1
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Zhu S, Shen Z, Wu X, Han W, Jia B, Lu W, Zhang M. Demixing is a default process for biological condensates formed via phase separation. Science 2024; 384:920-928. [PMID: 38781377 DOI: 10.1126/science.adj7066] [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: 07/11/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Excitatory and inhibitory synapses do not overlap even when formed on one submicron-sized dendritic protrusion. How excitatory and inhibitory postsynaptic cytomatrices or densities (e/iPSDs) are segregated is not understood. Broadly, why membraneless organelles are naturally segregated in cellular subcompartments is unclear. Using biochemical reconstitutions in vitro and in cells, we demonstrate that ePSDs and iPSDs spontaneously segregate into distinct condensed molecular assemblies through phase separation. Tagging iPSD scaffold gephyrin with a PSD-95 intrabody (dissociation constant ~4 nM) leads to mistargeting of gephyrin to ePSD condensates. Unexpectedly, formation of iPSD condensates forces the intrabody-tagged gephyrin out of ePSD condensates. Thus, instead of diffusion-governed spontaneous mixing, demixing is a default process for biomolecules in condensates. Phase separation can generate biomolecular compartmentalization specificities that cannot occur in dilute solutions.
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Affiliation(s)
- Shihan Zhu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zeyu Shen
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiandeng Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Wenyan Han
- Synapse and Neural Circuit Research Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824, USA
| | - Bowen Jia
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Wei Lu
- Synapse and Neural Circuit Research Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824, USA
| | - Mingjie Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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2
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Karger S, Miali ME, Solomonov A, Eliaz D, Varsano N, Shimanovich U. Protein Compartments Modulate Fibrillar Self-Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308069. [PMID: 38148317 DOI: 10.1002/smll.202308069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/04/2023] [Indexed: 12/28/2023]
Abstract
A notable feature of complex cellular environments is protein-rich compartments that are formed via liquid-liquid phase separation. Recent studies have shown that these biomolecular condensates can play both promoting and inhibitory roles in fibrillar protein self-assembly, a process that is linked to Alzheimer's, Parkinson's, Huntington's, and various prion diseases. Yet, the exact regulatory role of these condensates in protein aggregation remains unknown. By employing microfluidics to create artificial protein compartments, the self-assembly behavior of the fibrillar protein lysozyme within them can be characterized. It is observed that the volumetric parameters of protein-rich compartments can change the kinetics of protein self-assembly. Depending on the change in compartment parameters, the lysozyme fibrillation process either accelerated or decelerated. Furthermore, the results confirm that the volumetric parameters govern not only the nucleation and growth phases of the fibrillar aggregates but also affect the crosstalk between the protein-rich and protein-poor phases. The appearance of phase-separated compartments in the vicinity of natively folded protein complexes triggers their abrupt percolation into the compartments' core and further accelerates protein aggregation. Overall, the results of the study shed more light on the complex behavior and functions of protein-rich phases and, importantly, on their interaction with the surrounding environment.
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Affiliation(s)
- Shay Karger
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Marco E Miali
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Aleksei Solomonov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dror Eliaz
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ulyana Shimanovich
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
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3
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Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular determinants and signaling effects of PKA RIα phase separation. Mol Cell 2024; 84:1570-1584.e7. [PMID: 38537638 PMCID: PMC11031308 DOI: 10.1016/j.molcel.2024.03.002] [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: 02/21/2023] [Revised: 12/07/2023] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures proper cellular function. Liquid-liquid phase separation (LLPS) of the ubiquitous PKA regulatory subunit RIα promotes cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces, combined with the cAMP-induced unleashing of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence, drive RIα condensate formation in the cytosol of mammalian cells, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in forming a non-canonical R:C complex, which recruits active PKA-C to RIα condensates to maintain low basal PKA activity in the cytosol. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
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Affiliation(s)
- Julia C Hardy
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily H Pool
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica G H Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingrong Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daojia R Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Max Palay
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gerald Tan
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lisa Chen
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jaclyn L C Choi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ha Neul Lee
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stefan Strack
- Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Dong Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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4
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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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5
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Wan L, Zhu Y, Zhang W, Mu W. Recent advances in design and application of synthetic membraneless organelles. Biotechnol Adv 2024; 73:108355. [PMID: 38588907 DOI: 10.1016/j.biotechadv.2024.108355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
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6
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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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7
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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8
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Li P, Chen P, Qi F, Shi J, Zhu W, Li J, Zhang P, Xie H, Li L, Lei M, Ren X, Wang W, Zhang L, Xiang X, Zhang Y, Gao Z, Feng X, Du W, Liu X, Xia L, Liu BF, Li Y. High-throughput and proteome-wide discovery of endogenous biomolecular condensates. Nat Chem 2024:10.1038/s41557-024-01485-1. [PMID: 38499848 DOI: 10.1038/s41557-024-01485-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/23/2024] [Indexed: 03/20/2024]
Abstract
Phase separation inside mammalian cells regulates the formation of the biomolecular condensates that are related to gene expression, signalling, development and disease. However, a large population of endogenous condensates and their candidate phase-separating proteins have yet to be discovered in a quantitative and high-throughput manner. Here we demonstrate that endogenously expressed biomolecular condensates can be identified across a cell's proteome by sorting proteins across varying oligomeric states. We employ volumetric compression to modulate the concentrations of intracellular proteins and the degree of crowdedness, which are physical regulators of cellular biomolecular condensates. The changes in degree of the partition of proteins into condensates or phase separation led to varying oligomeric states of the proteins, which can be detected by coupling density gradient ultracentrifugation and quantitative mass spectrometry. In total, we identified 1,518 endogenous condensate proteins, of which 538 have not been reported before. Furthermore, we demonstrate that our strategy can identify condensate proteins that respond to specific biological processes.
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Affiliation(s)
- Pengjie Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Fukang Qi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jinyun Shi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wenjie Zhu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jiashuo Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Peng Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Han Xie
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Lina Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Mengcheng Lei
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xueqing Ren
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wenhui Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Liang Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xufu Xiang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yiwei Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zhaolong Gao
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Limin Xia
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
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9
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Unarta IC, Cao S, Goonetilleke EC, Niu J, Gellman SH, Huang X. Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. J Phys Chem B 2024; 128:2347-2359. [PMID: 38416758 PMCID: PMC11057999 DOI: 10.1021/acs.jpcb.3c08126] [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] [Indexed: 03/01/2024]
Abstract
Liquid-liquid phase separation mediated by proteins and/or nucleic acids is believed to underlie the formation of many distinct condensed phases, or membraneless organelles, within living cells. These condensates have been proposed to orchestrate a variety of important processes. Despite recent advances, the interactions that regulate the dynamics of molecules within a condensate remain poorly understood. We performed accumulated 564.7 μs all-atom molecular dynamics (MD) simulations (system size ∼200k atoms) of model condensates formed by a scaffold RNA oligomer and a scaffold peptide rich in arginine (Arg). These model condensates contained one of three possible guest peptides: the scaffold peptide itself or a variant in which six Arg residues were replaced by lysine (Lys) or asymmetric dimethyl arginine (ADMA). We found that the Arg-rich peptide can form the largest number of hydrogen bonds and bind the strongest to the scaffold RNA in the condensate, relative to the Lys- and ADMA-rich peptides. Our MD simulations also showed that the Arg-rich peptide diffused more slowly in the condensate relative to the other two guest peptides, which is consistent with a recent fluorescence microscopy study. There was no significant increase in the number of cation-π interactions between the Arg-rich peptide and the scaffold RNA compared to the Lys-rich and ADMA-rich peptides. Our results indicate that hydrogen bonds between the peptides and the RNA backbone, rather than cation-π interactions, play a major role in regulating peptide diffusion in the condensate.
