1
|
Zhao R, Huang S, Li J, Gu A, Fu M, Hua W, Mao Y, Lei QY, Lu B, Wen W. Excessive STAU1 condensate drives mTOR translation and autophagy dysfunction in neurodegeneration. J Cell Biol 2024; 223:e202311127. [PMID: 38913026 DOI: 10.1083/jcb.202311127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/20/2024] [Accepted: 05/03/2024] [Indexed: 06/25/2024] Open
Abstract
The double-stranded RNA-binding protein Staufen1 (STAU1) regulates a variety of physiological and pathological events via mediating RNA metabolism. STAU1 overabundance was observed in tissues from mouse models and fibroblasts from patients with neurodegenerative diseases, accompanied by enhanced mTOR signaling and impaired autophagic flux, while the underlying mechanism remains elusive. Here, we find that endogenous STAU1 forms dynamic cytoplasmic condensate in normal and tumor cell lines, as well as in mouse Huntington's disease knockin striatal cells. STAU1 condensate recruits target mRNA MTOR at its 5'UTR and promotes its translation both in vitro and in vivo, and thus enhanced formation of STAU1 condensate leads to mTOR hyperactivation and autophagy-lysosome dysfunction. Interference of STAU1 condensate normalizes mTOR levels, ameliorates autophagy-lysosome function, and reduces aggregation of pathological proteins in cellular models of neurodegenerative diseases. These findings highlight the importance of balanced phase separation in physiological processes, suggesting that modulating STAU1 condensate may be a strategy to mitigate the progression of neurodegenerative diseases with STAU1 overabundance.
Collapse
Affiliation(s)
- Ruiqian Zhao
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shijing Huang
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jingyu Li
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Aihong Gu
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Minjie Fu
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Hua
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qun-Ying Lei
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Boxun Lu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, New Cornerstone Science Laboratory, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, The Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
2
|
Wan L, Zhu Y, Zhang W, Mu W. Recent advances in design and application of synthetic membraneless organelles. Biotechnol Adv 2024; 73:108355. [PMID: 38588907 DOI: 10.1016/j.biotechadv.2024.108355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.
Collapse
Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
3
|
Geng Q, Keya JJ, Hotta T, Verhey KJ. The kinesin-3 KIF1C undergoes liquid-liquid phase separation for accumulation of specific transcripts at the cell periphery. EMBO J 2024:10.1038/s44318-024-00147-9. [PMID: 38898313 DOI: 10.1038/s44318-024-00147-9] [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: 03/19/2024] [Revised: 04/30/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
In cells, mRNAs are transported to and positioned at subcellular areas to locally regulate protein production. Recent studies have identified the kinesin-3 family member motor protein KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that the KIF1C C-terminal tail domain contains an intrinsically disordered region (IDR) that drives liquid-liquid phase separation (LLPS). KIF1C forms dynamic puncta in cells that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. Endogenous KIF1C forms condensates in cellular protrusions, where mRNAs are enriched in an IDR-dependent manner. Purified KIF1C tail constructs undergo LLPS in vitro at near-endogenous nM concentrations and in the absence of crowding agents and can directly recruit RNA molecules. Overall, our work uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role in mRNA positioning. In addition, the LLPS activity of KIF1C's tail represents a new mode of motor-cargo interaction that extends our current understanding of cytoskeletal motor proteins.
Collapse
Affiliation(s)
- Qi Geng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jakia Jannat Keya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
4
|
Passchier TC, White JBR, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 2024; 14:14099. [PMID: 38890308 PMCID: PMC11189427 DOI: 10.1038/s41598-024-58243-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 06/20/2024] Open
Abstract
We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent Ni and Ni+1 protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the Ni+1 N-terminus and Ni-1 C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions.
Collapse
Affiliation(s)
- Tim C Passchier
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
| | - Joshua B R White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel P Maskell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew J Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Exscientia, The Schrödinger Building Oxford Science Park, Oxford, OX4 4GE, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- College of Biomedical Sciences, Larkin University, 18301 N Miami Avenue, Miami, FL, 33169, USA.
| | - John N Barr
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
5
|
Liu J, Jiang Y, Liu R, Jin J, Wei S, Ji W, He X, Wu F, Yu P, Mao L. Vitamin C Drives Reentrant Actin Phase Transition: Biphasic Exocytosis Regulation Revealed by Single-Vesicle Electrochemistry. J Am Chem Soc 2024. [PMID: 38889317 DOI: 10.1021/jacs.4c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Unveiling molecular mechanisms that dominate protein phase dynamics has been a pressing need for deciphering the intricate intracellular modulation machinery. While ions and biomacromolecules have been widely recognized for modulating protein phase separations, effects of small molecules that essentially constitute the cytosolic chemical atmosphere on the protein phase behaviors are rarely understood. Herein, we report that vitamin C (VC), a key small molecule for maintaining a reductive intracellular atmosphere, drives reentrant phase transitions of myosin II/F-actin (actomyosin) cytoskeletons. The actomyosin bundle condensates dissemble in the low-VC regime and assemble in the high-VC regime in vitro or inside neuronal cells, through a concurrent myosin II protein aggregation-dissociation process with monotonic VC concentration increase. Based on this finding, we employ in situ single-cell and single-vesicle electrochemistry to demonstrate the quantitative modulation of catecholamine transmitter vesicle exocytosis by intracellular VC atmosphere, i.e., exocytotic release amount increases in the low-VC regime and decreases in the high-VC regime. Furthermore, we show how VC regulates cytomembrane-vesicle fusion pore dynamics through counteractive or synergistic effects of actomyosin phase transitions and the intracellular free calcium level on membrane tensions. Our work uncovers the small molecule-based reversive protein phase regulatory mechanism, paving a new way to chemical neuromodulation and therapeutic repertoire expansion.
Collapse
Affiliation(s)
- Jing Liu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Ying Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ran Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jing Jin
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Shiyi Wei
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Wenliang Ji
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiulan He
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Fei Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
6
|
Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024. [PMID: 38885177 DOI: 10.1021/acs.chemrev.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
Collapse
|
7
|
Lee K, Ku J, Ku D, Kim Y. Inverted Alu repeats: friends or foes in the human transcriptome. Exp Mol Med 2024:10.1038/s12276-024-01177-3. [PMID: 38871814 DOI: 10.1038/s12276-024-01177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/15/2024] Open
Abstract
Alu elements are highly abundant primate-specific short interspersed nuclear elements that account for ~10% of the human genome. Due to their preferential location in gene-rich regions, especially in introns and 3' UTRs, Alu elements can exert regulatory effects on the expression of both host and neighboring genes. When two Alu elements with inverse orientations are positioned in close proximity, their transcription results in the generation of distinct double-stranded RNAs (dsRNAs), known as inverted Alu repeats (IRAlus). IRAlus are key immunogenic self-dsRNAs and post-transcriptional cis-regulatory elements that play a role in circular RNA biogenesis, as well as RNA transport and stability. Recently, IRAlus dsRNAs have emerged as regulators of transcription and activators of Z-DNA-binding proteins. The formation and activity of IRAlus can be modulated through RNA editing and interactions with RNA-binding proteins, and misregulation of IRAlus has been implicated in several immune-associated disorders. In this review, we summarize the emerging functions of IRAlus dsRNAs, the regulatory mechanisms governing IRAlus activity, and their relevance in the pathogenesis of human diseases.
