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Ruan K, Bai G, Fang Y, Li D, Li T, Liu X, Lu B, Lu Q, Songyang Z, Sun S, Wang Z, Zhang X, Zhou W, Zhang H. Biomolecular condensates and disease pathogenesis. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2661-3. [PMID: 39037698 DOI: 10.1007/s11427-024-2661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Biomolecular condensates or membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) divide intracellular spaces into discrete compartments for specific functions. Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration, tumorigenesis, and many other pathological processes. Herein, we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation. We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders, hearing loss, cancers, and immunological diseases. Finally, we describe the emerging discovery of chemical modulators of phase separation.
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Affiliation(s)
- Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ge Bai
- Nanhu Brain-computer Interface Institute, Hangzhou, 311100, China.
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Qing Lu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuguo Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zheng Wang
- The Second Affiliated Hospital, School of Basic Medical Sciences, Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| | - Xin Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Jafarinia H, van der Giessen E, Onck PR. C9orf72 polyPR directly binds to various nuclear transport components. eLife 2024; 12:RP89694. [PMID: 38483313 PMCID: PMC10939497 DOI: 10.7554/elife.89694] [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] [Indexed: 03/17/2024] Open
Abstract
The disruption of nucleocytoplasmic transport (NCT) is an important mechanism in neurodegenerative diseases. In the case of C9orf72-ALS, trafficking of macromolecules through the nuclear pore complex (NPC) might get frustrated by the binding of C9orf72-translated arginine-containing dipeptide repeat proteins (R-DPRs) to the Kapβ family of nuclear transport receptors. Besides Kapβs, several other types of transport components have been linked to NCT impairments in R-DPR-expressed cells, but the molecular origin of these observations has not been clarified. Here, we adopt a coarse-grained molecular dynamics model at amino acid resolution to study the direct interaction between polyPR, the most toxic DPR, and various nuclear transport components to elucidate the binding mechanisms and provide a complete picture of potential polyPR-mediated NCT defects. We found polyPR to directly bind to several isoforms of the Impα family, CAS (the specific exporter of Impα) and RanGAP. We observe no binding between polyPR and Ran. Longer polyPRs at lower salt concentrations also make contact with RanGEF and NTF2. Analyzing the polyPR contact sites on the transport components reveals that polyPR potentially interferes with RanGTP/RanGDP binding, with nuclear localization signal (NLS)-containing cargoes (cargo-NLS) binding to Impα, with cargo-NLS release from Impα, and with Impα export from the nucleus. The abundance of polyPR-binding sites on multiple transport components combined with the inherent polyPR length dependence makes direct polyPR interference of NCT a potential mechanistic pathway of C9orf72 toxicity.
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Affiliation(s)
- Hamidreza Jafarinia
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
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3
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Klughammer N, Barth A, Dekker M, Fragasso A, Onck PR, Dekker C. Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores. eLife 2024; 12:RP87174. [PMID: 38376900 PMCID: PMC10942607 DOI: 10.7554/elife.87174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.
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Affiliation(s)
- Nils Klughammer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Maurice Dekker
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
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4
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Ortega JA, Sasselli IR, Boccitto M, Fleming AC, Fortuna TR, Li Y, Sato K, Clemons TD, Mckenna ED, Nguyen TP, Anderson EN, Asin J, Ichida JK, Pandey UB, Wolin SL, Stupp SI, Kiskinis E. CLIP-Seq analysis enables the design of protective ribosomal RNA bait oligonucleotides against C9ORF72 ALS/FTD poly-GR pathophysiology. SCIENCE ADVANCES 2023; 9:eadf7997. [PMID: 37948524 PMCID: PMC10637751 DOI: 10.1126/sciadv.adf7997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 10/11/2023] [Indexed: 11/12/2023]
Abstract
Amyotrophic lateral sclerosis and frontotemporal dementia patients with a hexanucleotide repeat expansion in C9ORF72 (C9-HRE) accumulate poly-GR and poly-PR aggregates. The pathogenicity of these arginine-rich dipeptide repeats (R-DPRs) is thought to be driven by their propensity to bind low-complexity domains of multivalent proteins. However, the ability of R-DPRs to bind native RNA and the significance of this interaction remain unclear. Here, we used computational and experimental approaches to characterize the physicochemical properties of R-DPRs and their interaction with RNA. We find that poly-GR predominantly binds ribosomal RNA (rRNA) in cells and exhibits an interaction that is predicted to be energetically stronger than that for associated ribosomal proteins. Critically, modified rRNA "bait" oligonucleotides restore poly-GR-associated ribosomal deficits and ameliorate poly-GR toxicity in patient neurons and Drosophila models. Our work strengthens the hypothesis that ribosomal function is impaired by R-DPRs, highlights a role for direct rRNA binding in mediating ribosomal dysfunction, and presents a strategy for protecting against C9-HRE pathophysiological mechanisms.