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Affiliation(s)
- Ilona C. Unarta
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Siqin Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Eshani C. Goonetilleke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
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10
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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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11
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Man J, Zhang Q, Zhao T, Sun D, Sun W, Long K, Zhang Z. Oxidative Stress Induced by Arsenite is Involved in YTHDF2 Phase Separation. Biol Trace Elem Res 2024; 202:885-899. [PMID: 37310554 DOI: 10.1007/s12011-023-03728-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) undergoes phase separation in response to the stimulation of high concentration of arsenite, suggesting that oxidative stress, the major mechanism of arsenite toxicity, may play a role in YTHDF2 phase separation. However, whether arsenite-induced oxidative stress is involved in phase separation of YTHDF2 has yet to be established. To explore the effect of arsenite-induced oxidative stress on YTHDF2 phase separation, the levels of oxidative stress, YTHDF2 phase separation, and N6-methyladenosine (m6A) in human keratinocytes were detected after exposure to various concentrations of sodium arsenite (0-500 µM; 1 h) and antioxidant N-acetylcysteine (0-10 mM; 2 h). We found that arsenite promoted oxidative stress and YTHDF2 phase separation in a concentration-dependent manner. In contrast, pretreatment with N-acetylcysteine significantly relieved arsenate-induced oxidative stress and inhibited YTHDF2 phase separation. As one of the key factors to YTHDF2 phase separation, N6-methyladenosine (m6A) levels in human keratinocytes were significantly increased after arsenite exposure, accompanied by upregulation of m6A methylesterase levels and downregulation of m6A demethylases levels. On the contrary, N-acetylcysteine mitigated the arsenite-induced increase of m6A and m6A methylesterase and the arsenite-induced decrease in m6A demethylase. Collectively, our study firstly revealed that oxidative stress induced by arsenite plays an important role in YTHDF2 phase separation driven by m6A modification, which provides new insights into the arsenite toxicity from the phase-separation perspective.
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Affiliation(s)
- Jin Man
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Weilian Sun
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Keyan Long
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China.
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12
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Yan X, Zhang M, Wang D. Interplay between posttranslational modifications and liquid‒liquid phase separation in tumors. Cancer Lett 2024; 584:216614. [PMID: 38246226 DOI: 10.1016/j.canlet.2024.216614] [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: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a general phenomenon recently recognized to be critically involved in the regulation of a variety of cellular biological processes, such as transcriptional regulation, heterochromatin formation and signal transduction, through the compartmentalization of proteins or nucleic acids into droplet-like condensates. These processes are directly or indirectly related to tumor initiation and treatment. Posttranslational modifications (PTMs), which represent a rapid and reversible mechanism involved in the functional regulation of proteins, have emerged as key events in modulating LLPS under physiological or pathophysiological conditions, including tumorigenesis and antitumor therapy. In this review, we introduce the biological functions participated in cancer-associated LLPS, discuss the potential roles of LLPS during tumor onset or therapy, and emphasize the mechanistic characteristics of LLPS regulated by PTMs and its effects on tumor progression. We then provide a perspective on further studies on LLPS and its regulation by PTMs in cancer research. This review aims to broaden the understanding of the functions of LLPS and its regulation by PTMs under normal or aberrant cellular conditions.
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Affiliation(s)
- Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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13
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Liu S, Bi Y, Han T, Li YE, Wang Q, Wu NN, Xu C, Ge J, Hu R, Zhang Y. The E3 ubiquitin ligase MARCH2 protects against myocardial ischemia-reperfusion injury through inhibiting pyroptosis via negative regulation of PGAM5/MAVS/NLRP3 axis. Cell Discov 2024; 10:24. [PMID: 38409220 PMCID: PMC10897310 DOI: 10.1038/s41421-023-00622-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/12/2023] [Indexed: 02/28/2024] Open
Abstract
Inflammasome activation and pyroptotic cell death are known to contribute to the pathogenesis of cardiovascular diseases, such as myocardial ischemia-reperfusion (I/R) injury, although the underlying regulatory mechanisms remain poorly understood. Here we report that expression levels of the E3 ubiquitin ligase membrane-associated RING finger protein 2 (MARCH2) were elevated in ischemic human hearts or mouse hearts upon I/R injury. Genetic ablation of MARCH2 aggravated myocardial infarction and cardiac dysfunction upon myocardial I/R injury. Single-cell RNA-seq analysis suggested that loss of MARCH2 prompted activation of NLRP3 inflammasome in cardiomyocytes. Mechanistically, phosphoglycerate mutase 5 (PGAM5) was found to act as a novel regulator of MAVS-NLRP3 signaling by forming liquid-liquid phase separation condensates with MAVS and fostering the recruitment of NLRP3. MARCH2 directly interacts with PGAM5 to promote its K48-linked polyubiquitination and proteasomal degradation, resulting in reduced PGAM5-MAVS co-condensation, and consequently inhibition of NLRP3 inflammasome activation and cardiomyocyte pyroptosis. AAV-based re-introduction of MARCH2 significantly ameliorated I/R-induced mouse heart dysfunction. Altogether, our findings reveal a novel mechanism where MARCH2-mediated ubiquitination negatively regulates the PGAM5/MAVS/NLRP3 axis to protect against cardiomyocyte pyroptosis and myocardial I/R injury.
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Affiliation(s)
- Shuolin Liu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Key Laboratory of Viral Heart Diseases, National Health Commission. Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yaguang Bi
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Key Laboratory of Viral Heart Diseases, National Health Commission. Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Tianting Han
- College of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yiran E Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Key Laboratory of Viral Heart Diseases, National Health Commission. Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Qihang Wang
- College of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ne Natalie Wu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Key Laboratory of Viral Heart Diseases, National Health Commission. Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Chenguo Xu
- College of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Key Laboratory of Viral Heart Diseases, National Health Commission. Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Ronggui Hu
- College of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai, China.
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science, Hangzhou Institute for Advance Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Yingmei Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Key Laboratory of Viral Heart Diseases, National Health Commission. Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
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14
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Mumford TR, Rae D, Brackhahn E, Idris A, Gonzalez-Martinez D, Pal AA, Chung MC, Guan J, Rhoades E, Bugaj LJ. Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter. Cell Syst 2024; 15:166-179.e7. [PMID: 38335954 PMCID: PMC10947474 DOI: 10.1016/j.cels.2024.01.005] [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: 08/22/2022] [Revised: 11/06/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Protein clustering plays numerous roles in cell physiology and disease. However, protein oligomers can be difficult to detect because they are often too small to appear as puncta in conventional fluorescence microscopy. Here, we describe a fluorescent reporter strategy that detects protein clusters with high sensitivity called CluMPS (clusters magnified by phase separation). A CluMPS reporter detects and visually amplifies even small clusters of a binding partner, generating large, quantifiable fluorescence condensates. We use computational modeling and optogenetic clustering to demonstrate that CluMPS can detect small oligomers and behaves rationally according to key system parameters. CluMPS detected small aggregates of pathological proteins where the corresponding GFP fusions appeared diffuse. CluMPS also detected and tracked clusters of unmodified and tagged endogenous proteins, and orthogonal CluMPS probes could be multiplexed in cells. CluMPS provides a powerful yet straightforward approach to observe higher-order protein assembly in its native cellular context. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Thomas R Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Diarmid Rae
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Brackhahn
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abbas Idris
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ayush Aditya Pal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Chung
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
| | - Juan Guan
- Department of Physics, University of Florida, Gainesville, FL 32611, USA; Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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Fu Q, Zhang B, Chen X, Chu L. Liquid-liquid phase separation in Alzheimer's disease. J Mol Med (Berl) 2024; 102:167-181. [PMID: 38167731 DOI: 10.1007/s00109-023-02407-3] [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: 04/17/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
The pathological aggregation and misfolding of tau and amyloid-β play a key role in Alzheimer's disease (AD). However, the underlying pathological mechanisms remain unclear. Emerging evidences indicate that liquid-liquid phase separation (LLPS) has great impacts on regulating human health and diseases, especially neurodegenerative diseases. A series of studies have revealed the significance of LLPS in AD. In this review, we summarize the latest progress of LLPS in AD, focusing on the impact of metal ions, small-molecule inhibitors, and proteinaceous partners on tau LLPS and aggregation, as well as toxic oligomerization, the role of LLPS on amyloid-β (Aβ) aggregation, and the cross-interactions between amyloidogenic proteins in AD. Eventually, the fundamental methods and techniques used in LLPS study are introduced. We expect to present readers a deeper understanding of the relationship between LLPS and AD.