Collapse
Affiliation(s)
- Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury (KIB), Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
8
|
Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures. Biophys J 2024; 123:1342-1355. [PMID: 37408305 PMCID: PMC11163273 DOI: 10.1016/j.bpj.2023.06.024] [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: 04/16/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Multiphasic architectures are found ubiquitously in biomolecular condensates and are thought to have important implications for the organization of multiple chemical reactions within the same compartment. Many of these multiphasic condensates contain RNA in addition to proteins. Here, we investigate the importance of different interactions in multiphasic condensates comprising two different proteins and RNA using computer simulations with a residue-resolution coarse-grained model of proteins and RNA. We find that in multilayered condensates containing RNA in both phases, protein-RNA interactions dominate, with aromatic residues and arginine forming the key stabilizing interactions. The total aromatic and arginine content of the two proteins must be appreciably different for distinct phases to form, and we show that this difference increases as the system is driven toward greater multiphasicity. Using the trends observed in the different interaction energies of this system, we demonstrate that we can also construct multilayered condensates with RNA preferentially concentrated in one phase. The "rules" identified can thus enable the design of synthetic multiphasic condensates to facilitate further study of their organization and function.
Collapse
Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jerelle A Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Physics, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
9
|
Ripin N, Macedo de Vasconcelos L, Ugay DA, Parker R. DDX6 modulates P-body and stress granule assembly, composition, and docking. J Cell Biol 2024; 223:e202306022. [PMID: 38536035 PMCID: PMC10978804 DOI: 10.1083/jcb.202306022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/20/2023] [Accepted: 03/04/2024] [Indexed: 04/01/2024] Open
Abstract
Stress granules and P-bodies are ribonucleoprotein (RNP) granules that accumulate during the stress response due to the condensation of untranslating mRNPs. Stress granules form in part by intermolecular RNA-RNA interactions and can be limited by components of the RNA chaperone network, which inhibits RNA-driven aggregation. Herein, we demonstrate that the DEAD-box helicase DDX6, a P-body component, can also limit the formation of stress granules, independent of the formation of P-bodies. In an ATPase, RNA-binding dependent manner, DDX6 limits the partitioning of itself and other RNPs into stress granules. When P-bodies are limited, proteins that normally partition between stress granules and P-bodies show increased accumulation within stress granules. Moreover, we show that loss of DDX6, 4E-T, and DCP1A increases P-body docking with stress granules, which depends on CNOT1 and PAT1B. Taken together, these observations identify a new role for DDX6 in limiting stress granules and demonstrate that P-body components can influence stress granule composition and docking with P-bodies.
Collapse
Affiliation(s)
- Nina Ripin
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Daniella A. Ugay
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
10
|
Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
Collapse
Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
| |
Collapse
|
11
|
Kiang KM, Ahad L, Zhong X, Lu QR. Biomolecular condensates: hubs of Hippo-YAP/TAZ signaling in cancer. Trends Cell Biol 2024:S0962-8924(24)00096-5. [PMID: 38806345 DOI: 10.1016/j.tcb.2024.04.009] [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: 07/27/2023] [Revised: 04/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
Biomolecular condensates, the membraneless cellular compartments formed by liquid-liquid phase separation (LLPS), represent an important mechanism for physiological and tumorigenic processes. Recent studies have advanced our understanding of how these condensates formed in the cytoplasm or nucleus regulate Hippo signaling, a central player in organogenesis and tumorigenesis. Here, we review recent findings on the dynamic formation and function of biomolecular condensates in regulating the Hippo-yes-associated protein (YAP)/transcription coactivator with PDZ-binding motif (TAZ) signaling pathway under physiological and pathological processes. We further discuss how the nuclear condensates of YAP- or TAZ-fusion oncoproteins compartmentalize crucial transcriptional co-activators and alter chromatin architecture to promote oncogenic programs. Finally, we highlight key questions regarding how these findings may pave the way for novel therapeutics to target cancer.
Collapse
Affiliation(s)
- Karrie M Kiang
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Leena Ahad
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaowen Zhong
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Q Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| |
Collapse
|
12
|
Wagner T, Priyanka P, Micheletti R, Friedman MJ, Nair SJ, Gamliel A, Taylor H, Song X, Cho M, Oh S, Li W, Han J, Ohgi KA, Abrass M, D'Antonio-Chronowska A, D'Antonio M, Hazuda H, Duggirala R, Blangero J, Ding S, Guzmann C, Frazer KA, Aggarwal AK, Zemljic-Harpf AE, Rosenfeld MG, Suh Y. Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594600. [PMID: 38798402 PMCID: PMC11118446 DOI: 10.1101/2024.05.17.594600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Because most DNA-binding transcription factors (dbTFs), including the architectural regulator CTCF, bind RNA and exhibit di-/multimerization, a central conundrum is whether these distinct properties are regulated post-transcriptionally to modulate transcriptional programs. Here, investigating stress-dependent activation of SIRT1, encoding an evolutionarily-conserved protein deacetylase, we show that induced phosphorylation of CTCF acts as a rheostat to permit CTCF occupancy of low-affinity promoter DNA sites to precisely the levels necessary. This CTCF recruitment to the SIRT1 promoter is eliciting a cardioprotective cardiomyocyte transcriptional activation program and provides resilience against the stress of the beating heart in vivo . Mice harboring a mutation in the conserved low-affinity CTCF promoter binding site exhibit an altered, cardiomyocyte-specific transcriptional program and a systolic heart failure phenotype. This transcriptional role for CTCF reveals that a covalent dbTF modification regulating signal-dependent transcription serves as a previously unsuspected component of the oxidative stress response.
Collapse
|
13
|
Earwood R, Ninomiya H, Wang H, Shimada IS, Stroud M, Perez D, Uuganbayar U, Yamada C, Akiyama-Miyoshi T, Stefanovic B, Kato Y. The binding of LARP6 and DNAAF6 in biomolecular condensates influences ciliogenesis of multiciliated cells. J Biol Chem 2024; 300:107373. [PMID: 38762183 DOI: 10.1016/j.jbc.2024.107373] [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: 12/08/2023] [Revised: 04/19/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
Motile cilia on the cell surface produce fluid flows in the body and abnormalities in motile cilia cause primary ciliary dyskinesia. Dynein axonemal assembly factor 6 (DNAAF6), a causative gene of primary ciliary dyskinesia, was isolated as an interacting protein with La ribonucleoprotein 6 (LARP6) that regulates ciliogenesis in multiciliated cells (MCCs). In MCCs of Xenopus embryos, LARP6 and DNAAF6 were colocalized in biomolecular condensates termed dynein axonemal particles and synergized to control ciliogenesis. Moreover, tubulin alpha 1c-like mRNA encoding α-tubulin protein, that is a major component of ciliary axoneme, was identified as a target mRNA regulated by binding LARP6. While DNAAF6 was necessary for high α-tubulin protein expression near the apical side of Xenopus MCCs during ciliogenesis, its mutant, which abolishes binding with LARP6, was unable to restore the expression of α-tubulin protein near the apical side of MCCs in Xenopus DNAAF6 morphant. These results indicated that the binding of LARP6 and DNAAF6 in dynein axonemal particles regulates highly expressed α-tubulin protein near the apical side of Xenopus MCCs during ciliogenesis.