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Affiliation(s)
- Juan A. Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Pathology and Experimental Therapy, Institute of Neurosciences, University of Barcelona, Barcelona 08907, Spain
| | - Ivan R. Sasselli
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Centro de Fisica de Materiales (CFM), CSIC-UPV/EHU, 20018 San Sebastián, Spain
| | - Marco Boccitto
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Andrew C. Fleming
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tyler R. Fortuna
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Yichen Li
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kohei Sato
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - Tristan D. Clemons
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth D. Mckenna
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Thao P. Nguyen
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric N. Anderson
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Jesus Asin
- Department of Statistical Methods, School of Engineering, University of Zaragoza, Zaragoza 50018, Spain
| | - Justin K. Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Udai B. Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Sandra L. Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Samuel I. Stupp
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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5
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Shakibi S, Onck PR, Van der Giessen E. A One-Bead-Per-Saccharide (1BPS) Model for Glycosaminoglycans. J Chem Theory Comput 2023; 19:5491-5502. [PMID: 37459601 PMCID: PMC10448712 DOI: 10.1021/acs.jctc.3c00238] [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: 02/28/2023] [Indexed: 08/23/2023]
Abstract
Glycosaminoglycans (GAGs) are polysaccharide compounds that play key roles in various biological processes. GAGs are important structural components of cartilage and the extracellular matrix of the brain. Due to the large size of these polysaccharides, coarse-grained approaches are indispensable for modeling these biopolymers. We develop a one-bead-per-saccharide model of chondroitin sulfates and hyaluronic acid based on an existing three-bead-per-saccharide coarse-grained model. Our coarse graining is carried out by using iterative Boltzmann inversion (IBI), including an additional coupling potential to incorporate the correlation between dihedral angles. The predictions of the model are verified against those of the existing three-bead-per-saccharin model and the experimental radius of gyration for hyaluronic acid.
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Affiliation(s)
- Saber Shakibi
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Patrick R. Onck
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Erik Van der Giessen
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
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Szała-Mendyk B, Phan TM, Mohanty P, Mittal J. Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations. Curr Opin Chem Biol 2023; 75:102333. [PMID: 37267850 PMCID: PMC10527940 DOI: 10.1016/j.cbpa.2023.102333] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 06/04/2023]
Abstract
"Membraneless organelles," also referred to as biomolecular condensates, perform a variety of cellular functions and their dysregulation is implicated in cancer and neurodegeneration. In the last two decades, liquid-liquid phase separation (LLPS) of intrinsically disordered and multidomain proteins has emerged as a plausible mechanism underlying the formation of various biomolecular condensates. Further, the occurrence of liquid-to-solid transitions within liquid-like condensates may give rise to amyloid structures, implying a biophysical link between phase separation and protein aggregation. Despite significant advances, uncovering the microscopic details of liquid-to-solid phase transitions using experiments remains a considerable challenge and presents an exciting opportunity for the development of computational models which provide valuable, complementary insights into the underlying phenomenon. In this review, we first highlight recent biophysical studies which provide new insights into the molecular mechanisms underlying liquid-to-solid (fibril) phase transitions of folded, disordered and multi-domain proteins. Next, we summarize the range of computational models used to study protein aggregation and phase separation. Finally, we discuss recent computational approaches which attempt to capture the underlying physics of liquid-to-solid transitions along with their merits and shortcomings.
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Affiliation(s)
- Beata Szała-Mendyk
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States; Department of Chemistry, Texas A&M University, TAMU 3255, College Station, 77843, Texas, United States; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, TAMU 3255, College Station, 77843, Texas, United States.