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Affiliation(s)
- Qinggang Fu
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Bixiang Zhang
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiaoping Chen
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Liang Chu
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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16
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Sipko EL, Chappell GF, Berlow RB. Multivalency emerges as a common feature of intrinsically disordered protein interactions. Curr Opin Struct Biol 2024; 84:102742. [PMID: 38096754 DOI: 10.1016/j.sbi.2023.102742] [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: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Intrinsically disordered proteins (IDPs) use their unique molecular properties and conformational plasticity to interact with cellular partners in a wide variety of biological contexts. Multivalency is an important feature of IDPs that allows for utilization of an expanded toolkit for interactions with other macromolecules and confers additional complexity to molecular recognition processes. Recent studies have offered insights into how multivalent interactions of IDPs enable responsive and sensitive regulation in the context of transcription and cellular signaling. Multivalency is also widely recognized as an important feature of IDP interactions that mediate formation of biomolecular condensates. We highlight recent examples of multivalent interactions of IDPs across diverse contexts to illustrate the breadth of biological processes that utilize multivalency in molecular interactions.
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Affiliation(s)
- Emily L Sipko
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett F Chappell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca B Berlow
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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17
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Sang CC, Moore G, Tereshchenko M, Nosella ML, Zhang H, Alderson TR, Dasovich M, Leung A, Finkelstein IJ, Forman-Kay JD, Lee HO. PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.575817. [PMID: 38328070 PMCID: PMC10849519 DOI: 10.1101/2024.01.20.575817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is one of the first responders to DNA damage and plays crucial roles in recruiting DNA repair proteins through its activity - poly(ADP-ribosyl)ation (PARylation). The enrichment of DNA repair proteins at sites of DNA damage has been described as the formation of a biomolecular condensate. However, it is not understood how PARP1 and PARylation contribute to the formation and organization of DNA repair condensates. Using recombinant human PARP1 in vitro, we find that PARP1 readily forms viscous biomolecular condensates in a DNA-dependent manner and that this depends on its three zinc finger (ZnF) domains. PARylation enhances PARP1 condensation in a PAR chain-length dependent manner and increases the internal dynamics of PARP1 condensates. DNA and single-strand break repair proteins XRCC1, LigIII, Polβ, and FUS partition in PARP1 condensates, although in different patterns. While Polβ and FUS are both homogeneously mixed within PARP1 condensates, FUS enrichment is greatly enhanced upon PARylation whereas Polβ partitioning is not. XRCC1 and LigIII display an inhomogeneous organization within PARP1 condensates; their enrichment in these multiphase condensates is enhanced by PARylation. Functionally, PARP1 condensates concentrate short DNA fragments and facilitate compaction of long DNA and bridge DNA ends. Furthermore, the presence of PARP1 condensates significantly promotes DNA ligation upon PARylation. These findings provide insight into how PARP1 condensation and PARylation regulate the assembly and biochemical activities in DNA repair foci, which may inform on how PARPs function in other PAR-driven condensates.
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Affiliation(s)
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Michael L. Nosella
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Hongshan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, TX, USA
| | - T. Reid Alderson
- Division of Molecular Biology and Biochemistry, Medizinische Universität Graz, Graz, 8010, Austria
| | - Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Department of Oncology, and Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, TX, USA
| | - Julie D. Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Hyun O. Lee
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
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18
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Wu H, Chen X, Shen Z, Li H, Liang S, Lu Y, Zhang M. Phosphorylation-dependent membraneless organelle fusion and fission illustrated by postsynaptic density assemblies. Mol Cell 2024; 84:309-326.e7. [PMID: 38096828 DOI: 10.1016/j.molcel.2023.11.011] [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: 12/23/2022] [Revised: 09/10/2023] [Accepted: 11/13/2023] [Indexed: 01/21/2024]
Abstract
Membraneless organelles formed by phase separation of proteins and nucleic acids play diverse cellular functions. Whether and, if yes, how membraneless organelles in ways analogous to membrane-based organelles also undergo regulated fusion and fission is unknown. Here, using a partially reconstituted mammalian postsynaptic density (PSD) condensate as a paradigm, we show that membraneless organelles can undergo phosphorylation-dependent fusion and fission. Without phosphorylation of the SAPAP guanylate kinase domain-binding repeats, the upper and lower layers of PSD protein mixtures form two immiscible sub-compartments in a phase-in-phase organization. Phosphorylation of SAPAP leads to fusion of the two sub-compartments into one condensate accompanied with an increased Stargazin density in the condensate. Dephosphorylation of SAPAP can reverse this event. Preventing SAPAP phosphorylation in vivo leads to increased separation of proteins from the lower and upper layers of PSD sub-compartments. Thus, analogous to membrane-based organelles, membraneless organelles can also undergo regulated fusion and fission.
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Affiliation(s)
- Haowei Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xudong Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zeyu Shen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hao Li
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shiqi Liang
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Youming Lu
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mingjie Zhang
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518036, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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19
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Xiao M, Wang F, Chen N, Zhang H, Cao J, Yu Y, Zhao B, Ji J, Xu P, Li L, Shen L, Lin X, Feng XH. Smad4 sequestered in SFPQ condensates prevents TGF-β tumor-suppressive signaling. Dev Cell 2024; 59:48-63.e8. [PMID: 38103553 DOI: 10.1016/j.devcel.2023.11.020] [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: 05/10/2023] [Revised: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Loss of TGF-β growth-inhibitory responses is a hallmark of human cancer. However, the molecular mechanisms underlying the TGF-β resistance of cancer cells remain to be fully elucidated. Splicing factor proline- and glutamine-rich (SFPQ) is a prion-like RNA-binding protein that is frequently upregulated in human cancers. In this study, we identified SFPQ as a potent suppressor of TGF-β signaling. The ability of SFPQ to suppress TGF-β responses depends on its prion-like domain (PrLD) that drives liquid-liquid phase separation (LLPS). Mechanistically, SFPQ physically restrained Smad4 in its condensates, which excluded Smad4 from the Smad complex and chromatin occupancy and thus functionally dampened Smad-dependent transcriptional responses. Accordingly, SFPQ deficiency or loss of phase separation activities rendered human cells hypersensitive to TGF-β responses. Together, our data identify an important function of SFPQ through LLPS that suppresses Smad transcriptional activation and TGF-β tumor-suppressive activity.
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Affiliation(s)
- Mu Xiao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Fei Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Nuo Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hanchenxi Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jin Cao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yi Yu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Bin Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Li Shen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xia Lin
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China; The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310009, China.
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20
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Shandilya E, Bains AS, Maiti S. Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media. J Phys Chem B 2023; 127:10508-10517. [PMID: 38052045 DOI: 10.1021/acs.jpcb.3c07074] [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: 12/07/2023]
Abstract
Temporal regulation between input and output signals is one of the hallmarks of complex biological processes. Herein, we report that the conformational disposition of a protein in macromolecularly crowded media can be controlled with time using enzymes. First, we demonstrate the pH dependence of bovine serum albumin (BSA) condensation and conformational alteration in the presence of poly(ethylene glycol) as a crowder. However, by exploiting the strength of pH-modulatory enzymatic reactions (glucose oxidase and urease), the conversion time between the condensed and free forms can be tuned. Additionally, we demonstrate that the trapping of intermediate states with respect to the overall system at a particular α-helix or β-sheet composition and rotational mobility can be possible simply by altering the substrate concentration. Finally, we show that the intrinsic catalytic ability of BSA toward the Kemp elimination (KE) reaction is inhibited in the aggregated form but regained in the free form. In fact, the rate of KE reaction can also be actuated enzymatically in a temporal fashion, therefore demonstrating the programmability of a cascade of biochemical events in crowded media.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Arshdeep Singh Bains
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular Determinants and Signaling Effects of PKA RIα Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570836. [PMID: 38168176 PMCID: PMC10760030 DOI: 10.1101/2023.12.10.570836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures the specific execution of various cellular functions. Liquid-liquid phase separation (LLPS) of the ubiquitously expressed PKA regulatory subunit RIα was recently identified as a major driver of cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces combined with the cAMP-induced release of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence are required to drive RIα condensate formation in cytosol, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in the formation of a non-canonical R:C complex, which serves to maintain low basal PKA activity in the cytosol by enabling the recruitment of active PKA-C to RIα condensates. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
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22
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Wang YL, Zhao WW, Shi J, Wan XB, Zheng J, Fan XJ. Liquid-liquid phase separation in DNA double-strand breaks repair. Cell Death Dis 2023; 14:746. [PMID: 37968256 PMCID: PMC10651886 DOI: 10.1038/s41419-023-06267-0] [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: 12/26/2022] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
DNA double-strand breaks (DSBs) are the fatal type of DNA damage mostly induced by exposure genome to ionizing radiation or genotoxic chemicals. DSBs are mainly repaired by homologous recombination (HR) and nonhomologous end joining (NHEJ). To repair DSBs, a large amount of DNA repair factors was observed to be concentrated at the end of DSBs in a specific spatiotemporal manner to form a repair center. Recently, this repair center was characterized as a condensate derived from liquid-liquid phase separation (LLPS) of key DSBs repair factors. LLPS has been found to be the mechanism of membraneless organelles formation and plays key roles in a variety of biological processes. In this review, the recent advances and mechanisms of LLPS in the formation of DSBs repair-related condensates are summarized.
