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Yin L, Yuan L, Li J, Jiang B. The liquid-liquid phase separation in programmed cell death. Cell Signal 2024; 120:111215. [PMID: 38740235 DOI: 10.1016/j.cellsig.2024.111215] [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: 03/25/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
In recent years, the physical phenomenon of liquid-liquid phase separation has been widely introduced into biological research. Membrane-free organelles have been found to exist in cells that were driven by liquid-liquid phase separation. Intermolecular multivalent interactions can drive liquid-liquid phase separation to form condensates that are independent of other substances in the environment and thus can play an effective role in regulating multiple biological processes in the cell. The way of cell death has also long been a focus in multiple research. In the face of various stresses, cell death-related mechanisms are crucial for maintaining cellular homeostasis and regulating cell fate. With the in-depth study of cell death pathways, it has been found that the process of cell death was also accompanied by the regulation of liquid-liquid phase separation and played a key role. Therefore, this review summarized the roles of liquid-liquid phase separation in various cell death pathways, and explored the regulation of cell fate by liquid-liquid phase separation, with the expectation that the exploration of the mechanism of liquid-liquid phase separation would provide new insights into the treatment of diseases caused by regulated cell death.
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Affiliation(s)
- Leijing Yin
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China.
| | - Ludong Yuan
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Jing Li
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China.
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2
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024; 26:851-858. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [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: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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3
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Chen X, Tsvetkov AS, Shen HM, Isidoro C, Ktistakis NT, Linkermann A, Koopman WJ, Simon HU, Galluzzi L, Luo S, Xu D, Gu W, Peulen O, Cai Q, Rubinsztein DC, Chi JT, Zhang DD, Li C, Toyokuni S, Liu J, Roh JL, Dai E, Juhasz G, Liu W, Zhang J, Yang M, Liu J, Zhu LQ, Zou W, Piacentini M, Ding WX, Yue Z, Xie Y, Petersen M, Gewirtz DA, Mandell MA, Chu CT, Sinha D, Eftekharpour E, Zhivotovsky B, Besteiro S, Gabrilovich DI, Kim DH, Kagan VE, Bayir H, Chen GC, Ayton S, Lünemann JD, Komatsu M, Krautwald S, Loos B, Baehrecke EH, Wang J, Lane JD, Sadoshima J, Yang WS, Gao M, Münz C, Thumm M, Kampmann M, Yu D, Lipinski MM, Jones JW, Jiang X, Zeh HJ, Kang R, Klionsky DJ, Kroemer G, Tang D. International consensus guidelines for the definition, detection, and interpretation of autophagy-dependent ferroptosis. Autophagy 2024; 20:1213-1246. [PMID: 38442890 PMCID: PMC11210914 DOI: 10.1080/15548627.2024.2319901] [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: 08/25/2023] [Accepted: 10/19/2023] [Indexed: 03/07/2024] Open
Abstract
Macroautophagy/autophagy is a complex degradation process with a dual role in cell death that is influenced by the cell types that are involved and the stressors they are exposed to. Ferroptosis is an iron-dependent oxidative form of cell death characterized by unrestricted lipid peroxidation in the context of heterogeneous and plastic mechanisms. Recent studies have shed light on the involvement of specific types of autophagy (e.g. ferritinophagy, lipophagy, and clockophagy) in initiating or executing ferroptotic cell death through the selective degradation of anti-injury proteins or organelles. Conversely, other forms of selective autophagy (e.g. reticulophagy and lysophagy) enhance the cellular defense against ferroptotic damage. Dysregulated autophagy-dependent ferroptosis has implications for a diverse range of pathological conditions. This review aims to present an updated definition of autophagy-dependent ferroptosis, discuss influential substrates and receptors, outline experimental methods, and propose guidelines for interpreting the results.Abbreviation: 3-MA:3-methyladenine; 4HNE: 4-hydroxynonenal; ACD: accidentalcell death; ADF: autophagy-dependentferroptosis; ARE: antioxidant response element; BH2:dihydrobiopterin; BH4: tetrahydrobiopterin; BMDMs: bonemarrow-derived macrophages; CMA: chaperone-mediated autophagy; CQ:chloroquine; DAMPs: danger/damage-associated molecular patterns; EMT,epithelial-mesenchymal transition; EPR: electronparamagnetic resonance; ER, endoplasmic reticulum; FRET: Försterresonance energy transfer; GFP: green fluorescent protein;GSH: glutathione;IF: immunofluorescence; IHC: immunohistochemistry; IOP, intraocularpressure; IRI: ischemia-reperfusion injury; LAA: linoleamide alkyne;MDA: malondialdehyde; PGSK: Phen Green™ SK;RCD: regulatedcell death; PUFAs: polyunsaturated fatty acids; RFP: red fluorescentprotein;ROS: reactive oxygen species; TBA: thiobarbituricacid; TBARS: thiobarbituric acid reactive substances; TEM:transmission electron microscopy.
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Affiliation(s)
- Xin Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Andrey S. Tsvetkov
- Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, USA
| | - Han-Ming Shen
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China
| | - Ciro Isidoro
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine 3, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Germany
- Division of Nephrology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Werner J.H. Koopman
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
- Institute of Biochemistry, Brandenburg Medical School, Neuruppin, Germany
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Shouqing Luo
- Peninsula Medical School, University of Plymouth, Plymouth, UK
| | - Daqian Xu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Gu
- Institute for Cancer Genetics, and Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA Cancer-University of Liège, Liège, Belgium
| | - Qian Cai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - David C. Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Donna D. Zhang
- Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - Changfeng Li
- Department of Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shinya Toyokuni
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
| | - Jinbao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Jong-Lyel Roh
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Enyong Dai
- The Second Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Gabor Juhasz
- Biological Research Center, Institute of Genetics, Szeged, Hungary
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest, Hungary
| | - Wei Liu
- Department of Orthopedics, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Minghua Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Pediatric Cancer, Changsha, China
| | - Jiao Liu
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiping Zou
- Departments of Surgery and Pathology, University of Michigan Medical School, Ann Arbor, USA
| | - Mauro Piacentini
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- National Institute for Infectious Diseases IRCCS “Lazzaro Spallanzani”, Rome, Italy
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yangchun Xie
- Department of Oncology, Central South University, Changsha, Hunan, China
| | - Morten Petersen
- Functional genomics, Department of Biology, Copenhagen University, Denmark
| | - David A. Gewirtz
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Massey Cancer Center, Richmond, VA, USA
| | - Michael A. Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, USA
| | - Charleen T. Chu
- Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Debasish Sinha
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Wilmer Eye lnstitute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eftekhar Eftekharpour
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Canada
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer, Villejuif, France; Gustave Roussy Cancer, Villejuif, France
| | - Boris Zhivotovsky
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden, Europe
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Sébastien Besteiro
- LPHI, University Montpellier, CNRS, Montpellier, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | | | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Valerian E. Kagan
- Department of Environmental Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hülya Bayir
- Department of Pediatrics, Columbia University, New York, USA
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Scott Ayton
- Florey Institute, University of Melbourne, Parkville, Australia
| | - Jan D. Lünemann
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University School of Medicine, Bunkyo-ku Tokyo, Japan
| | - Stefan Krautwald
- Department of Nephrology and Hypertension, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ben Loos
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Eric H. Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Thoracic Oncology Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Medical Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jon D. Lane
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Junichi Sadoshima
- Rutgers New Jersey Medical School, Department of Cell Biology and Molecular Medicine, Newark, USA
| | - Wan Seok Yang
- Department of Biological Sciences, St. John’s University, New York City, NY, USA
| | - Minghui Gao
- The HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Christian Münz
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Michael Thumm
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Martin Kampmann
- Department of Biochemistry & Biophysics, University of California, San Francisco, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, USA
| | - Di Yu
- Faculty of Medicine, Frazer Institute, University of Queensland, Brisbane, Australia
- Faculty of Medicine, Ian Frazer Centre for Children’s Immunotherapy Research, Child Health Research Centre, University of Queensland, Brisbane, Australia
| | - Marta M. Lipinski
- Department of Anesthesiology & Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jace W. Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert J. Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer, Villejuif, France; Gustave Roussy Cancer, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
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4
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Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [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: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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5
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Qiu H, Wu X, Ma X, Li S, Cai Q, Ganzella M, Ge L, Zhang H, Zhang M. Short-distance vesicle transport via phase separation. Cell 2024; 187:2175-2193.e21. [PMID: 38552623 DOI: 10.1016/j.cell.2024.03.003] [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: 01/31/2023] [Revised: 01/17/2024] [Accepted: 03/02/2024] [Indexed: 04/28/2024]
Abstract
In addition to long-distance molecular motor-mediated transport, cellular vesicles also need to be moved at short distances with defined directions to meet functional needs in subcellular compartments but with unknown mechanisms. Such short-distance vesicle transport does not involve molecular motors. Here, we demonstrate, using synaptic vesicle (SV) transport as a paradigm, that phase separation of synaptic proteins with vesicles can facilitate regulated, directional vesicle transport between different presynaptic bouton sub-compartments. Specifically, a large coiled-coil scaffold protein Piccolo, in response to Ca2+ and via its C2A domain-mediated Ca2+ sensing, can extract SVs from the synapsin-clustered reserve pool condensate and deposit the extracted SVs onto the surface of the active zone protein condensate. We further show that the Trk-fused gene, TFG, also participates in COPII vesicle trafficking from ER to the ER-Golgi intermediate compartment via phase separation. Thus, phase separation may play a general role in short-distance, directional vesicle transport in cells.