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7
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Roles of RNA-binding proteins in neurological disorders, COVID-19, and cancer. Hum Cell 2023; 36:493-514. [PMID: 36528839 PMCID: PMC9760055 DOI: 10.1007/s13577-022-00843-w] [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: 08/30/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
RNA-binding proteins (RBPs) have emerged as important players in multiple biological processes including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, biogenesis, and ribosome biogenesis. A large number of RBPs had already been identified by different approaches in various organisms and exhibited regulatory functions on RNAs' fate. RBPs can either directly or indirectly interact with their target RNAs or mRNAs to assume a key biological function whose outcome may trigger disease or normal biological events. They also exert distinct functions related to their canonical and non-canonical forms. This review summarizes the current understanding of a wide range of RBPs' functions and highlights their emerging roles in the regulation of diverse pathways, different physiological processes, and their molecular links with diseases. Various types of diseases, encompassing colorectal carcinoma, non-small cell lung carcinoma, amyotrophic lateral sclerosis, and Severe acute respiratory syndrome coronavirus 2, aberrantly express RBPs. We also highlight some recent advances in the field that could prompt the development of RBPs-based therapeutic interventions.
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8
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Jafarinia H, Van der Giessen E, Onck PR. Molecular basis of C9orf72 poly-PR interference with the β-karyopherin family of nuclear transport receptors. Sci Rep 2022; 12:21324. [PMID: 36494425 PMCID: PMC9734553 DOI: 10.1038/s41598-022-25732-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Nucleocytoplasmic transport (NCT) is affected in several neurodegenerative diseases including C9orf72-ALS. It has recently been found that arginine-containing dipeptide repeat proteins (R-DPRs), translated from C9orf72 repeat expansions, directly bind to several importins. To gain insight into how this can affect nucleocytoplasmic transport, we use coarse-grained molecular dynamics simulations to study the molecular interaction of poly-PR, the most toxic DPR, with several Kapβs (importins and exportins). We show that poly-PR-Kapβ binding depends on the net charge per residue (NCPR) of the Kapβ, salt concentration of the solvent, and poly-PR length. Poly-PR makes contact with the inner surface of most importins, which strongly interferes with Kapβ binding to cargo-NLS, IBB, and RanGTP in a poly-PR length-dependent manner. Longer poly-PRs at higher concentrations are also able to make contact with the outer surface of importins that contain several binding sites to FG-Nups. We also show that poly-PR binds to exportins, especially at lower salt concentrations, interacting with several RanGTP and FG-Nup binding sites. Overall, our results suggest that poly-PR might cause length-dependent defects in cargo loading, cargo release, Kapβ transport and Ran gradient across the nuclear envelope.
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Affiliation(s)
- Hamidreza Jafarinia
- grid.4830.f0000 0004 0407 1981Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Erik Van der Giessen
- grid.4830.f0000 0004 0407 1981Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Patrick R. Onck
- grid.4830.f0000 0004 0407 1981Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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9
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Kriachkov V, Ormsby AR, Kusnadi EP, McWilliam HE, Mintern JD, Amarasinghe SL, Ritchie ME, Furic L, Hatters DM. Arginine-rich C9ORF72 ALS proteins stall ribosomes in a manner distinct from a canonical ribosome-associated quality control substrate. J Biol Chem 2022; 299:102774. [PMID: 36481270 PMCID: PMC9830226 DOI: 10.1016/j.jbc.2022.102774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Hexanucleotide expansion mutations in C9ORF72 are a frequent cause of amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPRs), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mechanism of pathogenicity remains to be determined. Here, we explored the molecular features of DPR-induced stalling and examined whether known mechanisms such as ribosome quality control (RQC) regulate translation elongation on sequences that encode arginine-rich DPRs. We demonstrate that arginine-rich DPRs lead to stalling in a length-dependent manner, with lengths longer than 40 repeats invoking severe translation arrest. Mutational screening of 40×Gly-Xxx DPRs shows that stalling is most pronounced when Xxx is a charged amino acid (Arg, Lys, Glu, or Asp). Through a genome-wide knockout screen, we find that genes regulating stalling on polyadenosine mRNA coding for poly-Lys, a canonical RQC substrate, act differently in the case of arginine-rich DPRs. Indeed, these findings point to a limited scope for natural regulatory responses to resolve the arginine-rich DPR stalls, even though the stalls may be sensed, as evidenced by an upregulation of RQC gene expression. These findings therefore implicate arginine-rich DPR-mediated stalled ribosomes as a source of stress and toxicity and may be a crucial component in pathomechanisms.