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Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
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23
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Liu J, Zhao C, Xiao X, Li A, Liu Y, Zhao J, Fan L, Liang Z, Pang W, Yao W, Li W, Zhou J. Endothelial discoidin domain receptor 1 senses flow to modulate YAP activation. Nat Commun 2023; 14:6457. [PMID: 37833282 PMCID: PMC10576099 DOI: 10.1038/s41467-023-42341-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: 05/26/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Mechanotransduction in endothelial cells is critical to maintain vascular homeostasis and can contribute to disease development, yet the molecules responsible for sensing flow remain largely unknown. Here, we demonstrate that the discoidin domain receptor 1 (DDR1) tyrosine kinase is a direct mechanosensor and is essential for connecting the force imposed by shear to the endothelial responses. We identify the flow-induced activation of endothelial DDR1 to be atherogenic. Shear force likely causes conformational changes of DDR1 ectodomain by unfolding its DS-like domain to expose the buried cysteine-287, whose exposure facilitates force-induced receptor oligomerization and phase separation. Upon shearing, DDR1 forms liquid-like biomolecular condensates and co-condenses with YWHAE, leading to nuclear translocation of YAP. Our findings establish a previously uncharacterized role of DDR1 in directly sensing flow, propose a conceptual framework for understanding upstream regulation of the YAP signaling, and offer a mechanism by which endothelial activation of DDR1 promotes atherosclerosis.
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Affiliation(s)
- Jiayu Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China
| | - Chuanrong Zhao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Xue Xiao
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aohan Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yueqi Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China
| | - Jianan Zhao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China
| | - Linwei Fan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China
| | - Zhenhui Liang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China
| | - Wei Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
| | - Weijuan Yao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
| | - Wei Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China.
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China.
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24
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Parra AS, Moezzi CA, Johnston CA. Drosophila Adducin facilitates phase separation and function of a conserved spindle orientation complex. Front Cell Dev Biol 2023; 11:1220529. [PMID: 37655159 PMCID: PMC10467427 DOI: 10.3389/fcell.2023.1220529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
Asymmetric cell division (ACD) allows stem cells to generate differentiating progeny while simultaneously maintaining their own pluripotent state. ACD involves coupling mitotic spindle orientation with cortical polarity cues to direct unequal segregation of cell fate determinants. In Drosophila neural stem cells (neuroblasts; NBs), spindles orient along an apical-basal polarity axis through a conserved complex of Partner of Inscuteable (Pins; human LGN) and Mushroom body defect (Mud; human NuMA). While many details of its function are well known, the molecular mechanics that drive assembly of the cortical Pins/Mud complex remain unclear, particularly with respect to the mutually exclusive Pins complex formed with the apical scaffold protein Inscuteable (Insc). Here we identify Hu li tai shao (Hts; human Adducin) as a direct Mud-binding protein, using an aldolase fold within its head domain (HtsHEAD) to bind a short Mud coiled-coil domain (MudCC) that is adjacent to the Pins-binding domain (MudPBD). Hts is expressed throughout the larval central brain and apically polarizes in mitotic NBs where it is required for Mud-dependent spindle orientation. In vitro analyses reveal that Pins undergoes liquid-liquid phase separation with Mud, but not with Insc, suggesting a potential molecular basis for differential assembly mechanics between these two competing apical protein complexes. Furthermore, we find that Hts binds an intact Pins/Mud complex, reduces the concentration threshold for its phase separation, and alters the liquid-like property of the resulting phase separated droplets. Domain mapping and mutational analyses implicate critical roles for both multivalent interactions (via MudCC oligomerization) and protein disorder (via an intrinsically disordered region in Hts; HtsIDR) in phase separation of the Hts/Mud/Pins complex. Our study identifies a new component of the spindle positioning machinery in NBs and suggests that phase separation of specific protein complexes might regulate ordered assembly within the apical domain to ensure proper signaling output.
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Zhang L, Liu Z, Lu Y, Nie J, Chen Y. Phase Separation in Kidney Diseases: Autosomal Dominant Polycystic Kidney Disease and Beyond. KIDNEY DISEASES (BASEL, SWITZERLAND) 2023; 9:229-238. [PMID: 37899998 PMCID: PMC10601909 DOI: 10.1159/000530250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/15/2023] [Indexed: 10/31/2023]
Abstract
Background The formation of biomolecular condensates via phase separation has emerged as a fundamental principle underlying the spatiotemporal coordination of biological activities in cells. Aberrant biomolecular condensates often directly regulate key cellular process involved in the pathogenesis of human diseases, including kidney diseases. Summary In this review, we summarize the physiological roles of phase separation and methodologies for phase separation studies. Taking autosomal dominant polycystic kidney disease as an example, we discuss recent advances toward elucidating the multiple mechanisms involved in kidney pathology arising from aberrant phase separation. We suggest that dysregulation of phase separation contributes to the pathogenesis of other important kidney diseases, including kidney injury and fibrosis. Key Messages Phase separation provides a useful new concept to understand the mechanisms underlying kidney disease development. Targeting aberrant phase-separated condensates offers new therapeutic avenues for combating kidney diseases.
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Affiliation(s)
- Lirong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Zhiheng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Yumei Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Jing Nie
- Division of Nephrology, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yupeng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
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26
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Miao Y, Guo X, Zhu K, Zhao W. Biomolecular condensates tunes immune signaling at the Host-Pathogen interface. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102374. [PMID: 37148673 DOI: 10.1016/j.pbi.2023.102374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
Membraneless organelles participate in diverse spatiotemporal regulation of cellular signal transduction by recruiting necessary signaling factors. During host-pathogen interactions, the plasma membrane (PM) at the interface between the plant and microbes serves as a central platform for forming multicomponent immune signaling hubs. The macromolecular condensation of the immune complex and regulators is important in regulating immune signaling outputs regarding strength, timing, and crosstalk between signaling pathways. This review discusses mechanisms that regulate specific and crosstalk of plant immune signal transduction pathways through macromolecular assembly and condensation.
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Affiliation(s)
- Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore.
| | - Xiangfu Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
| | - Kexin Zhu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore
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27
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Gao XK, Sheng ZK, Lu YH, Sun YT, Rao XS, Shi LJ, Cong XX, Chen X, Wu HB, Huang M, Zheng Q, Guo JS, Jiang LJ, Zheng LL, Zhou YT. VAPB-mediated ER-targeting stabilizes IRS-1 signalosomes to regulate insulin/IGF signaling. Cell Discov 2023; 9:83. [PMID: 37528084 PMCID: PMC10394085 DOI: 10.1038/s41421-023-00576-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/08/2023] [Indexed: 08/03/2023] Open
Abstract
The scaffold protein IRS-1 is an essential node in insulin/IGF signaling. It has long been recognized that the stability of IRS-1 is dependent on its endomembrane targeting. However, how IRS-1 targets the intracellular membrane, and what type of intracellular membrane is actually targeted, remains poorly understood. Here, we found that the phase separation-mediated IRS-1 puncta attached to endoplasmic reticulum (ER). VAPB, an ER-anchored protein that mediates tethers between ER and membranes of other organelles, was identified as a direct interacting partner of IRS-1. VAPB mainly binds active IRS-1 because IGF-1 enhanced the VAPB-IRS-1 association and replacing of the nine tyrosine residues of YXXM motifs disrupted the VAPB-IRS-1 association. We further delineated that the Y745 and Y746 residues in the FFAT-like motif of IRS-1 mediated the association with VAPB. Notably, VAPB targeted IRS-1 to the ER and subsequently maintained its stability. Consistently, ablation of VAPB in mice led to downregulation of IRS-1, suppression of insulin signaling, and glucose intolerance. The amyotrophic lateral sclerosis (ALS)-derived VAPB P56S mutant also impaired IRS-1 stability by interfering with the ER-tethering of IRS-1. Our findings thus revealed a previously unappreciated condensate-membrane contact (CMC), by which VAPB stabilizes the membraneless IRS-1 signalosome through targeting it to ER membrane.