Collapse
Affiliation(s)
- Ryan Earwood
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Hiromasa Ninomiya
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Hao Wang
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Issei S Shimada
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Mia Stroud
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Diana Perez
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Udval Uuganbayar
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Chisato Yamada
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Toru Akiyama-Miyoshi
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Branko Stefanovic
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA.
| | - Yoichi Kato
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA; Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan.
| |
Collapse
|
14
|
Shelkovnikova TA, Hautbergue GM. RNP granules in ALS and neurodegeneration: From multifunctional membraneless organelles to therapeutic opportunities. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:455-479. [PMID: 38802180 DOI: 10.1016/bs.irn.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and related neurodegenerative diseases are characterised by dysfunction of a host of RNA-binding proteins (RBPs) and a severely disrupted RNA metabolism. Recently, RBP-harbouring phase-separated complexes, ribonucleoprotein (RNP) granules, have come into the limelight as "crucibles" of neuronal pathology in ALS. RNP granules are indispensable for the multitude of regulatory processes underlying cellular RNA metabolism and serve as critical organisers of cellular biochemistry. Neurons, highly specialised cells, heavily rely on RNP granules for efficient trafficking, signalling and stress responses. Multiple RNP granule components, primarily RBPs such as TDP-43 and FUS, are affected by ALS mutations. However, even in the absence of mutations, RBP proteinopathies represent pathophysiological hallmarks of ALS. Given the high local concentrations of RBPs and RNAs, their weakened or enhanced interactions within RNP granules disrupt their homeostasis. Thus, the physiological process of phase separation and RNP granule formation, vital for maintaining the high-functioning state of neuronal cells, becomes their Achilles heel. Here, we will review the recent literature on the causes and consequences of abnormal RNP granule functioning in ALS and related disorders. In particular, we will summarise the evidence for the network-level dysfunction of RNP granules in these conditions and discuss considerations for therapeutic interventions to target RBPs, RNP granules and their network as a whole.
Collapse
Affiliation(s)
- Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom; Healthy Lifespan Institute (HELSI), University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| |
Collapse
|
15
|
Ramachandran V, Potoyan DA. Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning. Biophys J 2024; 123:1152-1163. [PMID: 38571310 PMCID: PMC11079944 DOI: 10.1016/j.bpj.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/03/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024] Open
Abstract
Conformational dynamics of RNA plays important roles in a variety of cellular functions such as transcriptional regulation, catalysis, scaffolding, and sensing. Recently, RNAs with low-complexity sequences have been shown to phase separate and form condensate phases similar to lowcomplexity protein domains. The affinity for phase separation and the material characteristics of RNA condensates are strongly dependent on sequence composition and patterning. We hypothesize that differences in the affinities for RNA phase separation can be uncovered by studying sequence-dependent conformational dynamics of single RNA chains. To this end, we have employed atomistic simulations and deep dimensionality reduction techniques to map temperature-dependent conformational free energy landscapes for 20 base-long homopolymeric RNA sequences: poly(U), poly(G), poly(C), and poly(A). The energy landscapes of homopolymeric RNAs reveal a plethora of metastable states with qualitatively different populations stemming from differences in base chemistry. Through detailed analysis of base, phosphate, and sugar interactions, we show that experimentally observed temperature-driven shifts in metastable state populations align with experiments on RNA phase transitions. Specifically, we find that the thermodynamics of unfolding of homopolymeric RNA follows the poly(G) > poly(A) > poly(C) > poly(U) order of stability, mirroring the propensity of RNA to form condensates. To conclude, this work shows that at least for homopolymeric RNA sequences the single-chain conformational dynamics contains sufficient information for predicting and quantifying condensate forming affinities of RNAs. Thus, we anticipate that atomically detailed studies of temeprature -dependent energy landscapes of RNAs will be a useful guide for understanding the propensity of various RNA molecules to form condensates.
Collapse
Affiliation(s)
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa; Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, Iowa.
| |
Collapse
|
16
|
Lerra L, Panatta M, Bär D, Zanini I, Tan JY, Pisano A, Mungo C, Baroux C, Panse VG, Marques AC, Santoro R. An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains. Mol Cell 2024; 84:1667-1683.e10. [PMID: 38599210 PMCID: PMC11065421 DOI: 10.1016/j.molcel.2024.03.015] [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: 02/23/2023] [Revised: 10/19/2023] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
The nucleus is composed of functionally distinct membraneless compartments that undergo phase separation (PS). However, whether different subnuclear compartments are connected remains elusive. We identified a type of nuclear body with PS features composed of BAZ2A that associates with active chromatin. BAZ2A bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space, BAZ2A bodies contact H3K27me3 bodies. BAZ2A-body disruption promotes BAZ2A invasion into H3K27me3 domains, causing H3K27me3-body loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A bodies, whereas the strong binder long non-coding RNA (lncRNA) Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unraveling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process, contributing to nuclear organization and the regulation of chromatin and gene expression.
Collapse
Affiliation(s)
- Luigi Lerra
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Isabella Zanini
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Agnese Pisano
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Chiara Mungo
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8057, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland.
| |
Collapse
|
17
|
De Sota RE, Quake SR, Sninsky JJ, Toden S. Decoding bioactive signals of the RNA secretome: the cell-free messenger RNA catalogue. Expert Rev Mol Med 2024; 26:e12. [PMID: 38682644 PMCID: PMC11140549 DOI: 10.1017/erm.2024.12] [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: 08/08/2023] [Revised: 01/18/2024] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Despite gene-expression profiling being one of the most common methods to evaluate molecular dysregulation in tissues, the utilization of cell-free messenger RNA (cf-mRNA) as a blood-based non-invasive biomarker analyte has been limited compared to other RNA classes. Recent advancements in low-input RNA-sequencing and normalization techniques, however, have enabled characterization as well as accurate quantification of cf-mRNAs allowing direct pathological insights. The molecular profile of the cell-free transcriptome in multiple diseases has subsequently been characterized including, prenatal diseases, neurological disorders, liver diseases and cancers suggesting this biological compartment may serve as a disease agnostic platform. With mRNAs packaged in a myriad of extracellular vesicles and particles, these signals may be used to develop clinically actionable, non-invasive disease biomarkers. Here, we summarize the recent scientific developments of extracellular mRNA, biology of extracellular mRNA carriers, clinical utility of cf-mRNA as disease biomarkers, as well as proposed functions in cell and tissue pathophysiology.
Collapse
Affiliation(s)
- Rhys E. De Sota
- Superfluid Dx., 259 E Grand Avenue, South San Francisco, CA 94080, USA
| | - Stephen R. Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - John J. Sninsky
- Superfluid Dx., 259 E Grand Avenue, South San Francisco, CA 94080, USA
| | - Shusuke Toden
- Superfluid Dx., 259 E Grand Avenue, South San Francisco, CA 94080, USA
| |
Collapse
|
18
|
Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
Collapse
Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
19
|
Buggiani J, Meinnel T, Giglione C, Frottin F. Advances in nuclear proteostasis of metazoans. Biochimie 2024:S0300-9084(24)00081-6. [PMID: 38642824 DOI: 10.1016/j.biochi.2024.04.006] [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: 01/29/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
The proteostasis network and associated protein quality control (PQC) mechanisms ensure proteome functionality and are essential for cell survival. A distinctive feature of eukaryotic cells is their high degree of compartmentalization, requiring specific and adapted proteostasis networks for each compartment. The nucleus, essential for maintaining the integrity of genetic information and gene transcription, is one such compartment. While PQC mechanisms have been investigated for decades in the cytoplasm and the endoplasmic reticulum, our knowledge of nuclear PQC pathways is only emerging. Recent developments in the field have underscored the importance of spatially managing aberrant proteins within the nucleus. Upon proteotoxic stress, misfolded proteins and PQC effectors accumulate in various nuclear membrane-less organelles. Beyond bringing together effectors and substrates, the biophysical properties of these organelles allow novel PQC functions. In this review, we explore the specificity of the nuclear compartment, the effectors of the nuclear proteostasis network, and the PQC roles of nuclear membrane-less organelles in metazoans.
