1
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [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: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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2
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Sun J, Chen Y, Bi R, Yuan Y, Yu H. Bioinformatic approaches of liquid-liquid phase separation in human disease. Chin Med J (Engl) 2024; 137:1912-1925. [PMID: 39033393 PMCID: PMC11332758 DOI: 10.1097/cm9.0000000000003249] [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: 04/28/2024] [Indexed: 07/23/2024] Open
Abstract
ABSTRACT Biomolecular aggregation within cellular environments via liquid-liquid phase separation (LLPS) spontaneously forms droplet-like structures, which play pivotal roles in diverse biological processes. These structures are closely associated with a range of diseases, including neurodegenerative disorders, cancer and infectious diseases, highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis, and exploring potential therapeutic interventions. In this review, we delineate recent advancements in LLPS research, emphasizing its pathological relevance, therapeutic considerations, and the pivotal role of bioinformatic tools and databases in facilitating LLPS investigations. Additionally, we undertook a comprehensive analysis of bioinformatic resources dedicated to LLPS research in order to elucidate their functionality and applicability. By providing comprehensive insights into current LLPS-related bioinformatics resources, this review highlights its implications for human health and disease.
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Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yilong Chen
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ruiye Bi
- Department of Orthognathic and TMJ Surgery, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
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3
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Chuang HY, He RY, Huang YA, Hsu WT, Cheng YJ, Guo ZR, Wali N, Hwang IS, Shie JJ, Huang JJT. Engineered droplet-forming peptide as photocontrollable phase modulator for fused in sarcoma protein. Nat Commun 2024; 15:5686. [PMID: 38971830 PMCID: PMC11227587 DOI: 10.1038/s41467-024-50025-5] [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: 10/19/2023] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
The assembly and disassembly of biomolecular condensates are crucial for the subcellular compartmentalization of biomolecules in the control of cellular reactions. Recently, a correlation has been discovered between the phase transition of condensates and their maturation (aggregation) process in diseases. Therefore, modulating the phase of condensates to unravel the roles of condensation has become a matter of interest. Here, we create a peptide-based phase modulator, JSF1, which forms droplets in the dark and transforms into amyloid-like fibrils upon photoinitiation, as evidenced by their distinctive nanomechanical and dynamic properties. JSF1 is found to effectively enhance the condensation of purified fused in sarcoma (FUS) protein and, upon light exposure, induce its fibrilization. We also use JSF1 to modulate the biophysical states of FUS condensates in live cells and elucidate the relationship between FUS phase transition and FUS proteinopathy, thereby shedding light on the effect of protein phase transition on cellular function and malfunction.
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Affiliation(s)
- Hao-Yu Chuang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Ting Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ya-Jen Cheng
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Zheng-Rong Guo
- Institute of Physics, Academia Sinica, Taipei, 115, Taiwan
| | - Niaz Wali
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | | | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
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4
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Di Timoteo G, Giuliani A, Setti A, Biagi MC, Lisi M, Santini T, Grandioso A, Mariani D, Castagnetti F, Perego E, Zappone S, Lattante S, Sabatelli M, Rotili D, Vicidomini G, Bozzoni I. M 6A reduction relieves FUS-associated ALS granules. Nat Commun 2024; 15:5033. [PMID: 38866783 PMCID: PMC11169559 DOI: 10.1038/s41467-024-49416-5] [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: 10/04/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease due to gradual motoneurons (MN) degeneration. Among the processes associated to ALS pathogenesis, there is the formation of cytoplasmic inclusions produced by aggregation of mutant proteins, among which the RNA binding protein FUS. Here we show that, in neuronal cells and in iPSC-derived MN expressing mutant FUS, such inclusions are significantly reduced in number and dissolve faster when the RNA m6A content is diminished. Interestingly, stress granules formed in ALS conditions showed a distinctive transcriptome with respect to control cells, which reverted to similar to control after m6A downregulation. Notably, cells expressing mutant FUS were characterized by higher m6A levels suggesting a possible link between m6A homeostasis and pathological aggregates. Finally, we show that FUS inclusions are reduced also in patient-derived fibroblasts treated with STM-2457, an inhibitor of METTL3 activity, paving the way for its possible use for counteracting aggregate formation in ALS.
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Grants
- ERC-2019-SyG 855923-ASTRA EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- ERC-2018-CoG 818669-BrightEyes EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- AIRC IG 2019 Id. 23053 Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)
- PRIN 2017 2017P352Z4 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- NextGenerationEU PNRR MUR Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "National Center for Gene Therapy and Drugbased on RNA Technology" (CN00000041) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "National Center for Gene Therapy and Drug based on RNA Technology" (CN00000041) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- NextGenerationEU PNRR MUR Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "Sapienza" Ateneo Project 2021 n. RM12117A61C811CE Sapienza Università di Roma (Sapienza University of Rome)
- Regione Lazio PROGETTI DI GRUPPI DI RICERCA 2020 - A0375-2020-36597 Regione Lazio (Region of Lazio)
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Andrea Giuliani
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Martina C Biagi
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy
| | - Michela Lisi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Alessia Grandioso
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Davide Mariani
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Francesco Castagnetti
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Eleonora Perego
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Sabrina Zappone
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Mario Sabatelli
- Section of Neurology, Department of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Adult NEMO Clinical Center, Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Giuseppe Vicidomini
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy.