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Affiliation(s)
- Xiu Kui Gao
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Zu Kang Sheng
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ye Hong Lu
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Ting Sun
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xi Sheng Rao
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lin Jing Shi
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiao Xia Cong
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiao Chen
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hao Bo Wu
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Man Huang
- Department of Biochemistry and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejinag, China
- Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, China
| | - Qiang Zheng
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian-Sheng Guo
- Department of Pathology of Sir Run Run Shaw Hospital, Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liang Jun Jiang
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Li Ling Zheng
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Department of Biochemistry and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejinag, China.
- Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, China.
| | - Yi Ting Zhou
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, China.
- ZJU-UoE Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Hangzhou, Zhejiang, China.
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28
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He Y, Wang S, Liu S, Qin D, Liu Z, Wang L, Chen X, Zhang L. MSL1 Promotes Liver Regeneration by Driving Phase Separation of STAT3 and Histone H4 and Enhancing Their Acetylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301094. [PMID: 37279389 PMCID: PMC10427353 DOI: 10.1002/advs.202301094] [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: 02/17/2023] [Revised: 04/25/2023] [Indexed: 06/08/2023]
Abstract
Male-specific lethal 1 (MSL1) is critical for the formation of MSL histone acetyltransferase complex which acetylates histone H4 Lys16 (H4K16ac) to activate gene expression. However, the role of MSL1 in liver regeneration is poorly understood. Here, this work identifies MSL1 as a key regulator of STAT3 and histone H4 (H4) in hepatocytes. MSL1 forms condensates with STAT3 or H4 through liquid-liquid phase separation to enrich acetyl-coenzyme A (Ac-CoA), and Ac-CoA in turn enhances MSL1 condensate formation, synergetically promoting the acetylation of STAT3 K685 and H4K16, thus stimulating liver regeneration after partial hepatectomy (PH). Additionally, increasing Ac-CoA level can enhance STAT3 and H4 acetylation, thus promoting liver regeneration in aged mice. The results demonstrate that MSL1 condensate-mediated STAT3 and H4 acetylation play an important role in liver regeneration. Thus, promoting the phase separation of MSL1 and increasing Ac-CoA level may be a novel therapeutic strategy for acute liver diseases and transplantation.
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Affiliation(s)
- Yucheng He
- College of Veterinary Medicine/Bio‐medical CenterHuazhong Agricultural UniversityWuhanHubei430070China
| | - Shichao Wang
- College of Veterinary Medicine/Bio‐medical CenterHuazhong Agricultural UniversityWuhanHubei430070China
| | - Shenghui Liu
- College of Veterinary Medicine/Bio‐medical CenterHuazhong Agricultural UniversityWuhanHubei430070China
| | - Dan Qin
- College of Veterinary Medicine/Bio‐medical CenterHuazhong Agricultural UniversityWuhanHubei430070China
| | - Zhangmei Liu
- College of Veterinary Medicine/Bio‐medical CenterHuazhong Agricultural UniversityWuhanHubei430070China
| | - Liqiang Wang
- Department of NephrologyChinese PLA General HospitalChinese PLA Institute of NephrologyState Key Laboratory of Kidney DiseasesNational Clinical Research Center for Kidney Diseases28th Fuxing RoadBeijing100853China
| | - Xiangmei Chen
- Department of NephrologyChinese PLA General HospitalChinese PLA Institute of NephrologyState Key Laboratory of Kidney DiseasesNational Clinical Research Center for Kidney Diseases28th Fuxing RoadBeijing100853China
| | - Lisheng Zhang
- College of Veterinary Medicine/Bio‐medical CenterHuazhong Agricultural UniversityWuhanHubei430070China
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Kang JE, Jun JH, Kwon JH, Lee JH, Hwang K, Kim S, Jeong N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool-Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes (Basel) 2023; 14:1476. [PMID: 37510380 PMCID: PMC10379056 DOI: 10.3390/genes14071476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool-liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein-nucleic acid interaction (PNI) and protein-protein interaction (PPI) analysis based on domain-domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain-motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms.
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Affiliation(s)
- Jee Eun Kang
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Ji Hae Jun
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Jung Hyun Kwon
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Ju-Hyun Lee
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Kidong Hwang
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Sungjong Kim
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Namhee Jeong
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
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30
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Elias RD, Zhu Y, Su Q, Ghirlando R, Zhang J, Deshmukh L. Reversible phase separation of ESCRT protein ALIX through tyrosine phosphorylation. SCIENCE ADVANCES 2023; 9:eadg3913. [PMID: 37450591 PMCID: PMC10348681 DOI: 10.1126/sciadv.adg3913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Cytokinetic abscission, the last step of cell division, is regulated by the ESCRT machinery. In response to mitotic errors, ESCRT proteins, namely, ALIX, CHMP4B, and CHMP4C, accumulate in the cytosolic compartments termed "abscission checkpoint bodies" (ACBs) to delay abscission and prevent tumorigenesis. ALIX contributes to the biogenesis and stability of ACBs via an unknown mechanism. We show that ALIX phase separates into nondynamic condensates in vitro and in vivo, mediated by the amyloidogenic portion of its proline-rich domain. ALIX condensates confined CHMP4 paralogs in vitro. These condensates dissolved and reformed upon reversible tyrosine phosphorylation of ALIX, mediated by Src kinase and PTP1B, and sequestration of CHMP4C altered their Src-mediated dissolution. NMR analysis revealed how ALIX triggers the activation of CHMP4 proteins, which is required for successful abscission. These results implicate ALIX's phase separation in the modulation of ACBs. This study also highlights how posttranslational modifications can control protein phase separation.
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Affiliation(s)
- Ruben D. Elias
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yingqi Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qi Su
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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31
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Hurtle BT, Xie L, Donnelly CJ. Disrupting pathologic phase transitions in neurodegeneration. J Clin Invest 2023; 133:e168549. [PMID: 37395272 DOI: 10.1172/jci168549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Solid-like protein deposits found in aged and diseased human brains have revealed a relationship between insoluble protein accumulations and the resulting deficits in neurologic function. Clinically diverse neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis, exhibit unique and disease-specific biochemical protein signatures and abnormal protein depositions that often correlate with disease pathogenesis. Recent evidence indicates that many pathologic proteins assemble into liquid-like protein phases through the highly coordinated process of liquid-liquid phase separation. Over the last decade, biomolecular phase transitions have emerged as a fundamental mechanism of cellular organization. Liquid-like condensates organize functionally related biomolecules within the cell, and many neuropathology-associated proteins reside within these dynamic structures. Thus, examining biomolecular phase transitions enhances our understanding of the molecular mechanisms mediating toxicity across diverse neurodegenerative diseases. This Review explores the known mechanisms contributing to aberrant protein phase transitions in neurodegenerative diseases, focusing on tau and TDP-43 proteinopathies and outlining potential therapeutic strategies to regulate these pathologic events.
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Affiliation(s)
- Bryan T Hurtle
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Longxin Xie
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Christopher J Donnelly
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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32
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Ziethen N, Kirschbaum J, Zwicker D. Nucleation of Chemically Active Droplets. PHYSICAL REVIEW LETTERS 2023; 130:248201. [PMID: 37390433 DOI: 10.1103/physrevlett.130.248201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/10/2023] [Indexed: 07/02/2023]
Abstract
Driven chemical reactions can control the macroscopic properties of droplets, like their size. Such active droplets are critical in structuring the interior of biological cells. Cells also need to control where and when droplets appear, so they need to control droplet nucleation. Our numerical simulations demonstrate that reactions generally suppress nucleation if they stabilize the homogeneous state. An equilibrium surrogate model reveals that reactions increase the effective energy barrier of nucleation, enabling quantitative predictions of the increased nucleation times. Moreover, the surrogate model allows us to construct a phase diagram, which summarizes how reactions affect the stability of the homogeneous phase and the droplet state. This simple picture provides accurate predictions of how driven reactions delay nucleation, which is relevant for understanding droplets in biological cells and chemical engineering.