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Affiliation(s)
- Hua Qiu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiandeng Wu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiaoli Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qixu Cai
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Marcelo Ganzella
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, 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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6
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Lizarrondo J, Wilfling F. Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken? J Mol Biol 2024:168574. [PMID: 38636617 DOI: 10.1016/j.jmb.2024.168574] [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: 01/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
Proteins are known to perform an astonishing array of functions thanks to their ability to cooperate and modulate each other's properties. Inside cells, proteins can assemble into large multi-subunit complexes to carry out complex cellular functions. The correct assembly and maintenance of the functional state of macromolecular protein complexes is crucial for human health. Failure to do so leads to loss of function and potential accumulation of harmful materials, which is associated with a variety of human diseases such as neurodegeneration and cancer. Autophagy engulfs cytosolic material in autophagosomes, and therefore is best suited to eliminate intact macromolecular complexes without disassembling them, which could interfere with de novo assembly. In this review, we discuss the role of autophagy in the selective degradation of macromolecular complexes. We highlight the current state of knowledge for different macromolecular complexes and their selective autophagic degradation. We emphasize the gaps in our understanding of what it takes for these large macromolecular complexes to be degraded and point to future work that may shed light on the regulation of the selective degradation of macromolecular complexes by autophagy.
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Affiliation(s)
- Javier Lizarrondo
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt a.M. 60598, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, Frankfurt a.M. 60438, Germany.
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7
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Chakraborty S, Nandi P, Mishra J, Niharika, Roy A, Manna S, Baral T, Mishra P, Mishra PK, Patra SK. Molecular mechanisms in regulation of autophagy and apoptosis in view of epigenetic regulation of genes and involvement of liquid-liquid phase separation. Cancer Lett 2024; 587:216779. [PMID: 38458592 DOI: 10.1016/j.canlet.2024.216779] [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: 01/13/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Cellular physiology is critically regulated by multiple signaling nexuses, among which cell death mechanisms play crucial roles in controlling the homeostatic landscape at the tissue level within an organism. Apoptosis, also known as programmed cell death, can be induced by external and internal stimuli directing the cells to commit suicide in unfavourable conditions. In contrast, stress conditions like nutrient deprivation, infection and hypoxia trigger autophagy, which is lysosome-mediated processing of damaged cellular organelle for recycling of the degraded products, including amino acids. Apparently, apoptosis and autophagy both are catabolic and tumor-suppressive pathways; apoptosis is essential during development and cancer cell death, while autophagy promotes cell survival under stress. Moreover, autophagy plays dual role during cancer development and progression by facilitating the survival of cancer cells under stressed conditions and inducing death in extreme adversity. Despite having two different molecular mechanisms, both apoptosis and autophagy are interconnected by several crosslinking intermediates. Epigenetic modifications, such as DNA methylation, post-translational modification of histone tails, and miRNA play a pivotal role in regulating genes involved in both autophagy and apoptosis. Both autophagic and apoptotic genes can undergo various epigenetic modifications and promote or inhibit these processes under normal and cancerous conditions. Epigenetic modifiers are uniquely important in controlling the signaling pathways regulating autophagy and apoptosis. Therefore, these epigenetic modifiers of both autophagic and apoptotic genes can act as novel therapeutic targets against cancers. Additionally, liquid-liquid phase separation (LLPS) also modulates the aggregation of misfolded proteins and provokes autophagy in the cytosolic environment. This review deals with the molecular mechanisms of both autophagy and apoptosis including crosstalk between them; emphasizing epigenetic regulation, involvement of LLPS therein, and possible therapeutic approaches against cancers.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Prahallad Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bypass Road, Bhauri, Bhopal, 462 030, MP, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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8
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Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
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Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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9
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar EH, Abu Zeid IM, Bouback TA, Bamagoos A, Uversky VN, Rubio-Casillas A, Redwan EM. Intrinsic factors behind long COVID: IV. Hypothetical roles of the SARS-CoV-2 nucleocapsid protein and its liquid-liquid phase separation. J Cell Biochem 2024; 125:e30530. [PMID: 38349116 DOI: 10.1002/jcb.30530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
When the SARS-CoV-2 virus infects humans, it leads to a condition called COVID-19 that has a wide spectrum of clinical manifestations, from no symptoms to acute respiratory distress syndrome. The virus initiates damage by attaching to the ACE-2 protein on the surface of endothelial cells that line the blood vessels and using these cells as hosts for replication. Reactive oxygen species levels are increased during viral replication, which leads to oxidative stress. About three-fifths (~60%) of the people who get infected with the virus eradicate it from their body after 28 days and recover their normal activity. However, a large fraction (~40%) of the people who are infected with the virus suffer from various symptoms (anosmia and/or ageusia, fatigue, cough, myalgia, cognitive impairment, insomnia, dyspnea, and tachycardia) beyond 12 weeks and are diagnosed with a syndrome called long COVID. Long-term clinical studies in a group of people who contracted SARS-CoV-2 have been contrasted with a noninfected matched group of people. A subset of infected people can be distinguished by a set of cytokine markers to have persistent, low-grade inflammation and often self-report two or more bothersome symptoms. No medication can alleviate their symptoms efficiently. Coronavirus nucleocapsid proteins have been investigated extensively as potential drug targets due to their key roles in virus replication, among which is their ability to bind their respective genomic RNAs for incorporation into emerging virions. This review highlights basic studies of the nucleocapsid protein and its ability to undergo liquid-liquid phase separation. We hypothesize that this ability of the nucleocapsid protein for phase separation may contribute to long COVID. This hypothesis unlocks new investigation angles and could potentially open novel avenues for a better understanding of long COVID and treating this condition.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab H Mattar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Moscow Region, Russia
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, Jalisco, Mexico
- Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, Jalisco, Mexico
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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10
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Zheng H, Zhang H. More than a bystander: RNAs specify multifaceted behaviors of liquid-liquid phase-separated biomolecular condensates. Bioessays 2024; 46:e2300203. [PMID: 38175843 DOI: 10.1002/bies.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid-liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid-like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of RNP condensates, such as dynamic assembly and/or disassembly and biophysical properties. RNA properties - including concentration, sequence, length and structure - also determine the phase behaviors of RNP condensates. RNA is also involved in specifying autophagic degradation of RNP condensates. Unraveling the role of RNA in RNPs provides novel insights into pathological accumulation of RNPs in various diseases. This new understanding can potentially be harnessed to develop therapeutic strategies.
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Affiliation(s)
- Hui Zheng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
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11
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Wang X, Liu J, Mao C, Mao Y. Phase separation-mediated biomolecular condensates and their relationship to tumor. Cell Commun Signal 2024; 22:143. [PMID: 38383403 PMCID: PMC10880379 DOI: 10.1186/s12964-024-01518-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.