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy.
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy.
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5
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Hernandez-Candia CN, Brady BR, Harrison E, Tucker CL. A platform to induce and mature biomolecular condensates using chemicals and light. Nat Chem Biol 2024; 20:452-462. [PMID: 38191942 PMCID: PMC10978248 DOI: 10.1038/s41589-023-01520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Biomolecular condensates are membraneless compartments that impart spatial and temporal organization to cells. Condensates can undergo maturation, transitioning from dynamic liquid-like states into solid-like states associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Huntington's disease. Despite their important roles, many aspects of condensate biology remain incompletely understood, requiring tools for acutely manipulating condensate-relevant processes within cells. Here we used the BCL6 BTB domain and its ligands BI-3802 and BI-3812 to create a chemical genetic platform, BTBolig, allowing inducible condensate formation and dissolution. We also developed optogenetic and chemical methods for controlled induction of condensate maturation, where we surprisingly observed recruitment of chaperones into the condensate core and formation of dynamic biphasic condensates. Our work provides insights into the interaction of condensates with proteostasis pathways and introduces a suite of chemical-genetic approaches to probe the role of biomolecular condensates in health and disease.
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Affiliation(s)
| | - Brian R Brady
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Evan Harrison
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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6
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Chen R, Glauninger H, Kahan DN, Shangguan J, Sachleben JR, Riback JA, Drummond DA, Sosnick TR. HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker. Proc Natl Acad Sci U S A 2024; 121:e2321606121. [PMID: 38513106 PMCID: PMC10990091 DOI: 10.1073/pnas.2321606121] [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: 12/12/2023] [Accepted: 01/29/2024] [Indexed: 03/23/2024] Open
Abstract
Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen, Nat. Rev. Mol. Cell Biol. 18, 285-298 (2017), H. Yoo, C. Triandafillou, D. A. Drummond, J. Biol. Chem. 294, 7151-7159 (2019)]. Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation [J. A. Riback et al., Cell 168, 1028-1040.e19 (2017)]. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. We apply hydrogen-deuterium exchange/mass spectrometry to investigate the mechanism of Pab1's condensation. Pab1's four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe populations allows us to identify which regions contribute to the condensate's interaction network. Our data yield a picture of Pab1's stress-triggered condensation, which we term sequential activation (Fig. 1A), wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. Subsequent association is dictated more by the underlying free energy surface than specific interactions, an effect we refer to as thermodynamic specificity. Our study represents an advance for elucidating the interactions that drive condensation. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.
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Affiliation(s)
- Ruofan Chen
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Hendrik Glauninger
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Graduate Program in Biophysical Sciences, Division of Physical Sciences, University of Chicago, Chicago, IL60637
| | - Darren N. Kahan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
| | - Julia Shangguan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
| | | | - Joshua A. Riback
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Graduate Program in Biophysical Sciences, Division of Physical Sciences, University of Chicago, Chicago, IL60637
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
| | - Tobin R. Sosnick
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
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7
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Chen L, Wu M, Zhou Y. HSPB8 binding to c-Myc alleviates hypoxia/reoxygenation-induced trophoblast cell dysfunction. Exp Ther Med 2024; 27:114. [PMID: 38361516 PMCID: PMC10867730 DOI: 10.3892/etm.2024.12402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/01/2023] [Indexed: 02/17/2024] Open
Abstract
Preeclampsia (PE) is a pregnancy-specific syndrome with complex pathogenesis. The present study aimed to explore the role of heat shock protein B8 (HSPB8) and c-Myc in trophoblast cell dysfunction using a hypoxia/reoxygenation (H/R)-treated HTR8/SVneo cell model. HSPB8 expression in tissues of patients with PE was analyzed using the Gene Expression Omnibus database. Following detection of HSPB8 expression in H/R-stimulated HTR8/SVneo cells, HSPB8 was overexpressed by transfection of the gene with a HSPB8-specific plasmid. Cell Counting Kit-8, wound healing and Transwell assays were used to evaluate the proliferation, migration and invasion of HTR8/SVneo cells exposed to H/R conditions. Reactive oxygen species (ROS) were determined by 2,7-dichlorodihydrofluorescein diacetate staining. 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolocarbo-cyanine iodide (JC-1) staining was applied to assess mitochondrial membrane potential. Malondialdehyde (MDA) and superoxide dismutase (SOD) levels were detected using the corresponding commercial kits. In addition, the induction of apoptosis was assessed by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. Moreover, the Biogrid database predicted that HSPB8 was bound to c-Myc, and a co-immunoprecipitation (Co-IP) assay was used to verify this interaction. Subsequently, c-Myc expression was silenced to conduct rescue experiments in HTR8/SVneo cells exposed to H/R conditions and upregulated HSPB8 expression. Notably, reduced HSPB8 expression was noted in PE tissues and H/R-stimulated HTR8/SVneo cells. HSPB8 enforced expression promoted the proliferation, migration and invasion of HTR8/SVneo cells. Moreover, H/R caused an increase in ROS and MDA levels as well as in TUNEL staining and a decrease in aggregated JC-1 fluorescence and SOD activity levels, which were restored following HSPB8 overexpression. Co-IP confirmed the interaction between HSPB8 and c-Myc. Moreover, knockdown of c-Myc expression compromised the effects of HSPB8 upregulation on trophoblast cell dysfunction following induction of H/R. Collectively, the data indicated that HSPB8 could improve mitochondrial oxidative stress by binding to c-Myc to alleviate trophoblast cell dysfunction. The findings may provide new insights into the pathogenesis of PE and highlight the role of HSPB8/c-Myc in the prevention and treatment of PE in the future.