Collapse
Affiliation(s)
- Julia Buggiani
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Frédéric Frottin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| |
Collapse
|
20
|
Song J. Adenosine Triphosphate: The Primordial Molecule That Controls Protein Homeostasis and Shapes the Genome-Proteome Interface. Biomolecules 2024; 14:500. [PMID: 38672516 PMCID: PMC11048592 DOI: 10.3390/biom14040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Adenosine triphosphate (ATP) acts as the universal energy currency that drives various biological processes, while nucleic acids function to store and transmit genetic information for all living organisms. Liquid-liquid phase separation (LLPS) represents the common principle for the formation of membrane-less organelles (MLOs) composed of proteins rich in intrinsically disordered regions (IDRs) and nucleic acids. Currently, while IDRs are well recognized to facilitate LLPS through dynamic and multivalent interactions, the precise mechanisms by which ATP and nucleic acids affect LLPS still remain elusive. This review summarizes recent NMR results on the LLPS of human FUS, TDP-43, and the viral nucleocapsid (N) protein of SARS-CoV-2, as modulated by ATP and nucleic acids, revealing the following: (1) ATP binds to folded domains overlapping with nucleic-acid-binding interfaces; (2) ATP and nucleic acids interplay to biphasically modulate LLPS by competitively binding to overlapping pockets of folded domains and Arg/Lys within IDRs; (3) ATP energy-independently induces protein folding with the highest efficiency known so far. As ATP likely emerged in the prebiotic monomeric world, while LLPS represents a pivotal mechanism to concentrate and compartmentalize rare molecules for forming primordial cells, ATP appears to control protein homeostasis and shape genome-proteome interfaces throughout the evolutionary trajectory, from prebiotic origins to modern cells.
Collapse
Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
| |
Collapse
|
21
|
Lee M, Moon HC, Jeong H, Kim DW, Park HY, Shin Y. Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions. Nat Commun 2024; 15:3216. [PMID: 38622120 PMCID: PMC11018775 DOI: 10.1038/s41467-024-47442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Biomolecular condensates, often assembled through phase transition mechanisms, play key roles in organizing diverse cellular activities. The material properties of condensates, ranging from liquid droplets to solid-like glasses or gels, are key features impacting the way resident components associate with one another. However, it remains unclear whether and how different material properties would influence specific cellular functions of condensates. Here, we combine optogenetic control of phase separation with single-molecule mRNA imaging to study relations between phase behaviors and functional performance of condensates. Using light-activated condensation, we show that sequestering target mRNAs into condensates causes translation inhibition. Orthogonal mRNA imaging reveals highly transient nature of interactions between individual mRNAs and condensates. Tuning condensate composition and material property towards more solid-like states leads to stronger translational repression, concomitant with a decrease in molecular mobility. We further demonstrate that β-actin mRNA sequestration in neurons suppresses spine enlargement during chemically induced long-term potentiation. Our work highlights how the material properties of condensates can modulate functions, a mechanism that may play a role in fine-tuning the output of condensate-driven cellular activities.
Collapse
Affiliation(s)
- Min Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Hyungseok C Moon
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hyeonjeong Jeong
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, USA
| | - Dong Wook Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea.
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, USA.
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea.
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea.
| |
Collapse
|
22
|
Chin KY, Ishida S, Sasaki Y, Terayama K. Predicting condensate formation of protein and RNA under various environmental conditions. BMC Bioinformatics 2024; 25:143. [PMID: 38566033 PMCID: PMC10988968 DOI: 10.1186/s12859-024-05764-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Liquid-liquid phase separation (LLPS) by biomolecules plays a central role in various biological phenomena and has garnered significant attention. The behavior of LLPS is strongly influenced by the characteristics of RNAs and environmental factors such as pH and temperature, as well as the properties of proteins. Recently, several databases recording LLPS-related biomolecules have been established, and prediction models of LLPS-related phenomena have been explored using these databases. However, a prediction model that concurrently considers proteins, RNAs, and experimental conditions has not been developed due to the limited information available from individual experiments in public databases. RESULTS To address this challenge, we have constructed a new dataset, RNAPSEC, which serves each experiment as a data point. This dataset was accomplished by manually collecting data from public literature. Utilizing RNAPSEC, we developed two prediction models that consider a protein, RNA, and experimental conditions. The first model can predict the LLPS behavior of a protein and RNA under given experimental conditions. The second model can predict the required conditions for a given protein and RNA to undergo LLPS. CONCLUSIONS RNAPSEC and these prediction models are expected to accelerate our understanding of the roles of proteins, RNAs, and environmental factors in LLPS.
Collapse
Affiliation(s)
- Ka Yin Chin
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Shoichi Ishida
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yukio Sasaki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kei Terayama
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- RIKEN Center for Advanced Intelligence Project, 1-4-1, Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
- MDX Research Center for Element Strategy, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
| |
Collapse
|
23
|
Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
Collapse
|
24
|
Schieweck R, Götz M. Pan-cellular organelles and suborganelles-from common functions to cellular diversity? Genes Dev 2024; 38:98-114. [PMID: 38485267 PMCID: PMC10982711 DOI: 10.1101/gad.351337.123] [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: 04/02/2024]
Abstract
Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles. For instance, centrosomes or mitochondria differ significantly in their protein composition in different, sometimes closely related, cell types. This has relevance for development and disease. Particularly striking is the high amount and diversity of RNA-binding proteins at these and other organelles, which brings us to review the evidence for RNA at different organelles and suborganelles. We include a discussion about (sub)organelles involved in translation, such as the nucleolus and ribosomes, for which unexpected cell type-specific diversity has also been reported. We propose here that the heterogeneity of these organelles and compartments represents a novel mechanism for regulating cell diversity. One reason is that protein functions can be multiplied by their different contributions in distinct organelles, as also exemplified by proteins with moonlighting function. The specialized organelles still perform pan-cellular functions but in a cell type-specific mode, as discussed here for centrosomes, mitochondria, vesicles, and other organelles. These can serve as regulatory hubs for the storage and transport of specific and functionally important regulators. In this way, they can control cell differentiation, plasticity, and survival. We further include examples highlighting the relevance for disease and propose to examine organelles in many more cell types for their possible differences with functional relevance.
Collapse
Affiliation(s)
- Rico Schieweck
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy;
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Magdalena Götz
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany;
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, 82152 Planegg-Martinsried, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
25
|
Bermudez Y, Hatfield D, Muller M. A Balancing Act: The Viral-Host Battle over RNA Binding Proteins. Viruses 2024; 16:474. [PMID: 38543839 PMCID: PMC10974049 DOI: 10.3390/v16030474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of a productive viral infection is the co-opting of host cell resources for viral replication. Despite the host repertoire of molecular functions and biological counter measures, viruses still subvert host defenses to take control of cellular factors such as RNA binding proteins (RBPs). RBPs are involved in virtually all steps of mRNA life, forming ribonucleoprotein complexes (mRNPs) in a highly ordered and regulated process to control RNA fate and stability in the cell. As such, the hallmark of the viral takeover of a cell is the reshaping of RNA fate to modulate host gene expression and evade immune responses by altering RBP interactions. Here, we provide an extensive review of work in this area, particularly on the duality of the formation of RNP complexes that can be either pro- or antiviral. Overall, in this review, we highlight the various ways viruses co-opt RBPs to regulate RNA stability and modulate the outcome of infection by gathering novel insights gained from research studies in this field.