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Affiliation(s)
- Viacheslav Kriachkov
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Angelique R. Ormsby
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eric P. Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Hamish E.G. McWilliam
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia,Department of Microbiology and Immunology, Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justine D. Mintern
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia,Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, Victoria, Australia
| | - Danny M. Hatters
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia,For correspondence: Danny M. Hatters
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10
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PolyGA targets the ER stress-adaptive response by impairing GRP75 function at the MAM in C9ORF72-ALS/FTD. Acta Neuropathol 2022; 144:939-966. [PMID: 36121477 PMCID: PMC9547809 DOI: 10.1007/s00401-022-02494-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
ER stress signaling is linked to the pathophysiological and clinical disease manifestations in amyotrophic lateral sclerosis (ALS). Here, we have investigated ER stress-induced adaptive mechanisms in C9ORF72-ALS/FTD, focusing on uncovering early endogenous neuroprotective mechanisms and the crosstalk between pathological and adaptive responses in disease onset and progression. We provide evidence for the early onset of ER stress-mediated adaptive response in C9ORF72 patient-derived motoneurons (MNs), reflected by the elevated increase in GRP75 expression. These transiently increased GRP75 levels enhance ER-mitochondrial association, boosting mitochondrial function and sustaining cellular bioenergetics during the initial stage of disease, thereby counteracting early mitochondrial deficits. In C9orf72 rodent neurons, an abrupt reduction in GRP75 expression coincided with the onset of UPR, mitochondrial dysfunction and the emergence of PolyGA aggregates, which co-localize with GRP75. Similarly, the overexpression of PolyGA in WT cortical neurons or C9ORF72 patient-derived MNs led to the sequestration of GRP75 within PolyGA inclusions, resulting in mitochondrial calcium (Ca2+) uptake impairments. Corroborating these findings, we found that PolyGA aggregate-bearing human post-mortem C9ORF72 hippocampal dentate gyrus neurons not only display reduced expression of GRP75 but also exhibit GRP75 sequestration within inclusions. Sustaining high GRP75 expression in spinal C9orf72 rodent MNs specifically prevented ER stress, normalized mitochondrial function, abrogated PolyGA accumulation in spinal MNs, and ameliorated ALS-associated behavioral phenotype. Taken together, our results are in line with the notion that neurons in C9ORF72-ALS/FTD are particularly susceptible to ER-mitochondrial dysfunction and that GRP75 serves as a critical endogenous neuroprotective factor. This neuroprotective pathway, is eventually targeted by PolyGA, leading to GRP75 sequestration, and its subsequent loss of function at the MAM, compromising mitochondrial function and promoting disease onset.
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11
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Shillcock JC, Lagisquet C, Alexandre J, Vuillon L, Ipsen JH. Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules. SOFT MATTER 2022; 18:6674-6693. [PMID: 36004748 DOI: 10.1039/d2sm00387b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biomolecular condensates play numerous roles in cells by selectively concentrating client proteins while excluding others. These functions are likely to be sensitive to the spatial organization of the scaffold proteins forming the condensate. We use coarse-grained molecular simulations to show that model intrinsically-disordered proteins phase separate into a heterogeneous, structured fluid characterized by a well-defined length scale. The proteins are modelled as semi-flexible polymers with punctate, multifunctional binding sites in good solvent conditions. Their dense phase is highly solvated with a spatial structure that is more sensitive to the separation of the binding sites than their affinity. We introduce graph theoretic measures to quantify their heterogeneity, and find that it increases with increasing binding site number, and exhibits multi-timescale dynamics. The model proteins also swell on passing from the dilute solution to the dense phase. The simulations predict that the structure of the dense phase is modulated by the location and affinity of binding sites distant from the termini of the proteins, while sites near the termini more strongly affect its phase behaviour. The relations uncovered between the arrangement of weak interaction sites on disordered proteins and the material properties of their dense phase can be experimentally tested to give insight into the biophysical properties, pathological effects, and rational design of biomolecular condensates.