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Affiliation(s)
- Ling Chen
- Department of Gynecology and Obstetrics, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Meiting Wu
- Department of Gynecology and Obstetrics, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yu Zhou
- Department of Gynecology and Obstetrics, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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8
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Zhang Z, Zhao Q, Gong Z, Du R, Liu M, Zhang Y, Zhang L, Li C. Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology. JACS AU 2024; 4:369-383. [PMID: 38425916 PMCID: PMC10900494 DOI: 10.1021/jacsau.3c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution identification of these protein structures and interactions within living cells presents a technical challenge. In this Perspective, we summarize the recent advancements in in-cell nuclear magnetic resonance (NMR) and in vivo cross-linking mass spectrometry (XL-MS) for studying protein structures and interactions within a cellular context. Additionally, we discuss the challenges, opportunities, and potential benefits of integrating in-cell NMR and in vivo XL-MS in future research to offer an exhaustive approach to studying proteins in their natural habitat.
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Affiliation(s)
- Zeting Zhang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Zhao
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruichen Du
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yukui Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
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9
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Zhang R, Jalali S, Dias CL, Haataja MP. Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach. PNAS NEXUS 2024; 3:pgae045. [PMID: 38725528 PMCID: PMC11079572 DOI: 10.1093/pnasnexus/pgae045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/19/2024] [Indexed: 05/12/2024]
Abstract
Amyloid fibrils have long been associated with many neurodegenerative diseases. The conventional picture of the formation and proliferation of fibrils from unfolded proteins comprises primary and secondary nucleation of oligomers followed by elongation and fragmentation thereof. In this work, we first employ extensive all-atom molecular dynamics (MD) simulations of short peptides to investigate the governing processes of fibril growth at the molecular scale. We observe that the peptides in the bulk solution can bind onto and subsequently diffuse along the fibril surface, which leads to fibril elongation via either bulk- or surface-mediated docking mechanisms. Then, to guide the quantitative interpretation of these observations and to provide a more comprehensive picture of the growth kinetics of single fibrils, a continuum model which incorporates the key processes observed in the MD simulations is formulated. The model is employed to investigate how relevant physical parameters affect the kinetics of fibril growth and identify distinct growth regimes. In particular, it is shown that fibrils which strongly bind peptides may undergo a transient exponential growth phase in which the entire fibril surface effectively acts as a sink for peptides. We also demonstrate how the relevant model parameters can be estimated from the MD trajectories. Our results provide compelling evidence that the overall fibril growth rates are determined by both bulk and surface peptide fluxes, thereby contributing to a more fundamental understanding of the growth kinetics of amyloid-like fibrils.