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Affiliation(s)
- Xi Wang
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jiameng Liu
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Chaoming Mao
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Yufei Mao
- Department of Ultrasound Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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12
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Restrepo LJ, Baehrecke EH. Regulation and Functions of Autophagy During Animal Development. J Mol Biol 2024:168473. [PMID: 38311234 DOI: 10.1016/j.jmb.2024.168473] [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: 12/12/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Autophagy is used to degrade cytoplasmic materials, and is critical to maintain cell and organismal health in diverse animals. Here we discuss the regulation, utilization and impact of autophagy on development, including roles in oogenesis, spermatogenesis and embryogenesis in animals. We also describe how autophagy influences postembryonic development in the context of neuronal and cardiac development, wound healing, and tissue regeneration. We describe recent studies of selective autophagy during development, including mitochondria-selective autophagy and endoplasmic reticulum (ER)-selective autophagy. Studies of developing model systems have also been used to discover novel regulators of autophagy, and we explain how studies of autophagy in these physiologically relevant systems are advancing our understanding of this important catabolic process.
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Affiliation(s)
- Lucas J Restrepo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA.
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13
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Nambiar A, Manjithaya R. Driving autophagy - the role of molecular motors. J Cell Sci 2024; 137:jcs260481. [PMID: 38329417 DOI: 10.1242/jcs.260481] [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] [Indexed: 02/09/2024] Open
Abstract
Most of the vesicular transport pathways inside the cell are facilitated by molecular motors that move along cytoskeletal networks. Autophagy is a well-explored catabolic pathway that is initiated by the formation of an isolation membrane known as the phagophore, which expands to form a double-membraned structure that captures its cargo and eventually moves towards the lysosomes for fusion. Molecular motors and cytoskeletal elements have been suggested to participate at different stages of the process as the autophagic vesicles move along cytoskeletal tracks. Dynein and kinesins govern autophagosome trafficking on microtubules through the sequential recruitment of their effector proteins, post-translational modifications and interactions with LC3-interacting regions (LIRs). In contrast, myosins are actin-based motors that participate in various stages of the autophagic flux, as well as in selective autophagy pathways. However, several outstanding questions remain with regard to how the dominance of a particular motor protein over another is controlled, and to the molecular mechanisms that underlie specific disease variants in motor proteins. In this Review, we aim to provide an overview of the role of molecular motors in autophagic flux, as well as highlight their dysregulation in diseases, such as neurodegenerative disorders and pathogenic infections, and ageing.
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Affiliation(s)
- Akshaya Nambiar
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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14
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陶 若, 张 水, 郭 文, 闫 志. [Research Progress in the Role of Liquid-Liquid Phase Separation in Human Cancer]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:24-30. [PMID: 38322521 PMCID: PMC10839487 DOI: 10.12182/20240160503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Indexed: 02/08/2024]
Abstract
Liquid-liquid phase separation (LLPS) is a reversible process, during which biological macromolecules, including proteins and nucleic acids, condense into liquid membraneless organelles under the influence of weak multivalent interactions. Currently, fluorescence recovery after photobleaching is the primary method used to detect the phase separation of biological macromolecules. Recent studies have revealed the link between abnormal LLPS and the pathogenesis and development of various human cancers. Through phase separation or abnormal phase separation, tumor-related biological macromolecules, such as mRNA, long noncoding RNAs (lncRNAs), and tumor-related proteins, can affect transcriptional translation and DNA damage repair, regulate the autophagy and ferroptosis functions of cells, and thus regulate the development of various tumors. In this review, we summarized the latest research findings on the mechanism of LLPS in the pathogenesis and progression of tumors and elaborated on the promotion or inhibition of autophagy, tumor immunity, DNA damage repair, and cell ferroptosis after abnormal phase separation of biomolecules, including mRNA, lncRNA, and proteins, which subsequently affects the pathogenesis and progression of tumors. According to published findings, many biological macromolecules can regulate transcriptional translation, expression, post-transcriptional modification, cell signal transduction, and other biological processes through phase separation. Therefore, further expansion of the research field of phase separation and in-depth investigation of its molecular mechanisms and regulatory processes hold extensive research potential.
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Affiliation(s)
- 若琳 陶
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
| | - 水军 张
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
| | - 文治 郭
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
| | - 志平 闫
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
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15
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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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16
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Hoffmann ME, Jacomin AC, Popovic D, Kalina D, Covarrubias-Pinto A, Dikic I. TBC1D2B undergoes phase separation and mediates autophagy initiation. J Cell Biochem 2024. [PMID: 38226533 DOI: 10.1002/jcb.30481] [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: 02/08/2023] [Revised: 08/28/2023] [Accepted: 09/17/2023] [Indexed: 01/17/2024]
Abstract
Small ubiquitin-like modifiers from the ATG8 family regulate autophagy initiation and progression in mammalian cells. Their interaction with LC3-interacting region (LIR) containing proteins promotes cargo sequestration, phagophore assembly, or even fusion between autophagosomes and lysosomes. Previously, we have shown that RabGAP proteins from the TBC family directly bind to LC3/GABARAP proteins. In the present study, we focus on the function of TBC1D2B. We show that TBC1D2B contains a functional canonical LIR motif and acts at an early stage of autophagy by binding to both LC3/GABARAP and ATG12 conjugation complexes. Subsequently, TBC1D2B is degraded by autophagy. TBC1D2B condensates into liquid droplets upon autophagy induction. Our study suggests that phase separation is an underlying mechanism of TBC1D2B-dependent autophagy induction.
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Affiliation(s)
- Marina E Hoffmann
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Anne-Claire Jacomin
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Doris Popovic
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Daniel Kalina
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
- Biomedical Research Laboratory, Department of Internal Medicine, Goethe University Clinic Frankfurt, Frankfurt, Germany
| | - Adriana Covarrubias-Pinto
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Ivan Dikic
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
- Molecular Signaling Group, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
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17
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Liu Q, Liu W, Niu Y, Wang T, Dong J. Liquid-liquid phase separation in plants: Advances and perspectives from model species to crops. PLANT COMMUNICATIONS 2024; 5:100663. [PMID: 37496271 PMCID: PMC10811348 DOI: 10.1016/j.xplc.2023.100663] [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: 02/14/2023] [Revised: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Membraneless biomolecular condensates play important roles in both normal biological activities and responses to environmental stimuli in living organisms. Liquid‒liquid phase separation (LLPS) is an organizational mechanism that has emerged in recent years to explain the formation of biomolecular condensates. In the past decade, advances in LLPS research have contributed to breakthroughs in disease fields. By contrast, although LLPS research in plants has progressed over the past 5 years, it has been concentrated on the model plant Arabidopsis, which has limited relevance to agricultural production. In this review, we provide an overview of recently reported advances in LLPS in plants, with a particular focus on photomorphogenesis, flowering, and abiotic and biotic stress responses. We propose that many potential LLPS proteins also exist in crops and may affect crop growth, development, and stress resistance. This possibility presents a great challenge as well as an opportunity for rigorous scientific research on the biological functions and applications of LLPS in crops.
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Affiliation(s)
- Qianwen Liu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Tao Wang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiangli Dong
- College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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18
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Hoffmann C, Milovanovic D. Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes. J Cell Sci 2023; 136:jcs261413. [PMID: 38149872 PMCID: PMC10785658 DOI: 10.1242/jcs.261413] [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] [Indexed: 12/28/2023] Open
Abstract
Liquid-liquid phase separation is a major mechanism for organizing macromolecules, particularly proteins with intrinsically disordered regions, in compartments not limited by a membrane or a scaffold. The cell can therefore be perceived as a complex emulsion containing many of these membraneless organelles, also referred to as biomolecular condensates, together with numerous membrane-bound organelles. It is currently unclear how such a complex concoction operates to allow for intracellular trafficking, signaling and metabolic processes to occur with high spatiotemporal precision. Based on experimental observations of synaptic vesicle condensates - a membraneless organelle that is in fact packed with membranes - we present here the framework of dipping contacts: a novel type of contact site between membraneless organelles and membranes. In this Hypothesis, we propose that our framework of dipping contacts can serve as a foundation to investigate the interface that couples the diffusion and material properties of condensates to biochemical processes occurring in membranes. The identity and regulation of this interface is especially critical in the case of neurodegenerative diseases, where aberrant inclusions of misfolded proteins and damaged organelles underlie cellular pathology.