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Affiliation(s)
- Noah Ziethen
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17 37077, Göttingen, Germany
| | - Jan Kirschbaum
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17 37077, Göttingen, Germany
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17 37077, Göttingen, Germany
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33
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Bertrand E, Demongin C, Dobra I, Rengifo-Gonzalez JC, Singatulina AS, Sukhanova MV, Lavrik OI, Pastré D, Hamon L. FUS fibrillation occurs through a nucleation-based process below the critical concentration required for liquid-liquid phase separation. Sci Rep 2023; 13:7772. [PMID: 37179431 PMCID: PMC10183042 DOI: 10.1038/s41598-023-34558-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
FUS is an RNA-binding protein involved in familiar forms of ALS and FTLD that also assembles into fibrillar cytoplasmic aggregates in some neurodegenerative diseases without genetic causes. The self-adhesive prion-like domain in FUS generates reversible condensates via the liquid-liquid phase separation process (LLPS) whose maturation can lead to the formation of insoluble fibrillar aggregates in vitro, consistent with the appearance of cytoplasmic inclusions in ageing neurons. Using a single-molecule imaging approach, we reveal that FUS can assemble into nanofibrils at concentrations in the nanomolar range. These results suggest that the formation of fibrillar aggregates of FUS could occur in the cytoplasm at low concentrations of FUS, below the critical ones required to trigger the liquid-like condensate formation. Such nanofibrils may serve as seeds for the formation of pathological inclusions. Interestingly, the fibrillation of FUS at low concentrations is inhibited by its binding to mRNA or after the phosphorylation of its prion-like domain, in agreement with previous models.
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Affiliation(s)
- Emilie Bertrand
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Clément Demongin
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Ioana Dobra
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | | | - Anastasia S Singatulina
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France.
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34
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Shi Y, Liao Y, Liu Q, Ni Z, Zhang Z, Shi M, Li P, Li H, Rao Y. BRD4-targeting PROTAC as a unique tool to study biomolecular condensates. Cell Discov 2023; 9:47. [PMID: 37156794 PMCID: PMC10167318 DOI: 10.1038/s41421-023-00544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/14/2023] [Indexed: 05/10/2023] Open
Abstract
Biomolecular condensates play key roles in various biological processes. However, specific condensation modulators are currently lacking. PROTAC is a new technology that can use small molecules to degrade target proteins specifically. PROTAC molecules are expected to regulate biomolecular condensates dynamically by degrading/recovering key molecules in biomolecular condensates. In this study, we employed a BRD4-targeting PROTAC molecule to regulate the super-enhancer (SE) condensate and monitored the changes of SE condensate under PROTAC treatment using live-cell imaging and high-throughput sequencing technologies. As a result, we found that BRD4-targeting PROTACs can significantly reduce the BRD4 condensates, and we established a quantitative method for tracking BRD4 condensates by PROTAC and cellular imaging. Surprisingly and encouragingly, BRD4 condensates were observed to preferentially form and play specialized roles in biological process regulation for the first time. Additionally, BRD4 PROTAC makes it possible to observe the dynamics of other condensate components under the continued disruption of BRD4 condensates. Together, these results shed new light on research methods for liquid-liquid phase separation (LLPS), and specifically demonstrate that PROTAC presents a powerful and distinctive tool for the study of biomolecular condensates.
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Affiliation(s)
- Yi Shi
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuan Liao
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Beijing, China
| | - Qianlong Liu
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zhihao Ni
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Zhenzhen Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.
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35
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Wang L, Liu Q, Wang N, Li S, Bian W, Sun Z, Wang L, Wang L, Liu C, Song C, Liu Q, Yang Q. Oleic Acid Dissolves cGAS-DNA Phase Separation to Inhibit Immune Surveillance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206820. [PMID: 36950761 DOI: 10.1002/advs.202206820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/23/2023] [Indexed: 05/18/2023]
Abstract
Phase separation (PS) is a fundamental principle in diverse life processes including immunosurveillance. Despite numerous studies on PS, little is known about its dissolution. Here, it is shown that oleic acid (OA) dissolves the cyclic GMP-AMP synthase (cGAS)-deoxyribonucleic acid (DNA) PS and inhibits immune surveillance of DNA. As solvent components control PS and metabolites are abundant cellular components, it is speculated that some metabolite(s) may dissolve PS. Metabolite-screening reveals that the cGAS-DNA condensates formed via PS are markedly dissolved by long-chain fatty acids, including OA. OA revokes intracellular cGAS-PS and DNA-induced activation. OA attenuates cGAS-mediated antiviral and anticancer immunosurveillance. These results link metabolism and immunity by dissolving PS, which may be targeted for therapeutic interventions.
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Affiliation(s)
- Lina Wang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Qiaoling Liu
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Na Wang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Siru Li
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Wei Bian
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Zhen Sun
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Lulu Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116 024, P. R. China
| | - Li Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116 023, P. R. China
| | - Caigang Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110 004, P. R. China
| | - Chengli Song
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510 060, P. R. China
| | - Qingkai Yang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, 116 044, P. R. China
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36
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Cermakova K, Hodges HC. Interaction modules that impart specificity to disordered protein. Trends Biochem Sci 2023; 48:477-490. [PMID: 36754681 PMCID: PMC10106370 DOI: 10.1016/j.tibs.2023.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
Intrinsically disordered regions (IDRs) are especially enriched among proteins that regulate chromatin and transcription. As a result, mechanisms that influence specificity of IDR-driven interactions have emerged as exciting unresolved issues for understanding gene regulation. We review the molecular elements frequently found within IDRs that confer regulatory specificity. In particular, we summarize the differing roles of disordered low-complexity regions (LCRs) and short linear motifs (SLiMs) towards selective nuclear regulation. Examination of IDR-driven interactions highlights SLiMs as organizers of selectivity, with widespread roles in gene regulation and integration of cellular signals. Analysis of recurrent interactions between SLiMs and folded domains suggests diverse avenues for SLiMs to influence phase-separated condensates and highlights opportunities to manipulate these interactions for control of biological activity.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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37
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Morishita K, Watanabe K, Naguro I, Ichijo H. Sodium ion influx regulates liquidity of biomolecular condensates in hyperosmotic stress response. Cell Rep 2023; 42:112315. [PMID: 37019112 DOI: 10.1016/j.celrep.2023.112315] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/17/2023] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Biomolecular condensates are membraneless structures formed through phase separation. Recent studies have demonstrated that the material properties of biomolecular condensates are crucial for their biological functions and pathogenicity. However, the phase maintenance of biomolecular condensates in cells remains elusive. Here, we show that sodium ion (Na+) influx regulates the condensate liquidity under hyperosmotic stress. ASK3 condensates have higher fluidity at the high intracellular Na+ concentration derived from extracellular hyperosmotic solution. Moreover, we identified TRPM4 as a cation channel that allows Na+ influx under hyperosmotic stress. TRPM4 inhibition causes the liquid-to-solid phase transition of ASK3 condensates, leading to impairment of the ASK3 osmoresponse. In addition to ASK3 condensates, intracellular Na+ widely regulates the condensate liquidity and aggregate formation of biomolecules, including DCP1A, TAZ, and polyQ-protein, under hyperosmotic stress. Our findings demonstrate that changes in Na+ contribute to the cellular stress response via liquidity maintenance of biomolecular condensates.
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Affiliation(s)
- Kazuhiro Morishita
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kengo Watanabe
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Isao Naguro
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hidenori Ichijo
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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38
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Yang S, Yu H, Xu X, Yang T, Wei Y, Zan R, Zhang X, Ma Q, Shum HC, Song Y. AIEgen-Conjugated Phase-Separating Peptides Illuminate Intracellular RNA through Coacervation-Induced Emission. ACS NANO 2023; 17:8195-8203. [PMID: 37093110 DOI: 10.1021/acsnano.2c12072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Intrinsically disordered peptides drive dynamic liquid-liquid phase separation (LLPS) in membraneless organelles and encode cellular functions in response to environmental stimuli. Engineering design on phase-separating peptides (PSPs) holds great promise for bioimaging, vaccine delivery, and disease theranostics. However, recombinant PSPs are devoid of robust luminogen or suitable cell permeability required for intracellular applications. Here, we synthesize a peptide-based RNA sensor by covalently connecting tetraphenylethylene (TPE), an aggregation-induced emission luminogen (AIEgens), to tandem peptide repeats of (RRASL)n (n = 1, 2, 3). Interestingly, the conjugation of TPE luminogen promotes liquid-liquid phase separation of the peptide repeats, and the minimum coacervation concentration (MCC) of TPE-(RRASL)n is decreased by an order of magnitude, compared to that of the untagged, TPE-free counterparts. Moreover, the luminescence of TPE-(RRASL)n is enhanced by up to 700-fold with increasing RNA concentration, which is attributed to the constricted rotation of the TPE moiety as a result of peptide/RNA coacervates within the droplet phase. Besides, at concentrations above MCC, TPE-(RRASL)n can efficiently penetrate through human gallbladder carcinoma cells (SGC-996), translocate into the cell nucleus, and colocalize with intracellular RNA. These observations suggest that AIEgen-conjugated PSPs can be used as droplet-based biosensors for intracellular RNA imaging through a regime of coacervation-induced emission.