Collapse
Affiliation(s)
| | | | - Mandy Muller
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (Y.B.); (D.H.)
| |
Collapse
|
26
|
de Vries T, Novakovic M, Ni Y, Smok I, Inghelram C, Bikaki M, Sarnowski CP, Han Y, Emmanouilidis L, Padroni G, Leitner A, Allain FHT. Specific protein-RNA interactions are mostly preserved in biomolecular condensates. SCIENCE ADVANCES 2024; 10:eadm7435. [PMID: 38446881 PMCID: PMC10917357 DOI: 10.1126/sciadv.adm7435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
Collapse
Affiliation(s)
- Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Yinan Ni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Clara Inghelram
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Chris P. Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yaning Han
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Giacomo Padroni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|
27
|
Chen L, Gai X, Yu X. Pre-rRNA facilitates the recruitment of RAD51AP1 to DNA double-strand breaks. J Biol Chem 2024; 300:107115. [PMID: 38403248 PMCID: PMC10959706 DOI: 10.1016/j.jbc.2024.107115] [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: 01/04/2024] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
RAD51-associated protein 1 (RAD51AP1) is known to promote homologous recombination (HR) repair. However, the precise mechanism of RAD51AP1 in HR repair is unclear. Here, we identify that RAD51AP1 associates with pre-rRNA. Both the N terminus and C terminus of RAD51AP1 recognize pre-rRNA. Pre-rRNA not only colocalizes with RAD51AP1 at double-strand breaks (DSBs) but also facilitates the recruitment of RAD51AP1 to DSBs. Consistently, transient inhibition of pre-rRNA synthesis by RNA polymerase I inhibitor suppresses the recruitment of RAD51AP1 as well as HR repair. Moreover, RAD51AP1 forms liquid-liquid phase separation in the presence of pre-rRNA in vitro, which may be the molecular mechanism of RAD51AP1 foci formation. Taken together, our results demonstrate that pre-rRNA mediates the relocation of RAD51AP1 to DSBs for HR repair.
Collapse
Affiliation(s)
- Linlin Chen
- School of Life Sciences, Fudan University, Shanghai, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaochen Gai
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Man J, Zhang Q, Zhao T, Sun D, Sun W, Long K, Zhang Z. Oxidative Stress Induced by Arsenite is Involved in YTHDF2 Phase Separation. Biol Trace Elem Res 2024; 202:885-899. [PMID: 37310554 DOI: 10.1007/s12011-023-03728-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) undergoes phase separation in response to the stimulation of high concentration of arsenite, suggesting that oxidative stress, the major mechanism of arsenite toxicity, may play a role in YTHDF2 phase separation. However, whether arsenite-induced oxidative stress is involved in phase separation of YTHDF2 has yet to be established. To explore the effect of arsenite-induced oxidative stress on YTHDF2 phase separation, the levels of oxidative stress, YTHDF2 phase separation, and N6-methyladenosine (m6A) in human keratinocytes were detected after exposure to various concentrations of sodium arsenite (0-500 µM; 1 h) and antioxidant N-acetylcysteine (0-10 mM; 2 h). We found that arsenite promoted oxidative stress and YTHDF2 phase separation in a concentration-dependent manner. In contrast, pretreatment with N-acetylcysteine significantly relieved arsenate-induced oxidative stress and inhibited YTHDF2 phase separation. As one of the key factors to YTHDF2 phase separation, N6-methyladenosine (m6A) levels in human keratinocytes were significantly increased after arsenite exposure, accompanied by upregulation of m6A methylesterase levels and downregulation of m6A demethylases levels. On the contrary, N-acetylcysteine mitigated the arsenite-induced increase of m6A and m6A methylesterase and the arsenite-induced decrease in m6A demethylase. Collectively, our study firstly revealed that oxidative stress induced by arsenite plays an important role in YTHDF2 phase separation driven by m6A modification, which provides new insights into the arsenite toxicity from the phase-separation perspective.
Collapse
Affiliation(s)
- Jin Man
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Weilian Sun
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Keyan Long
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
30
|
Liu HN, Wang T, Hu JJ, Chen L, Shi X, Li YM, Luo SZ. The disordered protein SERF promotes α-Synuclein aggregation through liquid-liquid phase separation. J Biol Chem 2024; 300:105667. [PMID: 38272228 PMCID: PMC10877630 DOI: 10.1016/j.jbc.2024.105667] [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: 03/01/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024] Open
Abstract
The aggregation of α-Synuclein (α-Syn) into amyloid fibrils is the hallmark of Parkinson's disease. Under stress or other pathological conditions, the accumulation of α-Syn oligomers is the main contributor to the cytotoxicity. A potential approach for treating Parkinson's disease involves preventing the accumulation of these α-Syn oligomers. In this study, we present a novel mechanism involving a conserved group of disorderly proteins known as small EDRK-rich factor (SERF), which promotes the aggregation of α-Syn through a cophase separation process. Using diverse methods like confocal microscopy, fluorescence recovery after photobleaching assays, solution-state NMR spectroscopy, and Western blot, we determined that the N-terminal domain of SERF1a plays a role in the interactions that occur during cophase separation. Within these droplets, α-Syn undergoes a gradual transformation from solid condensates to amyloid fibrils, while SERF1a is excluded from the condensates and dissolves into the solution. Notably, in vivo experiments show that SERF1a cophase separation with α-Syn significantly reduces the deposition of α-Syn oligomers and decreases its cellular toxicity under stress. These findings suggest that SERF1a accelerates the conversion of α-Syn from highly toxic oligomers to less toxic fibrils through cophase separation, thereby mitigating the biological damage of α-Syn aggregation.
Collapse
Affiliation(s)
- He-Ning Liu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ting Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jin-Jian Hu
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Long Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China.
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China.
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| |
Collapse
|
31
|
Ahangama Liyanage L, Ditlev JA. Mesoscale condensates organize the cytoplasm. Nat Cell Biol 2024; 26:310-312. [PMID: 38424272 DOI: 10.1038/s41556-023-01331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Affiliation(s)
- Leshani Ahangama Liyanage
- Programs in Molecular Medicine and Cell Biology, Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jonathon A Ditlev
- Programs in Molecular Medicine and Cell Biology, Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Wang S, Sun H, Chen G, Wu C, Sun B, Lin J, Lin D, Zeng D, Lin B, Huang G, Lu X, Lin H, Liang Y. RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities. Crit Rev Oncol Hematol 2024; 195:104271. [PMID: 38272151 DOI: 10.1016/j.critrevonc.2024.104271] [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: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.