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Affiliation(s)
- Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- National Center for X-ray Tomography, Advanced Light Source, Berkeley, CA 94720, USA
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Berlin and Berlin Institute of Health, 10117 Berlin, Germany
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19
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Chen Y, Wang Y, Wang T, Pei X, Zhang J, Liu Y. TRIM21 undergoes phase separation dependent CC domain to regulate autophagy. Biochem Biophys Res Commun 2023; 684:149101. [PMID: 37879251 DOI: 10.1016/j.bbrc.2023.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
Tripartite motif (TRIM) family proteins as E3-ligases participate in various biological processes. TRIM21, as the first autoantibody protein, has been found to be associated with autophagy. However, the role of TRIM21 engaging in autophagy is still unclear. In this study, TRIM21 forms significate puncta in the cytoplasm and undergoes liquid-liquid phase separation in vitro. Furthermore, we identify phase separation of the coiled-coil (CC) domain is essential for autophagosome to mediate autophagy-related protein recruited. These findings show that phase separation of the CC domain of TRIM21 promotes autophagosome to impact cell fate.
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Affiliation(s)
- Yatao Chen
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Tan Wang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoying Pei
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jun Zhang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China.
| | - Yan Liu
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China.
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20
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Liang P, Zhang J, Wang B. Emerging Roles of Ubiquitination in Biomolecular Condensates. Cells 2023; 12:2329. [PMID: 37759550 PMCID: PMC10527650 DOI: 10.3390/cells12182329] [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: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Biomolecular condensates are dynamic non-membrane-bound macromolecular high-order assemblies that participate in a growing list of cellular processes, such as transcription, the cell cycle, etc. Disturbed dynamics of biomolecular condensates are associated with many diseases, including cancer and neurodegeneration. Extensive efforts have been devoted to uncovering the molecular and biochemical grammar governing the dynamics of biomolecular condensates and establishing the critical roles of protein posttranslational modifications (PTMs) in this process. Here, we summarize the regulatory roles of ubiquitination (a major form of cellular PTM) in the dynamics of biomolecular condensates. We propose that these regulatory mechanisms can be harnessed to combat many diseases.
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Affiliation(s)
- Peigang Liang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (P.L.); (J.Z.)
| | - Jiaqi Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (P.L.); (J.Z.)
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (P.L.); (J.Z.)
- Shenzhen Research Institute of Xiamen University, Shenzhen 518057, China
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21
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Hou K, Liu T, Li J, Xian M, Sun L, Wei J. Liquid-liquid phase separation regulates alpha-synuclein aggregate and mitophagy in Parkinson's disease. Front Neurosci 2023; 17:1250532. [PMID: 37781241 PMCID: PMC10536155 DOI: 10.3389/fnins.2023.1250532] [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: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the world, and alpha-synuclein (α-syn) abnormal aggregate and mitochondrial dysfunction play a crucial role in its pathological development. Recent studies have revealed that proteins can form condensates through liquid-liquid phase separation (LLPS), and LLPS has been found to be widely present in α-syn aberrant aggregate and mitophagy-related protein physiological processes. This review summarizes the occurrence of α-syn LLPS and its influencing factors, introduces the production and transformation of the related protein LLPS during PINK1-Parkin-mediated mitophagy, hoping to provide new ideas and methods for the study of PD pathology.
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Affiliation(s)
- Kaiying Hou
- School of Life Sciences, Henan University, Kaifeng, China
| | - Tingting Liu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Jingwen Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Meiyan Xian
- School of Life Sciences, Henan University, Kaifeng, China
| | - Lin Sun
- College of Chemistry and Molecular Sciences, Henan University, Kaifeng, China
| | - Jianshe Wei
- School of Life Sciences, Henan University, Kaifeng, China
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22
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Nakagawa M, Tomioka Y, Sakuma C, Kurosawa Y, Shibata T, Arakawa T, Akuta T. Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis. Electrophoresis 2023; 44:1446-1460. [PMID: 37294166 DOI: 10.1002/elps.202200255] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023]
Abstract
A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first-dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native-PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS-PAGE gels or the edge of the flat SDS-MetaPhor high-resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen-antibody complexes, as well as complex proteins such as IgM pentamer and β-galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5-6 h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.
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Affiliation(s)
- Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
- Abwiz Bio Inc., San Diego, California, USA
| | - Takashi Shibata
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | | | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
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23
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Wang W, Wang C, Wang Y, Ma J, Wang T, Tao Z, Liu P, Li S, Hu Y, Gu A, Wang H, Qiu C, Li P. The P-body component DECAPPING5 and the floral repressor SISTER OF FCA regulate FLOWERING LOCUS C transcription in Arabidopsis. THE PLANT CELL 2023; 35:3303-3324. [PMID: 37220754 PMCID: PMC10473201 DOI: 10.1093/plcell/koad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 04/30/2023] [Indexed: 05/25/2023]
Abstract
Flowering is the transition from vegetative to reproductive growth and is critical for plant adaptation and reproduction. FLOWERING LOCUS C (FLC) plays a central role in flowering time control, and dissecting its regulation mechanism provides essential information for crop improvement. Here, we report that DECAPPING5 (DCP5), a component of processing bodies (P-bodies), regulates FLC transcription and flowering time in Arabidopsis (Arabidopsis thaliana). DCP5 and its interacting partner SISTER OF FCA (SSF) undergo liquid-liquid phase separation (LLPS) that is mediated by their prion-like domains (PrDs). Enhancing or attenuating the LLPS of both proteins using transgenic methods greatly affects their ability to regulate FLC and flowering time. DCP5 regulates FLC transcription by modulating RNA polymerase II enrichment at the FLC locus. DCP5 requires SSF for FLC regulation, and loss of SSF or its PrD disrupts DCP5 function. Our results reveal that DCP5 interacts with SSF, and the nuclear DCP5-SSF complex regulates FLC expression at the transcriptional level.
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Affiliation(s)
- Wanyi Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chuanhong Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yunhe Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Jing Ma
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Tengyue Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Zhen Tao
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Peipei Liu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Shuai Li
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yuanyuan Hu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Aiju Gu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Hui Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chunhong Qiu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Peijin Li
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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24
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Li J, Zhu K, Gu A, Zhang Y, Huang S, Hu R, Hu W, Lei QY, Wen W. Feedback regulation of ubiquitination and phase separation of HECT E3 ligases. Proc Natl Acad Sci U S A 2023; 120:e2302478120. [PMID: 37549262 PMCID: PMC10438380 DOI: 10.1073/pnas.2302478120] [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: 02/13/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Lipid homeostasis is essential for normal cellular functions and dysregulation of lipid metabolism is highly correlated with human diseases including neurodegenerative diseases. In the ubiquitin-dependent autophagic degradation pathway, Troyer syndrome-related protein Spartin activates and recruits HECT-type E3 Itch to lipid droplets (LDs) to regulate their turnover. In this study, we find that Spartin promotes the formation of Itch condensates independent of LDs. Spartin activates Itch through its multiple PPAY-motif platform generated by self-oligomerization, which targets the WW12 domains of Itch and releases the autoinhibition of the ligase. Spartin-induced activation and subsequent autoubiquitination of Itch lead to liquid-liquid phase separation (LLPS) of the poly-, but not oligo-, ubiquitinated Itch together with Spartin and E2 both in vitro and in living cells. LLPS-mediated condensation of the reaction components further accelerates the generation of polyubiquitin chains, thus forming a positive feedback loop. Such Itch-Spartin condensates actively promote the autophagy-dependent turnover of LDs. Moreover, we show that the catalytic HECT domain of Itch is sufficient to interact and phase separate with poly-, but not oligo-ubiquitin chains. HECT domains from other HECT E3 ligases also exhibit LLPS-mediated the promotion of ligase activity. Therefore, LLPS and ubiquitination are mutually interdependent and LLPS promotes the ligase activity of the HECT family E3 ligases.