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Affiliation(s)
- Shi Yang
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Han Yu
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiuli Xu
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ting Yang
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Wei
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Zan
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai 200032, China
| | - Xiaonong Zhang
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingming Ma
- School of Pharmacy, Qingdao University, Qingdao 266071, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Yang Song
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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39
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Huang Y, Huang J, Yin W, Xie F, Coleman B, Cao Y, Aya S, Zhu W, Yang Z, Jiang L. Encoding Coacervate Droplets with Paramagnetism for Dynamical Reconfigurability and Spatial Addressability. ACS NANO 2023; 17:6234-6246. [PMID: 36951305 DOI: 10.1021/acsnano.2c09617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
It is an ongoing endeavor in chemistry and materials science to regulate coacervate droplets on a physiologically relevant spatiotemporal scale to ultimately match or even surpass living cells' precision, complexity, and functionality. Herein, we develop a magnetic strategy orthogonal to the thermal, pH, light, or chemical counterparts that are commonly employed by biotic or artificial systems; its successful implementation thus adds a missing piece to the current arsenal of manipulative methodologies. Specifically, we paramagnetize the otherwise diamagnetic coacervate droplets by cooperatively combining paramagnetic ingredients (including organic radicals, metal ions, and Fe3O4 nanoparticles) and coacervate ingredients to obtain "MagCoa" droplets. A simple model is derived theoretically to account for migration and division of MagCoa droplets in an uneven magnetic field. Experimentally, we produce an array of compartmentalized and monodispersed droplets using microfluidics and magnetically steer them with uniformity and synchronicity. We design and fabricate spatial magnetic modulators to engineer the landscape of a magnetic field that, in turn, directs the MagCoa droplets into predesigned patterns in a reconfigurable fashion. These programmable liquid patterns can be potentially extended to dynamic assembly and information encryption. We envision that the toolbox established here is of generality and multitudes to serve as a practical guide to control droplets magnetically.
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Affiliation(s)
- Yangkun Huang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
| | - Jinpeng Huang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Wenxiang Yin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Fei Xie
- Institute of Information Technology, Handan University, Handan 056005, China
| | - Benjamin Coleman
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005-1892, United States
| | - Yaoyu Cao
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 511443, China
| | - Satoshi Aya
- College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhijie Yang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
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40
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Corbet GA, Burke JM, Parker R. Nucleic acid-protein condensates in innate immune signaling. EMBO J 2023; 42:e111870. [PMID: 36178199 PMCID: PMC10068312 DOI: 10.15252/embj.2022111870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/24/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
The presence of foreign nucleic acids in the cytosol is a marker of infection. Cells have sensors, also known as pattern recognition receptors (PRRs), in the cytosol that detect foreign nucleic acid and initiate an innate immune response. Recent studies have reported the condensation of multiple PRRs including PKR, NLRP6, and cGAS, with their nucleic acid activators into discrete nucleoprotein assemblies. Nucleic acid-protein condensates form due to multivalent interactions and can create high local concentrations of components. The formation of PRR-containing condensates may alter the magnitude or timing of PRR activation. In addition, unique condensates form following RNase L activation or during paracrine signaling from virally infected cells that may play roles in antiviral defense. These observations suggest that condensate formation may be a conserved mechanism that cells use to regulate activation of the innate immune response and open an avenue for further investigation into the composition and function of these condensates. Here we review the nucleic acid-protein granules that are implicated in the innate immune response, discuss general consequences of condensate formation and signal transduction, as well as what outstanding questions remain.
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Affiliation(s)
- Giulia A Corbet
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
| | - James M Burke
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
- Present address:
Department of Molecular MedicineUniversity of Florida Scripps Biomedical ResearchJupiterFLUSA
| | - Roy Parker
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
- Howard Hughes Medical InstituteChevy ChaseMDUSA
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Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid-Liquid Phase Separation for Biotechnology. BIOTECH 2023; 12:26. [PMID: 37092470 PMCID: PMC10123627 DOI: 10.3390/biotech12020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.
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Affiliation(s)
| | | | | | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
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Zhang K, Huang M, Li A, Wen J, Yan L, Li Y, Guo L, Senthil KS, Zhou Y, Chen G, Liu Y, Zhang X, Yao X, Qin D, Su H. DIAPH3 condensates formed by liquid-liquid phase separation act as a regulatory hub for stress-induced actin cytoskeleton remodeling. Cell Rep 2023; 42:111986. [PMID: 36640348 DOI: 10.1016/j.celrep.2022.111986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/24/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Membraneless condensates, such as stress granules (SGs) and processing bodies (P-bodies), have attracted wide attention due to their unique feature of rapid response to stress without first requiring nuclear feedback. In this study, we identify diaphanous-related formin 3 (DIAPH3), an actin nucleator, as a scaffold protein to initiate liquid-liquid phase separation (LLPS) and form abundant cytosolic phase-separated DIAPH3 granules (D-granules) in mammalian cells such as HeLa, HEK293, and fibroblasts under various stress conditions. Neither mRNAs nor known stress-associated condensate markers, such as G3BP1, G3BP2, and TIA1 for SGs and DCP1A for P-bodies, are detected in D-granules. Using overexpression and knockout of DIAPH3, pharmacological interventions, and optogenetics, we further demonstrate that stress-induced D-granules spatially sequester DIAPH3 within the condensation to inhibit the assembly of actin filaments in filopodia. This study reveals that D-granules formed by LLPS act as a regulatory hub for actin cytoskeletal remodeling in response to stress.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Miaodan Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ang Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Jing Wen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Lingli Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yunhao Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Liman Guo
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kumaran Satyanarayanan Senthil
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yangyang Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guobing Chen
- Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Yong Liu
- Laboratory of Neuroscience in Health and Disease Institute, Guangzhou First People's Hospital School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiaofei Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoli Yao
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Dajiang Qin
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huanxing Su
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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Phase separation of SGS3 drives siRNA body formation and promotes endogenous gene silencing. Cell Rep 2023; 42:111985. [PMID: 36640363 DOI: 10.1016/j.celrep.2022.111985] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/26/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
The generation of small interfering RNA (siRNA) involves many RNA processing components, including SUPPRESSOR OF GENE SILENCING 3 (SGS3), RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), and DICER-LIKE proteins (DCLs). Nonetheless, how these components are coordinated to produce siRNAs is unclear. Here, we show that SGS3 forms condensates via phase separation in vivo and in vitro. SGS3 interacts with RDR6 and drives it to form siRNA bodies in cytoplasm, which is promoted by SGS3-targeted RNAs. Disrupting SGS3 phase separation abrogates siRNA body assembly and siRNA biogenesis, whereas coexpression of SGS3 and RDR6 induces siRNA body formation in tobacco and yeast cells. Dysfunction in translation and mRNA decay increases the number of siRNA bodies, whereas DCL2/4 mutations enhance their size. Purification of SGS3 condensates identifies numerous RNA-binding proteins and siRNA processing components. Together, our findings reveal that SGS3 phase separation-mediated formation of siRNA bodies is essential for siRNA production and gene silencing.