Collapse
Affiliation(s)
- Shimeng Wang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Hexing Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Guanyuan Chen
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Chengyu Wu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Bingmei Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Jiajia Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Danping Lin
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - Baohang Lin
- Department of Thyroid, Breast and Vascular Surgery, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Xiaofeng Lu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Haoyu Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| | - Yuanke Liang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| |
Collapse
|
34
|
Erben E, Liao W, Minopoli A, Maghelli N, Lauga E, Kreysing M. Opto-fluidically multiplexed assembly and micro-robotics. LIGHT, SCIENCE & APPLICATIONS 2024; 13:59. [PMID: 38409110 PMCID: PMC10897173 DOI: 10.1038/s41377-024-01406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Techniques for high-definition micromanipulations, such as optical tweezers, hold substantial interest across a wide range of disciplines. However, their applicability remains constrained by material properties and laser exposure. And while microfluidic manipulations have been suggested as an alternative, their inherent capabilities are limited and further hindered by practical challenges of implementation and control. Here we show that the iterative application of laser-induced, localized flow fields can be used for the relative positioning of multiple micro-particles, irrespectively of their material properties. Compared to the standing theoretical proposal, our method keeps particles mobile, and we show that their precision manipulation is non-linearly accelerated via the multiplexing of temperature stimuli below the heat diffusion limit. The resulting flow fields are topologically rich and mathematically predictable. They represent unprecedented microfluidic control capabilities that are illustrated by the actuation of humanoid micro-robots with up to 30 degrees of freedom, whose motions are sufficiently well-defined to reliably communicate personal characteristics such as gender, happiness and nervousness. Our results constitute high-definition micro-fluidic manipulations with transformative potential for assembly, micro-manufacturing, the life sciences, robotics and opto-hydraulically actuated micro-factories.
Collapse
Affiliation(s)
- Elena Erben
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
- Center for Systems Biology, Dresden, 01307, Germany
- Institute of Biological and Chemical Systems - Biological Information Processing. Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, 76344, Germany
| | - Weida Liao
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Antonio Minopoli
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
- Center for Systems Biology, Dresden, 01307, Germany
| | - Nicola Maghelli
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
- Center for Systems Biology, Dresden, 01307, Germany
| | - Eric Lauga
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK
| | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.
- Center for Systems Biology, Dresden, 01307, Germany.
- Institute of Biological and Chemical Systems - Biological Information Processing. Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, 76344, Germany.
| |
Collapse
|
35
|
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.
Collapse
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.
| |
Collapse
|
36
|
Kharel P, Ivanov P. RNA G-quadruplexes and stress: emerging mechanisms and functions. Trends Cell Biol 2024:S0962-8924(24)00005-9. [PMID: 38341346 DOI: 10.1016/j.tcb.2024.01.005] [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: 09/30/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
RNA G-quadruplexes (rG4s) are noncanonical secondary structures formed by guanine-rich sequences that are found in different regions of RNA molecules. These structures have been implicated in diverse biological processes, including translation, splicing, and RNA stability. Recent studies have suggested that rG4s play a role in the cellular response to stress. This review summarizes the current knowledge on rG4s under stress, focusing on their formation, regulation, and potential functions in stress response pathways. We discuss the molecular mechanisms that regulate the formation of rG4 under different stress conditions and the impact of these structures on RNA metabolism, gene expression, and cell survival. Finally, we highlight the potential therapeutic implications of targeting rG4s for the treatment of stress-related diseases through modulating cell survival.
Collapse
Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; HMS Initiative for RNA Medicine, Boston, MA 02115, USA.
| |
Collapse
|
37
|
Kim J, Qin S, Zhou HX, Rosen MK. Surface Charge Can Modulate Phase Separation of Multidomain Proteins. J Am Chem Soc 2024; 146:3383-3395. [PMID: 38262618 PMCID: PMC10859935 DOI: 10.1021/jacs.3c12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Phase separation has emerged as an important mechanism explaining the formation of certain biomolecular condensates. Biological phase separation is often driven by the multivalent interactions of modular protein domains. Beyond valency, the physical features of folded domains that promote phase separation are poorly understood. We used a model system─the small ubiquitin modifier (SUMO) and its peptide ligand, the SUMO interaction motif (SIM)─to examine how domain surface charge influences multivalency-driven phase separation. Phase separation of polySUMO and polySIM was altered by pH via a change in the protonation state of SUMO surface histidines. These effects were recapitulated by histidine mutations, which modulated SUMO solubility and polySUMO-polySIM phase separation in parallel and were quantitatively explained by atomistic modeling of weak interactions among proteins in the system. Thus, surface charge can tune the phase separation of multivalent proteins, suggesting a means of controlling phase separation biologically, evolutionarily, and therapeutically.
Collapse
Affiliation(s)
- Jonggul Kim
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
| | - Sanbo Qin
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Huan-Xiang Zhou
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Department
of Physics, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Michael K. Rosen
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
| |
Collapse
|
38
|
Welles RM, Sojitra KA, Garabedian MV, Xia B, Wang W, Guan M, Regy RM, Gallagher ER, Hammer DA, Mittal J, Good MC. Determinants that enable disordered protein assembly into discrete condensed phases. Nat Chem 2024:10.1038/s41557-023-01423-7. [PMID: 38316988 DOI: 10.1038/s41557-023-01423-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024]
Abstract
Cells harbour numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein- and RNA-rich bodies are thought to form through multivalent interactions among proteins and nucleic acids, resulting in demixing via liquid-liquid phase separation. Proteins harbouring intrinsically disordered regions (IDRs) predominate in membraneless organelles. However, it is not known whether IDR sequence alone can dictate the formation of distinct condensed phases. We identified a pair of IDRs capable of forming spatially distinct condensates when expressed in cells. When reconstituted in vitro, these model proteins do not co-partition, suggesting condensation specificity is encoded directly in the polypeptide sequences. Through computational modelling and mutagenesis, we identified the amino acids and chain properties governing homotypic and heterotypic interactions that direct selective condensation. These results form the basis of physicochemical principles that may direct subcellular organization of IDRs into specific condensates and reveal an IDR code that can guide construction of orthogonal membraneless compartments.
Collapse
Affiliation(s)
- Rachel M Welles
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Mikael V Garabedian
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Boao Xia
- Bioengineering Graduate Program, Rice University, Houston, TX, USA
| | - Wentao Wang
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Muyang Guan
- Chemical and Biomolecular Engineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Roshan M Regy
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Elizabeth R Gallagher
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel A Hammer
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
- Chemical and Biomolecular Engineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
- Chemical and Biomolecular Engineering Department, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA.
| | - Matthew C Good
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
39
|
Burke JM, Ratnayake OC, Watkins JM, Perera R, Parker R. G3BP1-dependent condensation of translationally inactive viral RNAs antagonizes infection. SCIENCE ADVANCES 2024; 10:eadk8152. [PMID: 38295168 PMCID: PMC10830107 DOI: 10.1126/sciadv.adk8152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
G3BP1 is an RNA binding protein that condenses untranslating messenger RNAs into stress granules (SGs). G3BP1 is inactivated by multiple viruses and is thought to antagonize viral replication by SG-enhanced antiviral signaling. Here, we show that neither G3BP1 nor SGs generally alter the activation of innate immune pathways. Instead, we show that the RNAs encoded by West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 are prone to G3BP1-dependent RNA condensation, which is enhanced by limiting translation initiation and correlates with the disruption of viral replication organelles and viral RNA replication. We show that these viruses counteract condensation of their RNA genomes by inhibiting the RNA condensing function of G3BP proteins, hijacking the RNA decondensing activity of eIF4A, and/or maintaining efficient translation. These findings argue that RNA condensation can function as an intrinsic antiviral mechanism, which explains why many viruses inactivate G3BP proteins and suggests that SGs may have arisen as a vestige of this antiviral mechanism.