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Affiliation(s)
- Jingyu Li
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, National Center for Neurological Disorders, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Kang Zhu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, National Center for Neurological Disorders, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Aihong Gu
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, National Center for Neurological Disorders, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Yiqing Zhang
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, National Center for Neurological Disorders, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Shijing Huang
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, National Center for Neurological Disorders, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Ronggui Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai200032, China
| | - Weiguo Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Qun-Ying Lei
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, National Center for Neurological Disorders, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
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25
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Baechle JJ, Chen N, Makhijani P, Winer S, Furman D, Winer DA. Chronic inflammation and the hallmarks of aging. Mol Metab 2023; 74:101755. [PMID: 37329949 PMCID: PMC10359950 DOI: 10.1016/j.molmet.2023.101755] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Recently, the hallmarks of aging were updated to include dysbiosis, disabled macroautophagy, and chronic inflammation. In particular, the low-grade chronic inflammation during aging, without overt infection, is defined as "inflammaging," which is associated with increased morbidity and mortality in the aging population. Emerging evidence suggests a bidirectional and cyclical relationship between chronic inflammation and the development of age-related conditions, such as cardiovascular diseases, neurodegeneration, cancer, and frailty. How the crosstalk between chronic inflammation and other hallmarks of aging underlies biological mechanisms of aging and age-related disease is thus of particular interest to the current geroscience research. SCOPE OF REVIEW This review integrates the cellular and molecular mechanisms of age-associated chronic inflammation with the other eleven hallmarks of aging. Extra discussion is dedicated to the hallmark of "altered nutrient sensing," given the scope of Molecular Metabolism. The deregulation of hallmark processes during aging disrupts the delicate balance between pro-inflammatory and anti-inflammatory signaling, leading to a persistent inflammatory state. The resultant chronic inflammation, in turn, further aggravates the dysfunction of each hallmark, thereby driving the progression of aging and age-related diseases. MAIN CONCLUSIONS The crosstalk between chronic inflammation and other hallmarks of aging results in a vicious cycle that exacerbates the decline in cellular functions and promotes aging. Understanding this complex interplay will provide new insights into the mechanisms of aging and the development of potential anti-aging interventions. Given their interconnectedness and ability to accentuate the primary elements of aging, drivers of chronic inflammation may be an ideal target with high translational potential to address the pathological conditions associated with aging.
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Affiliation(s)
- Jordan J Baechle
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | - Nan Chen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada
| | - Priya Makhijani
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David Furman
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA; Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral, CONICET, Pilar, Argentina.
| | - Daniel A Winer
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada; Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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26
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Guo X, Zhu K, Zhu X, Zhao W, Miao Y. Two-dimensional molecular condensation in cell signaling and mechanosensing. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1064-1074. [PMID: 37475548 PMCID: PMC10423693 DOI: 10.3724/abbs.2023132] [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: 01/28/2023] [Accepted: 05/21/2023] [Indexed: 07/22/2023] Open
Abstract
Membraneless organelles (MLO) regulate diverse biological processes in a spatiotemporally controlled manner spanning from inside to outside of the cells. The plasma membrane (PM) at the cell surface serves as a central platform for forming multi-component signaling hubs that sense mechanical and chemical cues during physiological and pathological conditions. During signal transduction, the assembly and formation of membrane-bound MLO are dynamically tunable depending on the physicochemical properties of the surrounding environment and partitioning biomolecules. Biomechanical properties of MLO-associated membrane structures can control the microenvironment for biomolecular interactions and assembly. Lipid-protein complex interactions determine the catalytic region's assembly pattern and assembly rate and, thereby, the amplitude of activities. In this review, we will focus on how cell surface microenvironments, including membrane curvature, surface topology and tension, lipid-phase separation, and adhesion force, guide the assembly of PM-associated MLO for cell signal transductions.
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Affiliation(s)
- Xiangfu Guo
- School of ChemistryChemical Engineering and BiotechnologyNanyang Technological UniversitySingapore637457Singapore
| | - Kexin Zhu
- School of Biological SciencesNanyang Technological UniversitySingapore637551Singapore
| | - Xinlu Zhu
- School of Biological SciencesNanyang Technological UniversitySingapore637551Singapore
| | - Wenting Zhao
- School of ChemistryChemical Engineering and BiotechnologyNanyang Technological UniversitySingapore637457Singapore
- Institute for Digital Molecular Analytics and ScienceNanyang Technological UniversitySingapore636921Singapore
| | - Yansong Miao
- School of Biological SciencesNanyang Technological UniversitySingapore637551Singapore
- Institute for Digital Molecular Analytics and ScienceNanyang Technological UniversitySingapore636921Singapore
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27
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Rangachari V. Biomolecular condensates - extant relics or evolving microcompartments? Commun Biol 2023; 6:656. [PMID: 37344557 PMCID: PMC10284869 DOI: 10.1038/s42003-023-04963-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Unprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39402, USA.
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28
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Zheng H, Peng K, Gou X, Ju C, Zhang H. RNA recruitment switches the fate of protein condensates from autophagic degradation to accumulation. J Cell Biol 2023; 222:e202210104. [PMID: 37014300 PMCID: PMC10075224 DOI: 10.1083/jcb.202210104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/07/2023] [Accepted: 03/01/2023] [Indexed: 04/05/2023] Open
Abstract
Protein condensates can evade autophagic degradation under stress or pathological conditions. However, the underlying mechanisms are unclear. Here, we demonstrate that RNAs switch the fate of condensates in Caenorhabditis elegans. PGL granules undergo autophagic degradation in embryos laid under normal conditions and accumulate in embryos laid under heat stress conditions to confer stress adaptation. In heat-stressed embryos, mRNAs and RNA control factors partition into PGL granules. Depleting proteins involved in mRNA biogenesis and stability suppresses PGL granule accumulation and triggers their autophagic degradation, while loss of activity of proteins involved in RNA turnover facilitates accumulation. RNAs facilitate LLPS of PGL granules, enhance their liquidity, and also inhibit recruitment of the gelation-promoting scaffold protein EPG-2 to PGL granules. Thus, RNAs are important for controlling the susceptibility of phase-separated protein condensates to autophagic degradation. Our work provides insights into the accumulation of ribonucleoprotein aggregates associated with the pathogenesis of various diseases.
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Affiliation(s)
- Hui Zheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kangfu Peng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomeng Gou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Ju
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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29
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Park SH, Lee SE, Jeon JH, Lee JH, Itakura E, Chang S, Choi WH, Lee MJ. Formation of aggresomes with hydrogel-like characteristics by proteasome inhibition. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194932. [PMID: 36997115 DOI: 10.1016/j.bbagrm.2023.194932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/08/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
The spatiotemporal sequestration of misfolded proteins is a mechanism by which cells counterbalance proteome homeostasis upon exposure to various stress stimuli. Chronic inhibition of proteasomes results in a large, juxtanuclear, membrane-less inclusion, known as the aggresome. Although the molecular mechanisms driving its formation, clearance, and pathophysiological implications are continuously being uncovered, the biophysical aspects of aggresomes remain largely uncharacterized. Using fluorescence recovery after photobleaching and liquid droplet disruption assays, we found that the aggresomes are a homogeneously blended condensates with liquid-like properties similar to droplets formed via liquid-liquid phase separation. However, unlike fluidic liquid droplets, aggresomes have more viscosity and hydrogel-like characteristics. We also observed that the inhibition of aggresome formation using microtubule-disrupting agents resulted in less soluble and smaller cytoplasmic speckles, which was associated with marked cytotoxicity. Therefore, the aggresome appears to be cytoprotective and serves as a temporal reservoir for dysfunctional proteasomes and substrates that need to be degraded. Our results suggest that the aggresome assembles through distinct and potentially sequential processes of energy-dependent retrograde transportation and spontaneous condensation into a hydrogel.
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Affiliation(s)
- Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
| | - Sang-Eun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jun Hyoung Jeon
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Seegene, Inc., Seoul 05548, Republic of Korea
| | - Jung Hoon Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cellular Degradation Biology Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Eisuke Itakura
- Department of Biology, Graduate School of Science, Chiba University, Inage-ku, Chiba 263-8522, Japan
| | - Sunghoe Chang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea; Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cellular Degradation Biology Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cellular Degradation Biology Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
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30
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Ma Q, Huang F, Guo W, Feng K, Huang T, Cai Y. Identification of Phase-Separation-Protein-Related Function Based on Gene Ontology by Using Machine Learning Methods. Life (Basel) 2023; 13:1306. [PMID: 37374089 DOI: 10.3390/life13061306] [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: 03/23/2023] [Revised: 05/06/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Phase-separation proteins (PSPs) are a class of proteins that play a role in the process of liquid-liquid phase separation, which is a mechanism that mediates the formation of membranelle compartments in cells. Identifying phase separation proteins and their associated function could provide insights into cellular biology and the development of diseases, such as neurodegenerative diseases and cancer. Here, PSPs and non-PSPs that have been experimentally validated in earlier studies were gathered as positive and negative samples. Each protein's corresponding Gene Ontology (GO) terms were extracted and used to create a 24,907-dimensional binary vector. The purpose was to extract essential GO terms that can describe essential functions of PSPs and build efficient classifiers to identify PSPs with these GO terms at the same time. To this end, the incremental feature selection computational framework and an integrated feature analysis scheme, containing categorical boosting, least absolute shrinkage and selection operator, light gradient-boosting machine, extreme gradient boosting, and permutation feature importance, were used to build efficient classifiers and identify GO terms with classification-related importance. A set of random forest (RF) classifiers with F1 scores over 0.960 were established to distinguish PSPs from non-PSPs. A number of GO terms that are crucial for distinguishing between PSPs and non-PSPs were found, including GO:0003723, which is related to a biological process involving RNA binding; GO:0016020, which is related to membrane formation; and GO:0045202, which is related to the function of synapses. This study offered recommendations for future research aimed at determining the functional roles of PSPs in cellular processes by developing efficient RF classifiers and identifying the representative GO terms related to PSPs.