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [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: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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45
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Li W, Shu X, Zhang X, Zhang Z, Sun S, Li N, Long M. Potential Roles of YAP/TAZ Mechanotransduction in Spaceflight-Induced Liver Dysfunction. Int J Mol Sci 2023; 24:ijms24032197. [PMID: 36768527 PMCID: PMC9917057 DOI: 10.3390/ijms24032197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Microgravity exposure during spaceflight causes the disordered regulation of liver function, presenting a specialized mechano-biological coupling process. While YAP/TAZ serves as a typical mechanosensitive pathway involved in hepatocyte metabolism, it remains unclear whether and how it is correlated with microgravity-induced liver dysfunction. Here, we discussed liver function alterations induced by spaceflight or simulated effects of microgravity on Earth. The roles of YAP/TAZ serving as a potential bridge in connecting liver metabolism with microgravity were specifically summarized. Existing evidence indicated that YAP/TAZ target gene expressions were affected by mechanotransductive pathways and phase separation, reasonably speculating that microgravity might regulate YAP/TAZ activation by disrupting these pathways via cytoskeletal remodeling or nuclear deformation, or disturbing condensates formation via diffusion limit, and then breaking liver homeostasis.
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Affiliation(s)
- Wang Li
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Shu
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Zhang
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziliang Zhang
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shujin Sun
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Li
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (N.L.); (M.L.)
| | - Mian Long
- Center for Biomechanics and Bioengineering, Beijing Key Laboratory of Engineered Construction and Mechanobiology and Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (N.L.); (M.L.)
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Liu J, Wang J, Liu Y, Xie SA, Zhang J, Zhao C, Zhou Y, Pang W, Yao W, Peng Q, Wang X, Zhou J. Liquid-Liquid Phase Separation of DDR1 Counteracts the Hippo Pathway to Orchestrate Arterial Stiffening. Circ Res 2023; 132:87-105. [PMID: 36475898 DOI: 10.1161/circresaha.122.322113] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The Hippo-YAP (yes-associated protein) signaling pathway is modulated in response to various environmental cues. Activation of YAP in vascular smooth muscle cells conveys the extracellular matrix stiffness-induced changes in vascular smooth muscle cells phenotype and behavior. Recent studies have established a mechanoreceptive role of receptor tyrosine kinase DDR1 (discoidin domain receptor 1) in vascular smooth muscle cells. METHODS We conduced 5/6 nephrectomy in vascular smooth muscle cells-specific Ddr1-knockout mice, accompanied by pharmacological inhibition of the Hippo pathway kinase LATS1 (large tumor suppressor 1), to investigate DDR1 in YAP activation. We utilized polyacrylamide gels of varying stiffness or the DDR1 ligand, type I collagen, to stimulate the cells. We employed multiple molecular biological techniques to explore the role of DDR1 in controlling the Hippo pathway and to determine the mechanistic basis by which DDR1 exerts this effect. RESULTS We identified the requirement for DDR1 in stiffness/collagen-induced YAP activation. We uncovered that DDR1 underwent stiffness/collagen binding-stimulated liquid-liquid phase separation and co-condensed with LATS1 to inactivate LATS1. Mutagenesis experiments revealed that the transmembrane domain is responsible for DDR1 droplet formation. Purified DDR1 N-terminal and transmembrane domain was sufficient to drive its reversible condensation. Depletion of the DDR1 C-terminus led to failure in co-condensation with LATS1. Interaction between the DDR1 C-terminus and LATS1 competitively inhibited binding of MOB1 (Mps one binder 1) to LATS1 and thus the subsequent phosphorylation of LATS1. Introduction of the single-point mutants, histidine-745-proline and histidine-902-proline, to DDR1 on the C-terminus abolished the co-condensation. In mouse models, YAP activity was positively correlated with collagen I expression and arterial stiffness. LATS1 inhibition reactivated the YAP signaling in Ddr1-deficient vessels and abrogated the arterial softening effect of Ddr1 deficiency. CONCLUSIONS These findings identify DDR1 as a mediator of YAP activation by mechanical and chemical stimuli and demonstrate that DDR1 regulates LATS1 phosphorylation in an liquid-liquid phase separation-dependent manner.
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Affiliation(s)
- Jiayu Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.)
| | - Jin Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.).,Beijing Institute of Infectious Diseases, Beijing Key Laboratory of Emerging Infectious Diseases, National Center for Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing, China (J.W.)
| | - Yueqi Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.)
| | - Si-An Xie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.)
| | - Jianrui Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.)
| | - Chuanrong Zhao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.)
| | - Yuan Zhou
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China (Y.Z.)
| | - Wei Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.)
| | - Weijuan Yao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.)
| | - Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, China (Q.P.)
| | - Xiaohong Wang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China (X.W.)
| | - Jing Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., W.P., W.Y., J.Z.).,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., Y.Z., J.Z.).,National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China (J.L., J.W., Y.L., S.-A.X., J.Z., C.Z., J.Z.)
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Huai Y, Mao W, Wang X, Lin X, Li Y, Chen Z, Qian A. How do RNA binding proteins trigger liquid-liquid phase separation in human health and diseases? Biosci Trends 2022; 16:389-404. [PMID: 36464283 DOI: 10.5582/bst.2022.01449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
RNA-binding proteins (RBPs) lie at the center of post-transcriptional regulation and protein synthesis, adding complexity to RNA life cycle. RBPs also participate in the formation of membrane-less organelles (MLOs) via undergoing liquid-liquid phase separation (LLPS), which underlies the formation of MLOs in eukaryotic cells. RBPs-triggered LLPS mainly relies on the interaction between their RNA recognition motifs (RRMs) and capped mRNA transcripts and the heterotypic multivalent interactions between their intrinsically disordered regions (IDRs) or prion-like domains (PLDs). In turn, the aggregations of RBPs are also dependent on the process of LLPS. RBPs-driven LLPS is involved in many intracellular processes (regulation of translation, mRNA storage and stabilization and cell signaling) and serves as the heart of cellular physiology and pathology. Thus, it is essential to comprehend the potential roles and investigate the internal mechanism of RPBs-triggered LLPS. In this review, we primarily expound on our current understanding of RBPs and they-triggered LLPS and summarize their physiological and pathological functions. Furthermore, we also summarize the potential roles of RBPs-triggered LLPS as novel therapeutic mechanism for human diseases. This review will help understand the mechanisms underlying LLPS and downstream regulation of RBPs and provide insights into the pathogenesis and therapy of complex diseases.
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Affiliation(s)
- Ying Huai
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Wenjing Mao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xuehao Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xiao Lin
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Yu Li
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Zhihao Chen
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
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López-Palacios TP, Andersen JL. Kinase regulation by liquid–liquid phase separation. Trends Cell Biol 2022:S0962-8924(22)00260-4. [DOI: 10.1016/j.tcb.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
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Li H, Ernst C, Kolonko-Adamska M, Greb-Markiewicz B, Man J, Parissi V, Ng BWL. Phase separation in viral infections. Trends Microbiol 2022; 30:1217-1231. [PMID: 35902318 DOI: 10.1016/j.tim.2022.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Viruses rely on the reprogramming of cellular processes to enable efficient viral replication; this often requires subcompartmentalization within the host cell. Liquid-liquid phase separation (LLPS) has emerged as a fundamental principle to organize and subdivide cellular processes, and plays an important role in viral life cycles. Despite substantial advances in the field, elucidating the exact organization and function of these organelles remains a major challenge. In this review, we summarize the biochemical basis of condensate formation, the role of LLPS during viral infection, and interplay of LLPS with innate immune responses. Finally, we discuss possible strategies and molecules to modulate LLPS during viral infections.
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Affiliation(s)
- Haohua Li
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christina Ernst
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marta Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jackie Man
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; Faculty of Medicine, Imperial College, London, UK
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MPF), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, Bordeaux, France
| | - Billy Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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Wen Y, Ma J. Phase separation drives the formation of biomolecular condensates in the immune system. Front Immunol 2022; 13:986589. [PMID: 36439121 PMCID: PMC9685520 DOI: 10.3389/fimmu.2022.986589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/19/2022] [Indexed: 08/12/2023] Open
Abstract
When the external conditions change, such as the temperature or the pressure, the multi-component system sometimes separates into several phases with different components and structures, which is called phase separation. Increasing studies have shown that cells condense related biomolecules into independent compartments in order to carry out orderly and efficient biological reactions with the help of phase separation. Biomolecular condensates formed by phase separation play a significant role in a variety of cellular processes, including the control of signal transduction, the regulation of gene expression, and the stress response. In recent years, many phase separation events have been discovered in the immune response process. In this review, we provided a comprehensive and detailed overview of the role and mechanism of phase separation in the innate and adaptive immune responses, which will help the readers to appreciate the advance and importance of this field.
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Affiliation(s)
- Yuqing Wen
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
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