Collapse
Affiliation(s)
- James M. Burke
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Oshani C. Ratnayake
- Center for Vector-Borne and Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Center for Metabolism of Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - J. Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33438, USA
| | - Rushika Perera
- Center for Vector-Borne and Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Center for Metabolism of Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - Roy Parker
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| |
Collapse
|
40
|
Gregorich ZR, Yanghai Z, Kamp TJ, Granzier H, Guo W. Mechanisms of RBM20 Cardiomyopathy: Insights From Model Systems. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004355. [PMID: 38288598 PMCID: PMC10923161 DOI: 10.1161/circgen.123.004355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
RBM20 (RNA-binding motif protein 20) is a vertebrate- and muscle-specific RNA-binding protein that belongs to the serine-arginine-rich family of splicing factors. The RBM20 gene was first identified as a dilated cardiomyopathy-linked gene over a decade ago. Early studies in Rbm20 knockout rodents implicated disrupted splicing of RBM20 target genes as a causative mechanism. Clinical studies show that pathogenic variants in RBM20 are linked to aggressive dilated cardiomyopathy with early onset heart failure and high mortality. Subsequent studies employing pathogenic variant knock-in animal models revealed that variants in a specific portion of the arginine-serine-rich domain in RBM20 not only disrupt splicing but also hinder nucleocytoplasmic transport and lead to the formation of RBM20 biomolecular condensates in the sarcoplasm. Conversely, mice harboring a disease-associated variant in the RRM (RNA recognition motif) do not show evidence of adverse remodeling or exhibit sudden death despite disrupted splicing of RBM20 target genes. Thus, whether disrupted splicing, biomolecular condensates, or both contribute to dilated cardiomyopathy is under debate. Beyond this, additional questions remain, such as whether there is sexual dimorphism in the presentation of RBM20 cardiomyopathy. What are the clinical features of RBM20 cardiomyopathy and why do some individuals develop more severe disease than others? In this review, we summarize the reported observations and discuss potential mechanisms of RBM20 cardiomyopathy derived from studies employing in vivo animal models and in vitro human-induced pluripotent stem cell-derived cardiomyocytes. Potential therapeutic strategies to treat RBM20 cardiomyopathy are also discussed.
Collapse
Affiliation(s)
- Zachery R. Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI
| | - Zhang Yanghai
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI
| | - Timothy J. Kamp
- Cellular and Molecular Arrhythmia Research Program, University of Wisconsin-Madison, Madison, WI
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
- Cardiovascular Research Center, University of Wisconsin-Madison, Madison, WI
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI
- Cardiovascular Research Center, University of Wisconsin-Madison, Madison, WI
| |
Collapse
|
41
|
Heinrich S, Hondele M, Marchand D, Derrer CP, Zedan M, Oswald A, Malinovska L, Uliana F, Khawaja S, Mancini R, Grunwald D, Weis K. Glucose stress causes mRNA retention in nuclear Nab2 condensates. Cell Rep 2024; 43:113593. [PMID: 38113140 DOI: 10.1016/j.celrep.2023.113593] [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: 03/10/2022] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that, upon glucose withdrawal, the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. This coincides with a reduced abundance of the DEAD-box ATPase Dbp5 at the nuclear pore. Depleting Dbp5, and consequently blocking mRNA export, is necessary and sufficient to trigger Nab2 condensation. The state of Nab2 condensation influences the extent of nuclear mRNA accumulation and can be recapitulated in vitro, where Nab2 forms RNA-dependent liquid droplets. We hypothesize that cells use condensation to regulate mRNA export and control gene expression during stress.
Collapse
Affiliation(s)
- Stephanie Heinrich
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
| | - Maria Hondele
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland; Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Désirée Marchand
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Carina Patrizia Derrer
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Mostafa Zedan
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Alexandra Oswald
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Liliana Malinovska
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Sarah Khawaja
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Roberta Mancini
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - David Grunwald
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA 01605, USA
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
| |
Collapse
|
42
|
Geng Y, Cai Q. Role of C9orf72 hexanucleotide repeat expansions in ALS/FTD pathogenesis. Front Mol Neurosci 2024; 17:1322720. [PMID: 38318532 PMCID: PMC10838790 DOI: 10.3389/fnmol.2024.1322720] [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: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are progressive neurological disorders that share neurodegenerative pathways and features. The most prevalent genetic causes of ALS/FTD is the GGGGCC hexanucleotide repeat expansions in the first intron region of the chromosome 9 open reading frame 72 (C9orf72) gene. In this review, we comprehensively summarize the accumulating evidences elucidating the pathogenic mechanism associated with hexanucleotide repeat expansions in ALS/FTD. These mechanisms encompass the structural polymorphism of DNA and transcribed RNA, the formation of RNA foci via phase separation, and the cytoplasmic accumulation and toxicities of dipeptide-repeat proteins. Additionally, the formation of G-quadruplex structures significantly impairs the expression and normal function of the C9orf72 protein. We also discuss the sequestration of specific RNA binding proteins by GGGGCC RNA, which further contributes to the toxicity of C9orf72 hexanucleotide repeat expansions. The deeper understanding of the pathogenic mechanism of hexanucleotide repeat expansions in ALS/FTD provides multiple potential drug targets for these devastating diseases.
Collapse
Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
| |
Collapse
|
43
|
Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol 2024; 31:17-35. [PMID: 38199037 PMCID: PMC10842484 DOI: 10.1016/j.chembiol.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
RNA secondary structure plays essential roles in encoding RNA regulatory fate and function. Most RNAs populate ensembles of alternatively paired states and are continually unfolded and refolded by cellular processes. Measuring these structural ensembles and their contributions to cellular function has traditionally posed major challenges, but new methods and conceptual frameworks are beginning to fill this void. In this review, we provide a mechanism- and function-centric compendium of the roles of RNA secondary structural ensembles and minority states in regulating the RNA life cycle, from transcription to degradation. We further explore how dysregulation of RNA structural ensembles contributes to human disease and discuss the potential of drugging alternative RNA states to therapeutically modulate RNA activity. The emerging paradigm of RNA structural ensembles as central to RNA function provides a foundation for a deeper understanding of RNA biology and new therapeutic possibilities.
Collapse
Affiliation(s)
- Ritwika Bose
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Irfana Saleem
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M Mustoe
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
44
|
Moors TE, Milovanovic D. Defining a Lewy Body: Running Up the Hill of Shifting Definitions and Evolving Concepts. JOURNAL OF PARKINSON'S DISEASE 2024; 14:17-33. [PMID: 38189713 PMCID: PMC10836569 DOI: 10.3233/jpd-230183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Lewy bodies (LBs) are pathological hallmarks of Parkinson's disease and dementia with Lewy bodies, characterized by the accumulation of α-synuclein (αSyn) protein in the brain. While LBs were first described a century ago, their formation and morphogenesis mechanisms remain incompletely understood. Here, we present a historical overview of LB definitions and highlight the importance of semantic clarity and precise definitions when describing brain inclusions. Recent breakthroughs in imaging revealed shared features within LB subsets and the enrichment of membrane-bound organelles in these structures, challenging the conventional LB formation model. We discuss the involvement of emerging concepts of liquid-liquid phase separation, where biomolecules demix from a solution to form dense condensates, as a potential LB formation mechanism. Finally, we emphasize the need for the operational definitions of LBs based on morphological characteristics and detection protocols, particularly in studies investigating LB formation mechanisms. A better understanding of LB organization and ultrastructure can contribute to the development of targeted therapeutic strategies for synucleinopathies.