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Affiliation(s)
- Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China
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31
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Sakuta H, Nakatani N, Torisawa T, Sumino Y, Tsumoto K, Oiwa K, Yoshikawa K. Self-emergent vortex flow of microtubule and kinesin in cell-sized droplets under water/water phase separation. Commun Chem 2023; 6:80. [PMID: 37100870 PMCID: PMC10133263 DOI: 10.1038/s42004-023-00879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 04/11/2023] [Indexed: 04/28/2023] Open
Abstract
By facilitating a water/water phase separation (w/wPS), crowded biopolymers in cells form droplets that contribute to the spatial localization of biological components and their biochemical reactions. However, their influence on mechanical processes driven by protein motors has not been well studied. Here, we show that the w/wPS droplet spontaneously entraps kinesins as well as microtubules (MTs) and generates a micrometre-scale vortex flow inside the droplet. Active droplets with a size of 10-100 µm are generated through w/wPS of dextran and polyethylene glycol mixed with MTs, molecular-engineered chimeric four-headed kinesins and ATP after mechanical mixing. MTs and kinesin rapidly created contractile network accumulated at the interface of the droplet and gradually generated vortical flow, which can drive translational motion of a droplet. Our work reveals that the interface of w/wPS contributes not only to chemical processes but also produces mechanical motion by assembling species of protein motors in a functioning manner.
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Affiliation(s)
- Hiroki Sakuta
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Organization for Research Initiatives and Development, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
| | - Naoki Nakatani
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
| | - Takayuki Torisawa
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Sumino
- Department of Applied Physics, Faculty of Advanced Engineering, WaTUS and DCIS, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan.
| | - Kanta Tsumoto
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan.
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako, Hyogo, 678-1297, Japan.
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
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32
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Wang Z, Yang C, Guan D, Li J, Zhang H. Cellular proteins act as surfactants to control the interfacial behavior and function of biological condensates. Dev Cell 2023:S1534-5807(23)00157-0. [PMID: 37098348 DOI: 10.1016/j.devcel.2023.04.004] [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: 10/24/2022] [Revised: 03/02/2023] [Accepted: 04/01/2023] [Indexed: 04/27/2023]
Abstract
Interfacial tension governs the behaviors and physiological functions of multiple biological condensates during diverse biological processes. Little is known about whether there are cellular surfactant factors that regulate the interfacial tension and functions of biological condensates within physiological environments. TFEB, a master transcription factor that controls expression of autophagic-lysosomal genes, assembles into transcriptional condensates to control the autophagy-lysosome pathway (ALP). Here, we show that interfacial tension modulates the transcriptional activity of TFEB condensates. MLX, MYC, and IPMK act as synergistic surfactants to decrease the interfacial tension and consequent DNA affinity of TFEB condensates. The interfacial tension of TFEB condensates is quantitatively correlated to their DNA affinity and subsequent ALP activity. The interfacial tension and DNA affinity of condensates formed by TAZ-TEAD4 are also regulated by the synergistic surfactant proteins RUNX3 and HOXA4. Our results indicate that the interfacial tension and functions of biological condensates can be controlled by cellular surfactant proteins in human cells.
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Affiliation(s)
- Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.
| | - Chun Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Dongshi Guan
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Jiaqi Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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33
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Di Nunzio F, Uversky VN, Mouland AJ. Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle. Retrovirology 2023; 20:4. [PMID: 37029379 PMCID: PMC10081342 DOI: 10.1186/s12977-023-00619-6] [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: 12/07/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023] Open
Abstract
A rapidly evolving understanding of phase separation in the biological and physical sciences has led to the redefining of virus-engineered replication compartments in many viruses with RNA genomes. Condensation of viral, host and genomic and subgenomic RNAs can take place to evade the innate immunity response and to help viral replication. Divergent viruses prompt liquid-liquid phase separation (LLPS) to invade the host cell. During HIV replication there are several steps involving LLPS. In this review, we characterize the ability of individual viral and host partners that assemble into biomolecular condensates (BMCs). Of note, bioinformatic analyses predict models of phase separation in line with several published observations. Importantly, viral BMCs contribute to function in key steps retroviral replication. For example, reverse transcription takes place within nuclear BMCs, called HIV-MLOs while during late replication steps, retroviral nucleocapsid acts as a driver or scaffold to recruit client viral components to aid the assembly of progeny virions. Overall, LLPS during viral infections represents a newly described biological event now appreciated in the virology field, that can also be considered as an alternative pharmacological target to current drug therapies especially when viruses become resistant to antiviral treatment.
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Affiliation(s)
- Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Andrew J Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC, H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
- Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
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34
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Dong W, Tang C, Chu WT, Wang E, Wang J. Effects of Mass Change on Liquid–Liquid Phase Separation of the RNA-Binding Protein Fused in Sarcoma. Biomolecules 2023; 13:biom13040625. [PMID: 37189373 DOI: 10.3390/biom13040625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
In recent years, many experimental and theoretical studies of protein liquid–liquid phase separation (LLPS) have shown its important role in the processes of physiology and pathology. However, there is a lack of definite information on the regulation mechanism of LLPS in vital activities. Recently, we found that the intrinsically disordered proteins with the insertion/deletion of a non-interacting peptide segment or upon isotope replacement could form droplets, and the LLPS states are different from the proteins without those. We believed that there is an opportunity to decipher the LLPS mechanism with the mass change perspective. To investigate the effect of molecular mass on LLPS, we developed a coarse-grained model with different bead masses, including mass 1.0, mass 1.1, mass 1.2, mass 1.3, and mass 1.5 in atomic units or with the insertion of a non-interacting peptide (10 aa) and performed molecular dynamic simulations. Consequently, we found that the mass increase promotes the LLPS stability, which is based on decreasing the z motion rate and increasing the density and the inter-chain interaction of droplets. This insight into LLPS by mass change paves the way for the regulation and relevant diseases on LLPS.
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35
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Che X, Wu J, Liu H, Su J, Chen X. Cellular liquid-liquid phase separation: Concept, functions, regulations, and detections. J Cell Physiol 2023; 238:847-865. [PMID: 36870067 DOI: 10.1002/jcp.30980] [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: 06/06/2022] [Revised: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023]
Abstract
Liquid-liquid phase separation is a multicomponent system separated into phases with different compositions and structures. It has been identified and explored in organisms after being introduced from the thermodynamic field. Condensate, the product of phase separation, exists in different scales of cellular structures, such as nucleolus, stress granules, and other organelles in nuclei or cytoplasm. And also play critical roles in different cellular behaviors. Here, we review the concept, thermodynamical and biochemical principles of phase separation. We summarized the main functions including the adjustment of biochemical reaction rates, the regulation of macromolecule folding state, subcellular structural support, the mediation of subcellular location, and intimately linked to different kinds of diseases, such as cancer and neurodegeneration. Advanced detection methods to investigate phase separation are collected and analyzed. We conclude with the discussion of anxiety of phase separation, and thought about how progress can be made to develop precise detection methods and disclose the potential application of condensates.