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Affiliation(s)
- Julian C Shillcock
- Blue Brain Project and Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Clément Lagisquet
- LAMA, Univ. Savoie Mont Blanc, CNRS, LAMA, 73376 Le Bourget du Lac, France.
| | - Jérémy Alexandre
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Laurent Vuillon
- LAMA, Univ. Savoie Mont Blanc, CNRS, LAMA, 73376 Le Bourget du Lac, France.
| | - John H Ipsen
- Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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12
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C9orf72 Hexanucleotide Repeat Expansion-Related Neuropathology Is Attenuated by Nasal Rifampicin in Mice. Biomedicines 2022; 10:biomedicines10051080. [PMID: 35625816 PMCID: PMC9138602 DOI: 10.3390/biomedicines10051080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
The non-coding GGGGCC hexanucleotide repeat expansion (HRE) in C9orf72 gene is a dominant cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). This intronic mutation elicits the formation of nuclear and cytoplasmic inclusions containing RNA, RNA-binding proteins, and HRE-derived dipeptide repeat proteins (DPRs), leading to neurodegeneration via the gain-of-toxic function or loss-of-function of relevant proteins. Using C9-500 mice harboring ~500 repeats of the GGGGCC sequence in human C9orf72 gene, we investigated the effects of rifampicin against HRE-related pathological phenotypes. Rifampicin was administered intranasally to 4.5- to 5-month-old mice for 1 month, and their cognitive function and neuropathology were assessed by the Morris water maze test and immunohistochemical staining. Rifampicin treatment reduced the formation of RNA foci and cytoplasmic inclusions containing DPRs or phosphorylated TDP-43, and furthermore, the levels of phosphorylated double-strand RNA-dependent protein kinase (PKR) that regulates repeat-associated non-ATG (RAN) translation. Synapse loss in the hippocampus and neuronal loss and microglial activation in the prefrontal and motor cortices were also attenuated, and mouse memory was significantly improved. Our findings suggest a therapeutic potential of nasal rifampicin in the prevention of C9orf72-linked neurodegenerative disorders.
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13
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Van Lindt J, Lazar T, Pakravan D, Demulder M, Meszaros A, Van Den Bosch L, Maes D, Tompa P. F/YGG-motif is an intrinsically disordered nucleic-acid binding motif. RNA Biol 2022; 19:622-635. [PMID: 35491929 PMCID: PMC9067507 DOI: 10.1080/15476286.2022.2066336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNP) function in RNA processing, have RNA-recognition motifs (RRMs) and intrinsically disordered, low-complexity domains (LCDs). While RRMs are drivers of RNA binding, there is only limited knowledge about the RNA interaction by the LCD of some hnRNPs. Here, we show that the LCD of hnRNPA2 interacts with RNA via an embedded Tyr/Gly-rich region which is a disordered RNA-binding motif. RNA binding is maintained upon mutating tyrosine residues to phenylalanines, but abrogated by mutating to alanines, thus we term the RNA-binding region ‘F/YGG motif’. The F/YGG motif can bind a broad range of structured (e.g. tRNA) and disordered (e.g. polyA) RNAs, but not rRNA. As the F/YGG otif can also interact with DNA, we consider it a general nucleic acid-binding motif. hnRNPA2 LCD can form dense droplets, by liquid–liquid phase separation (LLPS). Their formation is inhibited by RNA binding, which is mitigated by salt and 1,6-hexanediol, suggesting that both electrostatic and hydrophobic interactions feature in the F/YGG motif. The D290V mutant also binds RNA, which interferes with both LLPS and aggregation thereof. We found homologous regions in a broad range of RNA- and DNA-binding proteins in the human proteome, suggesting that the F/YGG motif is a general nucleic acid-interaction motif.
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Affiliation(s)
- Joris Van Lindt
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tamas Lazar
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Donya Pakravan
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Manon Demulder
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Attila Meszaros
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ludo Van Den Bosch
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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14
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Tsanai M, Frederix PWJM, Schroer CFE, Souza PCT, Marrink SJ. Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chem Sci 2021; 12:8521-8530. [PMID: 34221333 PMCID: PMC8221187 DOI: 10.1039/d1sc00374g] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/17/2021] [Indexed: 01/30/2023] Open
Abstract
Complex coacervates are liquid-liquid phase separated systems, typically containing oppositely charged polyelectrolytes. They are widely studied for their functional properties as well as their potential involvement in cellular compartmentalization as biomolecular condensates. Diffusion and partitioning of solutes into a coacervate phase are important to address because their highly dynamic nature is one of their most important functional characteristics in real-world systems, but are difficult to study experimentally or even theoretically without an explicit representation of every molecule in the system. Here, we present an explicit-solvent, molecular dynamics coarse-grain model of complex coacervates, based on the Martini 3.0 force field. We demonstrate the accuracy of the model by reproducing the salt dependent coacervation of poly-lysine and poly-glutamate systems, and show the potential of the model by simulating the partitioning of ions and small nucleotides between the condensate and surrounding solvent phase. Our model paves the way for simulating coacervates and biomolecular condensates in a wide range of conditions, with near-atomic resolution.