Collapse
Affiliation(s)
- Tim E. Moors
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
45
|
Gorsheneva NA, Sopova JV, Azarov VV, Grizel AV, Rubel AA. Biomolecular Condensates: Structure, Functions, Methods of Research. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S205-S223. [PMID: 38621751 DOI: 10.1134/s0006297924140116] [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: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 04/17/2024]
Abstract
The term "biomolecular condensates" is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid-liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.
Collapse
Affiliation(s)
| | - Julia V Sopova
- St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | | |
Collapse
|
46
|
D'Ambra E, Vitiello E, Santini T, Bozzoni I. In Situ Hybridization of circRNAs in Cells and Tissues through BaseScope™ Strategy. Methods Mol Biol 2024; 2765:63-92. [PMID: 38381334 DOI: 10.1007/978-1-0716-3678-7_4] [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] [Indexed: 02/22/2024]
Abstract
Imaging-based approaches are powerful strategies that nowadays have been largely used to gain insight into the function of different types of macromolecules. As for RNA, it is becoming clear how important is its intracellular localization for the control of proper cell differentiation and development and how its perturbation can be linked to several pathological states. This aspect is even more important if one thinks of highly polarized cells such as neurons.In this chapter, we describe in detail an innovative RNA-FISH approach for the detection of circular RNAs (circRNAs), a recently discovered class of noncoding RNAs, which display different subcellular localizations and whose functions still largely remain to be elucidated. The detection of these molecules represents a great challenge, above all because they share most of their sequence with the corresponding linear counterparts, from which they differ only for the back-splicing junction (BSJ) originating from the circularization reaction. This implies the use of RNA-FISH probes capable of specifically binding the BSJ and avoiding the detection of the linear counterpart. This requirement imposes the design of probes on a very small region, which implies the risk of obtaining a low and undetectable signal. The BaseScope™ Assay RNA-FISH technology overpasses this problem since it is based on branched-DNA probes. With this approach it is possible to target a specific region of the RNA, even small such as a splicing junction, and at the same time to obtain a strong and well detectable signal. All this is possible thanks to subsequent series of probes that, starting from the first hybridization to the BSJ, build a branched tree of probes that greatly amplifies the signal. Here we provide a detailed step-by-step protocol of BaseScope™ RNA-FISH on circRNAs coupled with immunofluorescence, both in cells and tissues, and we address difficulties which may arise when using this methodology that depend on cell type, specific permeabilization, image acquisition, and post-acquisition analyses.
Collapse
Affiliation(s)
- Eleonora D'Ambra
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Erika Vitiello
- Center for Human Technology, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy.
- Center for Human Technology, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy.
| |
Collapse
|
47
|
Isozumi N, Sugie K, Mori E. [Biological phase separation in neuromuscular diseases]. Rinsho Shinkeigaku 2023; 63:799-805. [PMID: 37989290 DOI: 10.5692/clinicalneurol.cn-001877] [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] [Indexed: 11/23/2023]
Abstract
Biological phase separation refers to the liquid-liquid phase separation of biomolecules such as proteins in cells. Phase separation is driven by low-complexity domains of phase-separating proteins and strictly controlled by regulatory factors. Phase separation has also been found to be disrupted by genetic abnormalities. Abnormal aggregates of causative proteins accumulate in many neuromuscular diseases. In recent years, it has become clear that phase separating proteins are associated with neuromuscular diseases, and that abnormalities in the regulation of phase separation leads to the formation of aggregates. Gains in our knowledge of biological phase separation is gradually elucidating the pathogenesis of neuromuscular diseases.
Collapse
Affiliation(s)
| | - Kazuma Sugie
- Department of Neurology, Nara Medical University
| | - Eiichiro Mori
- Department of Future Basic Medicine, Nara Medical University
| |
Collapse
|
48
|
Zheng LW, Liu CC, Yu KD. Phase separations in oncogenesis, tumor progressions and metastasis: a glance from hallmarks of cancer. J Hematol Oncol 2023; 16:123. [PMID: 38110976 PMCID: PMC10726551 DOI: 10.1186/s13045-023-01522-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a novel principle for interpreting precise spatiotemporal coordination in living cells through biomolecular condensate (BMC) formation via dynamic aggregation. LLPS changes individual molecules into membrane-free, droplet-like BMCs with specific functions, which coordinate various cellular activities. The formation and regulation of LLPS are closely associated with oncogenesis, tumor progressions and metastasis, the specific roles and mechanisms of LLPS in tumors still need to be further investigated at present. In this review, we comprehensively summarize the conditions of LLPS and identify mechanisms involved in abnormal LLPS in cancer processes, including tumor growth, metastasis, and angiogenesis from the perspective of cancer hallmarks. We have also reviewed the clinical applications of LLPS in oncologic areas. This systematic summary of dysregulated LLPS from the different dimensions of cancer hallmarks will build a bridge for determining its specific functions to further guide basic research, finding strategies to intervene in LLPS, and developing relevant therapeutic approaches.
Collapse
Affiliation(s)
- Le-Wei Zheng
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
49
|
Tao J, Zeng Y, Dai B, Liu Y, Pan X, Wang LQ, Chen J, Zhou Y, Lu Z, Xie L, Liang Y. Excess PrP C inhibits muscle cell differentiation via miRNA-enhanced liquid-liquid phase separation implicated in myopathy. Nat Commun 2023; 14:8131. [PMID: 38065962 PMCID: PMC10709375 DOI: 10.1038/s41467-023-43826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The cellular prion protein (PrPC) is required for skeletal muscle function. Here, we report that a higher level of PrPC accumulates in the cytoplasm of the skeletal muscle of six myopathy patients compared to controls. PrPC inhibits skeletal muscle cell autophagy, and blocks myoblast differentiation. PrPC selectively binds to a subset of miRNAs during myoblast differentiation, and the colocalization of PrPC and miR-214-3p was observed in the skeletal muscle of six myopathy patients with excessive PrPC. We demonstrate that PrPC is overexpressed in skeletal muscle cells under pathological conditions, inhibits muscle cell differentiation by physically interacting with a subset of miRNAs, and selectively recruits these miRNAs into its phase-separated condensate in living myoblasts, which in turn enhances liquid-liquid phase separation of PrPC, promotes pathological aggregation of PrP, and results in the inhibition of autophagy-related protein 5-dependent autophagy and muscle bundle formation in myopathy patients characterized by incomplete muscle regeneration.
Collapse
Affiliation(s)
- Jing Tao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanping Zeng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Bin Dai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yin Liu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiaohan Pan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Li-Qiang Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Wuhan University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jie Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuneng Lu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Liwei Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
- Wuhan University Shenzhen Research Institute, Shenzhen, 518057, China.
| |
Collapse
|
50
|
Cai L, Wang GG. Through the lens of phase separation: intrinsically unstructured protein and chromatin looping. Nucleus 2023; 14:2179766. [PMID: 36821650 PMCID: PMC9980480 DOI: 10.1080/19491034.2023.2179766] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.
Collapse
Affiliation(s)
- Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Ling Cai Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Gang Greg Wang Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| |
Collapse
|