this work, we introduce PSPire, a machine learning predictor that incorporates both residue-level and structure-level features for the precise prediction of PSPs. Compared to current PSP predictors, PSPire shows a notable improvement in identifying PSPs without IDRs, which underscores the crucial role of non-IDR, structure-based characteristics in multivalent interactions throughout the PS process. Additionally, our biological validation experiments substantiate the predictive capacity of PSPire, with 9 out of 11 chosen candidate PSPs confirmed to form condensates within cells.
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Affiliation(s)
- Shuang Hou
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhaowei Yu
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yong Zhang
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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144
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de Vries T, Novakovic M, Ni Y, Smok I, Inghelram C, Bikaki M, Sarnowski CP, Han Y, Emmanouilidis L, Padroni G, Leitner A, Allain FHT. Specific protein-RNA interactions are mostly preserved in biomolecular condensates. SCIENCE ADVANCES 2024; 10:eadm7435. [PMID: 38446881 PMCID: PMC10917357 DOI: 10.1126/sciadv.adm7435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
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Affiliation(s)
- Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Yinan Ni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Clara Inghelram
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Chris P. Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yaning Han
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Giacomo Padroni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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145
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Pemberton JG, Tenkova T, Felgner P, Zimmerberg J, Balla T, Heuser J. Defining the EM-signature of successful cell-transfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583927. [PMID: 38496608 PMCID: PMC10942431 DOI: 10.1101/2024.03.07.583927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent structural changes after they have entered cells, changes that not only provide new insights into the mechanism of action of these particular transfection-reagents, but also provide a convenient and robust method for identifying by EM which cells in any culture have been successfully transfected. This also provides clues to the mechanism(s) of their toxic effects, when they are applied in excess. We demonstrate that after being bulk-endocytosed by cells, the cationic spheroids of Lipofectamine remain intact throughout the entire time of culturing, but escape from their endosomes and penetrate directly into the cytoplasm of the cell. In so doing, they provoke a stereotypical recruitment and rearrangement of endoplasmic reticulum (ER), and they ultimately end up escaping into the cytoplasm and forming unique 'inclusion-bodies.' Once free in the cytoplasm, they also invariably develop dense and uniform coatings of cytoplasmic ribosomes on their surfaces, and finally, they become surrounded by 'annulate' lamellae' of the ER. In the end, these annulate-lamellar enclosures become the ultrastructural 'signatures' of these inclusion-bodies, and serve to positively and definitively identify all cells that have been effectively transfected. Importantly, these new EM-observations define several new and unique properties of these classical Lipofectamines, and allow them to be discriminated from other lipoidal or particulate transfection-reagents, which we find do not physically break out of endosomes or end up in inclusion bodies, and in fact, provoke absolutely none of these 'signature' cytoplasmic reactions.
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146
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Ray S, Buell AK. Emerging experimental methods to study the thermodynamics of biomolecular condensate formation. J Chem Phys 2024; 160:091001. [PMID: 38445729 DOI: 10.1063/5.0190160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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147
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Dec R, Dzwolak W, Winter R. From a Droplet to a Fibril and from a Fibril to a Droplet: Intertwined Transition Pathways in Highly Dynamic Enzyme-Modulated Peptide-Adenosine Triphosphate Systems. J Am Chem Soc 2024; 146:6045-6052. [PMID: 38394622 DOI: 10.1021/jacs.3c13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Many cellular coassemblies of proteins and polynucleotides facilitate liquid-liquid phase separation (LLPS) and the subsequent self-assembly of disease-associated amyloid fibrils within the liquid droplets. Here, we explore the dynamics of coupled phase and conformational transitions of model adenosine triphosphate (ATP)-binding peptides, ACC1-13Kn, consisting of the potent amyloidogenic fragment of insulin's A-chain (ACC1-13) merged with oligolysine segments of various lengths (Kn, n = 16, 24, 40). The self-assembly of ATP-stabilized amyloid fibrils is preceded by LLPS for peptides with sufficiently long oligolysine segments. The two-component droplets and fibrils are in dynamic equilibria with free ATP and monomeric peptides, which makes them susceptible to ATP-hydrolyzing apyrase and ACC1-13Kn-digesting proteinase K. Both enzymes are capable of rapid disassembly of amyloid fibrils, producing either monomers of the peptide (apyrase) or free ATP released together with cleaved-off oligolysine segments (proteinase K). In the latter case, the enzyme-sequestered Kn segments form subsequent droplets with the co-released ATP, resulting in an unusual fibril-to-droplet transition. In support of the highly dynamic nature of the aggregate-monomer equilibria, addition of superstoichiometric amounts of free peptide to the ACC1-13Kn-ATP coaggregate causes its disassembly. Our results show that the droplet state is not merely an intermediate phase on the pathway to the amyloid aggregate but may also constitute the final phase of a complex amyloidogenic protein misfolding scenario rich in highly degraded protein fragments incompetent to transition again into fibrils.
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Affiliation(s)
- Robert Dec
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, Dortmund 44227, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, Warsaw 02-093, Poland
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, Dortmund 44227, Germany
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148
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Esteban-Hofer L, Emmanouilidis L, Yulikov M, Allain FHT, Jeschke G. Ensemble structure of the N-terminal domain (1-267) of FUS in a biomolecular condensate. Biophys J 2024; 123:538-554. [PMID: 38279531 PMCID: PMC10938082 DOI: 10.1016/j.bpj.2024.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/06/2023] [Accepted: 01/22/2024] [Indexed: 01/28/2024] Open
Abstract
Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π-sp2 interactions.
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Affiliation(s)
- Laura Esteban-Hofer
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Maxim Yulikov
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Gunnar Jeschke
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland.
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149
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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150
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Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain. Biopolymers 2024; 115:e23558. [PMID: 37399327 PMCID: PMC10831756 DOI: 10.1002/bip.23558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The well-known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA-binding protein, Fused in Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low-complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid-state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril structure (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C-terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site-specific. Simulations show that phosphorylation of residues within the fibril has a greater destabilization effect than residues that are outside the fibril region, which accords well with experiments. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular explanation.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Abhinaw Kumar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Mauro L Mugnai
- Institute for Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC, USA
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