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Affiliation(s)
- Maria Tsanai
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
| | - Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, University of Lyon Lyon France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
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15
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Lafarga V, Sirozh O, Díaz-López I, Galarreta A, Hisaoka M, Zarzuela E, Boskovic J, Jovanovic B, Fernandez-Leiro R, Muñoz J, Stoecklin G, Ventoso I, Fernandez-Capetillo O. Widespread displacement of DNA- and RNA-binding factors underlies toxicity of arginine-rich cell-penetrating peptides. EMBO J 2021; 40:e103311. [PMID: 33978236 DOI: 10.15252/embj.2019103311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 11/09/2022] Open
Abstract
Due to their capability to transport chemicals or proteins into target cells, cell-penetrating peptides (CPPs) are being developed as therapy delivery tools. However, and despite their interesting properties, arginine-rich CPPs often show toxicity for reasons that remain poorly understood. Using a (PR)n dipeptide repeat that has been linked to amyotrophic lateral sclerosis (ALS) as a model of an arginine-rich CPP, we here show that the presence of (PR)n leads to a generalized displacement of RNA- and DNA-binding proteins from chromatin and mRNA. Accordingly, any reaction involving nucleic acids, such as RNA transcription, translation, splicing and degradation, or DNA replication and repair, is impaired by the presence of the CPPs. Interestingly, the effects of (PR)n are fully mimicked by protamine, a small arginine-rich protein that displaces histones from chromatin during spermatogenesis. We propose that widespread coating of nucleic acids and consequent displacement of RNA- and DNA-binding factors from chromatin and mRNA accounts for the toxicity of arginine-rich CPPs, including those that have been recently associated with the onset of ALS.
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Affiliation(s)
- Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oleksandra Sirozh
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Irene Díaz-López
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Antonio Galarreta
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Misaru Hisaoka
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Eduardo Zarzuela
- ProteoRed-ISCIII, Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jasminka Boskovic
- Electron Microscopy Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bogdan Jovanovic
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Rafael Fernandez-Leiro
- Genomic Integrity and Structural Biology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jaime Muñoz
- ProteoRed-ISCIII, Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Iván Ventoso
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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16
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Solomon DA, Smikle R, Reid MJ, Mizielinska S. Altered Phase Separation and Cellular Impact in C9orf72-Linked ALS/FTD. Front Cell Neurosci 2021; 15:664151. [PMID: 33967699 PMCID: PMC8096919 DOI: 10.3389/fncel.2021.664151] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of the C9orf72 repeat expansion mutation as causative for chromosome 9-linked amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in 2011, a multitude of cellular pathways have been implicated. However, evidence has also been accumulating for a key mechanism of cellular compartmentalization—phase separation. Liquid-liquid phase separation (LLPS) is fundamental for the formation of membraneless organelles including stress granules, the nucleolus, Cajal bodies, nuclear speckles and the central channel of the nuclear pore. Evidence has now accumulated showing that the formation and function of these membraneless organelles is impaired by both the toxic arginine rich dipeptide repeat proteins (DPRs), translated from the C9orf72 repeat RNA transcript, and the repeat RNA itself. Both the arginine rich DPRs and repeat RNA themselves undergo phase separation and disrupt the physiological phase separation of proteins involved in the formation of these liquid-like organelles. Hence abnormal phase separation may explain a number of pathological cellular phenomena associated with C9orf72-ALS/FTD. In this review article, we will discuss the principles of phase separation, phase separation of the DPRs and repeat RNA themselves and how they perturb LLPS associated with membraneless organelles and the functional consequences of this. We will then discuss how phase separation may impact the major pathological feature of C9orf72-ALS/FTD, TDP-43 proteinopathy, and how LLPS may be targeted therapeutically in disease.
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Affiliation(s)
- Daniel A Solomon
- UK Dementia Research Institute at King's College London, London, United Kingdom.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Rebekah Smikle
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Matthew J Reid
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Sarah Mizielinska
- UK Dementia Research Institute at King's College London, London, United Kingdom.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
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