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Affiliation(s)
- Xuanlin Che
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Jiajun Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
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36
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Staples MI, Frazer C, Fawzi NL, Bennett RJ. Phase separation in fungi. Nat Microbiol 2023; 8:375-386. [PMID: 36782025 PMCID: PMC10081517 DOI: 10.1038/s41564-022-01314-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
Phase separation, in which macromolecules partition into a concentrated phase that is immiscible with a dilute phase, is involved with fundamental cellular processes across the tree of life. We review the principles of phase separation and highlight how it impacts diverse processes in the fungal kingdom. These include the regulation of autophagy, cell signalling pathways, transcriptional circuits and the establishment of asymmetry in fungal cells. We describe examples of stable, phase-separated assemblies including membraneless organelles such as the nucleolus as well as transient condensates that also arise through phase separation and enable cells to rapidly and reversibly respond to important environmental cues. We showcase how research into phase separation in model yeasts, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe, in conjunction with that in plant and human fungal pathogens, such as Ashbya gossypii and Candida albicans, is continuing to enrich our understanding of fundamental molecular processes.
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Affiliation(s)
- Mae I Staples
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Corey Frazer
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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37
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Takahashi D, Arimoto H. p62 Phase-Separation as the Foundation of Autophagy-Based Degraders. Biochemistry 2023; 62:559-560. [PMID: 35767697 DOI: 10.1021/acs.biochem.2c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Daiki Takahashi
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Hirokazu Arimoto
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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38
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Li Y, Chen T, You K, Peng T, Li T. Sequence determinants and solution conditions underlying liquid to solid phase transition. Am J Physiol Cell Physiol 2023; 324:C236-C246. [PMID: 36503242 DOI: 10.1152/ajpcell.00280.2022] [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: 12/15/2022]
Abstract
Life consists of numberless functional biomolecules that exist in various states. Besides well-dissolved phases, biomolecules especially proteins and nucleic acids can form liquid droplets through liquid-liquid phase separation (LLPS). Stronger interactions promote a solid-like state of biomolecular condensates, which are also formerly referred to as detergent-insoluble aggregates. Solid-like condensates exist in vivo physiologically and pathologically, and their formation has not been fully understood. Recently, more and more research has proven that liquid to solid phase transition (LST) is an essential way to form solid condensates. In this review, we summarized the regions in the sequence that have different impacts on phase transition and emphasized that the LST is affected by its sequence characteristics. Moreover, increasing evidence unveiled that LST is affected by various solution conditions. We discussed solution conditions like protein concentration, pH, ATP, ions, and small molecules in a solution. Methods have been established to study these solid phase components. Here, we summarized low-throughput experimental techniques and high-throughput omics methods in the study of the LST.
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Affiliation(s)
- Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Kaiqing You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Happy Life Technology, Beijing, China
| | - Tao Peng
- Happy Life Technology, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
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39
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Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
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Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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40
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Chen G, Wei T, Ju F, Li H. Protein quality control and aggregation in the endoplasmic reticulum: From basic to bedside. Front Cell Dev Biol 2023; 11:1156152. [PMID: 37152279 PMCID: PMC10154544 DOI: 10.3389/fcell.2023.1156152] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Endoplasmic reticulum (ER) is the largest membrane-bound compartment in all cells and functions as a key regulator in protein biosynthesis, lipid metabolism, and calcium balance. Mammalian endoplasmic reticulum has evolved with an orchestrated protein quality control system to handle defective proteins and ensure endoplasmic reticulum homeostasis. Nevertheless, the accumulation and aggregation of misfolded proteins in the endoplasmic reticulum may occur during pathological conditions. The inability of endoplasmic reticulum quality control system to clear faulty proteins and aggregates from the endoplasmic reticulum results in the development of many human disorders. The efforts to comprehensively understand endoplasmic reticulum quality control network and protein aggregation will benefit the diagnostics and therapeutics of endoplasmic reticulum storage diseases. Herein, we overview recent advances in mammalian endoplasmic reticulum protein quality control system, describe protein phase transition model, and summarize the approaches to monitor protein aggregation. Moreover, we discuss the therapeutic applications of enhancing endoplasmic reticulum protein quality control pathways in endoplasmic reticulum storage diseases.
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Affiliation(s)
- Guofang Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tingyi Wei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Furong Ju
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Sha Tin, Hong kong SAR, China
| | - Haisen Li
- School of Life Sciences, Fudan University, Shanghai, China
- AoBio Medical, Shanghai, China
- *Correspondence: Haisen Li,
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41
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HDAC1/3-dependent moderate liquid-liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation. Cell Death Dis 2022; 13:992. [PMID: 36424383 PMCID: PMC9691727 DOI: 10.1038/s41419-022-05435-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Abstract
Methyltransferase-like protein 3 (METTL3) plays critical roles in acute myeloid leukemia (AML) progression, however, the mechanism of abnormal overexpression of METTL3 in AML remain elusive. In the current study, we uncovered that Yin Yang 1 (YY1) binds to the promoter region of METTL3 as a transcription factor and promotes its expression, which in turn enhances the proliferation of AML cells. Mechanistically, YY1 binds to HDAC1/3 and regulates METTL3 expression in a moderate liquid-liquid phase separation (LLPS) manner. After mutation of the HDAC-binding site of YY1 or HDAC inhibitor (HDACi) treatment, YY1 was separated from HDAC1/3, which resulted in an excessive LLPS state, thereby inhibiting the expression of METTL3 and the proliferation of AML cells. In conclusion, our study clarified the regulatory mechanism of the abnormal expression of METTL3 in AML, revealed the precise "Yin-Yang" regulatory mechanism of YY1 from the perspective of LLPS degree, and provided new ideas for the precise diagnosis and treatment of AML.
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42
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Autophagy protein ULK1 interacts with and regulates SARM1 during axonal injury. Proc Natl Acad Sci U S A 2022; 119:e2203824119. [PMID: 36375051 PMCID: PMC9704737 DOI: 10.1073/pnas.2203824119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Autophagy is a cellular catabolic pathway generally thought to be neuroprotective. However, autophagy and in particular its upstream regulator, the ULK1 kinase, can also promote axonal degeneration. We examined the role and the mechanisms of autophagy in axonal degeneration using a mouse model of contusive spinal cord injury (SCI). Consistent with activation of autophagy during axonal degeneration following SCI, autophagosome marker LC3, ULK1 kinase, and ULK1 target, phospho-ATG13, accumulated in the axonal bulbs and injured axons. SARM1, a TIR NADase with a pivotal role in axonal degeneration, colocalized with ULK1 within 1 h after SCI, suggesting possible interaction between autophagy and SARM1-mediated axonal degeneration. In our in vitro experiments, inhibition of autophagy, including Ulk1 knockdown and ULK1 inhibitor, attenuated neurite fragmentation and reduced accumulation of SARM1 puncta in neurites of primary cortical neurons subjected to glutamate excitotoxicity. Immunoprecipitation data demonstrated that ULK1 physically interacted with SARM1 in vitro and in vivo and that SAM domains of SARM1 were necessary for ULK1-SARM1 complex formation. Consistent with a role in regulation of axonal degeneration, in primary cortical neurons ULK1-SARM1 interaction increased upon neurite damage. Supporting a role for autophagy and ULK1 in regulation of SARM1 in axonal degeneration in vivo, axonal ULK1 activation and accumulation of SARM1 were both decreased after SCI in Becn1+/- autophagy hypomorph mice compared to wild-type (WT) controls. These findings suggest a regulatory crosstalk between autophagy and axonal degeneration pathways, which is mediated through ULK1-SARM1 interaction and contributes to the ability of SARM1 to accumulate in injured axons.
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43
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Hill SE, Esquivel AR, Ospina SR, Rahal LM, Dickey CA, Blair LJ. Chaperoning activity of the cyclophilin family prevents tau aggregation. Protein Sci 2022; 31:e4448. [PMID: 36305768 PMCID: PMC9597375 DOI: 10.1002/pro.4448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/18/2022] [Accepted: 09/11/2022] [Indexed: 11/09/2022]
Abstract
Tauopathies, such as Alzheimer's disease, are characterized by the misfolding and progressive accumulation of the microtubule associated protein tau. Chaperones, tasked with maintaining protein homeostasis, can become imbalanced with age and contribute to the progression of neurodegenerative disease. Cyclophilins are a promising pool of underinvestigated chaperones with peptidyl-prolyl isomerase activity that may play protective roles in regulating tau aggregation. Using a Thioflavin T fluorescence-based assay to monitor in vitro tau aggregation, all eight cyclophilins, which include PPIA to PPIH prevent tau aggregation, with PPIB, PPIC, PPID, and PPIH showing the greatest inhibition. The low thermal stability of PPID and the strong heparin binding of PPIB undermines the simplistic interpretation of reduced tau aggregation. In a cellular model of tau accumulation, all cyclophilins, except PPID and PPIH, reduce insoluble tau. PPIB, PPIC, PPIE, and PPIF also reduce soluble tau levels with PPIC exclusively protecting cells from tau seeding. Overall, this study demonstrates cyclophilins prevent tau fibril formation and many reduce cellular insoluble tau accumulation with PPIC having the greatest potential as a molecular tool to mitigate tau seeding and accumulation.
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Affiliation(s)
- Shannon E. Hill
- USF Health Byrd Alzheimer's InstituteUniversity of South FloridaTampaFloridaUSA
- Department of Molecular MedicineUniversity of South FloridaTampaFloridaUSA
| | - Abigail R. Esquivel
- USF Health Byrd Alzheimer's InstituteUniversity of South FloridaTampaFloridaUSA
- Department of Molecular MedicineUniversity of South FloridaTampaFloridaUSA
| | - Santiago Rodriguez Ospina
- USF Health Byrd Alzheimer's InstituteUniversity of South FloridaTampaFloridaUSA
- Department of Molecular MedicineUniversity of South FloridaTampaFloridaUSA
| | - Lauren M. Rahal
- USF Health Byrd Alzheimer's InstituteUniversity of South FloridaTampaFloridaUSA
- Department of Molecular MedicineUniversity of South FloridaTampaFloridaUSA
| | - Chad A. Dickey
- USF Health Byrd Alzheimer's InstituteUniversity of South FloridaTampaFloridaUSA
- Department of Molecular MedicineUniversity of South FloridaTampaFloridaUSA
| | - Laura J. Blair
- USF Health Byrd Alzheimer's InstituteUniversity of South FloridaTampaFloridaUSA
- Department of Molecular MedicineUniversity of South FloridaTampaFloridaUSA
- Research ServiceJames A. Haley Veterans HospitalTampaFloridaUSA
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44
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Magné J, Green DR. LC3-associated endocytosis and the functions of Rubicon and ATG16L1. SCIENCE ADVANCES 2022; 8:eabo5600. [PMID: 36288306 PMCID: PMC9604520 DOI: 10.1126/sciadv.abo5600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
LC3-associated endocytosis (LANDO) is a noncanonical function of the autophagy machinery, in which LC3 (microtubule-associated protein light chain) is conjugated to rab5-positive endosomes, using a portion of the canonical autophagy pathway. LANDO was initially discovered in a murine model of Alzheimer's disease as a critical regulator of amyloid-β receptor recycling in microglial cells, playing a protective role against neuronal loss and memory impairment. Recent evidence suggests an emerging role of LANDO in cytokine receptor signaling and innate immunity. Here, we discuss the regulation of two crucial effectors of LANDO, Rubicon and ATG16L1, and their impact on endocytosis, autophagy, and phagocytosis.
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Abstract
Liquid-liquid phase separation (LLPS) triages protein cargoes for autophagic degradation. In this issue, Ohshima et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202203102) demonstrate that the autophagy receptor NCOA4 interacts with ferritin particles to form liquid-like condensates via LLPS. The NCOA4-ferritin condensates are delivered to lysosomes for degradation via either canonical macroautophagy or endosomal microautophagy to maintain intracellular iron homeostasis.
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Affiliation(s)
- Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Peng Q, Tan S, Xia L, Wu N, Oyang L, Tang Y, Su M, Luo X, Wang Y, Sheng X, Zhou Y, Liao Q. Phase separation in Cancer: From the Impacts and Mechanisms to Treatment potentials. Int J Biol Sci 2022; 18:5103-5122. [PMID: 35982902 PMCID: PMC9379413 DOI: 10.7150/ijbs.75410] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer is a public health problem of great concern, and it is also one of the main causes of death in the world. Cancer is a disease characterized by dysregulation of diverse cellular processes, including avoiding growth inhibitory factors, avoiding immune damage and promoting metastasis, etc. However, the precise mechanism of tumorigenesis and tumor progression still needs to be further elucidated. Formations of liquid-liquid phase separation (LLPS) condensates are a common strategy for cells to achieve diverse functions, such as chromatin organization, signal transduction, DNA repair and transcriptional regulation, etc. The biomolecular aggregates formed by LLPS are mainly driven by multivalent weak interactions mediated by intrinsic disordered regions (IDRs) in proteins. In recent years, aberrant phase separations and transition have been reported to be related to the process of various diseases, such as neurodegenerative diseases and cancer. Herein, we discussed recent findings that phase separation regulates tumor-related signaling pathways and thus contributes to tumor progression. We also reviewed some tumor virus-associated proteins to regulate the development of virus-associated tumors via phase separation. Finally, we discussed some possible strategies for treating tumors by targeting phase separation.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
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Chen X, Zhang M. Chaperonin-containing TCP-1 subunit 2-mediated aggrephagy: A potential target for treating neurodegeneration. Clin Transl Med 2022; 12:e1027. [PMID: 35988155 PMCID: PMC9393055 DOI: 10.1002/ctm2.1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xueshen Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Min Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
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Puca F, Fedele M, Rasio D, Battista S. Role of Diet in Stem and Cancer Stem Cells. Int J Mol Sci 2022; 23:ijms23158108. [PMID: 35897685 PMCID: PMC9330301 DOI: 10.3390/ijms23158108] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Diet and lifestyle factors greatly affect health and susceptibility to diseases, including cancer. Stem cells’ functions, including their ability to divide asymmetrically, set the rules for tissue homeostasis, contribute to health maintenance, and represent the entry point of cancer occurrence. Stem cell properties result from the complex integration of intrinsic, extrinsic, and systemic factors. In this context, diet-induced metabolic changes can have a profound impact on stem cell fate determination, lineage specification and differentiation. The purpose of this review is to provide a comprehensive description of the multiple “non-metabolic” effects of diet on stem cell functions, including little-known effects such as those on liquid-liquid phase separation and on non-random chromosome segregation (asymmetric division). A deep understanding of the specific dietetic requirements of normal and cancer stem cells may pave the way for the development of nutrition-based targeted therapeutic approaches to improve regenerative and anticancer therapies.
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Affiliation(s)
- Francesca Puca
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 78705, USA;
- Department of Oncology, IRBM Science Park SpA, 00071 Pomezia, Italy
| | - Monica Fedele
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), 80131 Naples, Italy;
| | - Debora Rasio
- Department of Clinical and Molecular Medicine, La Sapienza University, 00185 Rome, Italy;
| | - Sabrina Battista
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), 80131 Naples, Italy;
- Correspondence:
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Liquid-liquid phase separation in tumor biology. Signal Transduct Target Ther 2022; 7:221. [PMID: 35803926 PMCID: PMC9270353 DOI: 10.1038/s41392-022-01076-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids into micron-scale, liquid-like, membraneless bodies with specific functions, which were recently termed biomolecular condensates. Biomolecular condensates are executors underlying the intracellular spatiotemporal coordination of various biological activities, including chromatin organization, genomic stability, DNA damage response and repair, transcription, and signal transduction. Dysregulation of these cellular processes is a key event in the initiation and/or evolution of cancer, and emerging evidence has linked the formation and regulation of LLPS to malignant transformations in tumor biology. In this review, we comprehensively summarize the detailed mechanisms of biomolecular condensate formation and biophysical function and review the recent major advances toward elucidating the multiple mechanisms involved in cancer cell pathology driven by aberrant LLPS. In addition, we discuss the therapeutic perspectives of LLPS in cancer research and the most recently developed drug candidates targeting LLPS modulation that can be used to combat tumorigenesis.
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50
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Majeed ST, Majeed R, Andrabi KI. Expanding the view of the molecular mechanisms of autophagy pathway. J Cell Physiol 2022; 237:3257-3277. [DOI: 10.1002/jcp.30819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Sheikh Tahir Majeed
- Department of Biotechnology Central University of Kashmir Ganderbal Jammu and Kashmir India
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
| | - Rabiya Majeed
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
- Department of Biochemistry University of Kashmir Srinagar Jammu and Kashmir India
| | - Khurshid I. Andrabi
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
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