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Affiliation(s)
- Ruoyao Zhang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Cristiano Luis Dias
- Department of Physics, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ 08544, USA
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10
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Shao Y, Shu X, Lu Y, Zhu W, Li R, Fu H, Li C, Sun W, Li Z, Zhang Y, Cao X, Ye X, Ajiboye E, Zhao B, Zhang L, Wu H, Feng XH, Yang B, Lu H. A chaperone-like function of FUS ensures TAZ condensate dynamics and transcriptional activation. Nat Cell Biol 2024; 26:86-99. [PMID: 38172614 DOI: 10.1038/s41556-023-01309-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
The Hippo pathway has important roles in organ development, tissue homeostasis and tumour growth. Its downstream effector TAZ is a transcriptional coactivator that promotes target gene expression through the formation of biomolecular condensates. However, the mechanisms that regulate the biophysical properties of TAZ condensates to enable Hippo signalling are not well understood. Here using chemical crosslinking combined with an unbiased proteomics approach, we show that FUS associates with TAZ condensates and exerts a chaperone-like effect to maintain their proper liquidity and robust transcriptional activity. Mechanistically, the low complexity sequence domain of FUS targets the coiled-coil domain of TAZ in a phosphorylation-regulated manner, which ensures the liquidity and dynamicity of TAZ condensates. In cells lacking FUS, TAZ condensates transition into gel-like or solid-like assembles with immobilized TAZ, which leads to reduced expression of target genes and inhibition of pro-tumorigenic activity. Thus, our findings identify a chaperone-like function of FUS in Hippo regulation and demonstrate that appropriate biophysical properties of transcriptional condensates are essential for gene activation.
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Affiliation(s)
- Yangqing Shao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Yi Lu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenxuan Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ran Li
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Huanyi Fu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wei Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Zhuo Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yitong Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaolei Cao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xifu Ye
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Emmanuel Ajiboye
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA
| | - Bin Zhao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA
| | - Xin-Hua Feng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
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11
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Sahin C, Leppert A, Landreh M. Advances in mass spectrometry to unravel the structure and function of protein condensates. Nat Protoc 2023; 18:3653-3661. [PMID: 37907762 DOI: 10.1038/s41596-023-00900-0] [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: 04/18/2023] [Accepted: 08/09/2023] [Indexed: 11/02/2023]
Abstract
Membrane-less organelles assemble through liquid-liquid phase separation (LLPS) of partially disordered proteins into highly specialized microenvironments. Currently, it is challenging to obtain a clear understanding of the relationship between the structure and function of phase-separated protein assemblies, owing to their size, dynamics and heterogeneity. In this Perspective, we discuss recent advances in mass spectrometry (MS) that offer several promising approaches for the study of protein LLPS. We survey MS tools that have provided valuable insights into other insoluble protein systems, such as amyloids, and describe how they can also be applied to study proteins that undergo LLPS. On the basis of these recent advances, we propose to integrate MS into the experimental workflow for LLPS studies. We identify specific challenges and future opportunities for the analysis of protein condensate structure and function by MS.
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Affiliation(s)
- Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden.
- Structural Biology and NMR laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Axel Leppert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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12
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Naskar A, Nayak A, Salaikumaran MR, Vishal SS, Gopal PP. Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders. Front Mol Neurosci 2023; 16:1242925. [PMID: 37720552 PMCID: PMC10502346 DOI: 10.3389/fnmol.2023.1242925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/21/2023] [Indexed: 09/19/2023] Open
Abstract
Liquid-liquid phase separation results in the formation of dynamic biomolecular condensates, also known as membrane-less organelles, that allow for the assembly of functional compartments and higher order structures within cells. Multivalent, reversible interactions between RNA-binding proteins (RBPs), including FUS, TDP-43, and hnRNPA1, and/or RNA (e.g., RBP-RBP, RBP-RNA, RNA-RNA), result in the formation of ribonucleoprotein (RNP) condensates, which are critical for RNA processing, mRNA transport, stability, stress granule assembly, and translation. Stress granules, neuronal transport granules, and processing bodies are examples of cytoplasmic RNP condensates, while the nucleolus and Cajal bodies are representative nuclear RNP condensates. In neurons, RNP condensates promote long-range mRNA transport and local translation in the dendrites and axon, and are essential for spatiotemporal regulation of gene expression, axonal integrity and synaptic function. Mutations of RBPs and/or pathologic mislocalization and aggregation of RBPs are hallmarks of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease. ALS/FTD-linked mutations of RBPs alter the strength and reversibility of multivalent interactions with other RBPs and RNAs, resulting in aberrant phase transitions. These aberrant RNP condensates have detrimental functional consequences on mRNA stability, localization, and translation, and ultimately lead to compromised axonal integrity and synaptic function in disease. Pathogenic protein aggregation is dependent on various factors, and aberrant dynamically arrested RNP condensates may serve as an initial nucleation step for pathologic aggregate formation. Recent studies have focused on identifying mechanisms by which neurons resolve phase transitioned condensates to prevent the formation of pathogenic inclusions/aggregates. The present review focuses on the phase separation of neurodegenerative disease-linked RBPs, physiological functions of RNP condensates, and the pathologic role of aberrant phase transitions in neurodegenerative disease, particularly ALS/FTD. We also examine cellular mechanisms that contribute to the resolution of aberrant condensates in neurons, and potential therapeutic approaches to resolve aberrantly phase transitioned condensates at a molecular level.
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Affiliation(s)
- Aditi Naskar
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Asima Nayak
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | | | - Sonali S. Vishal
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Pallavi P. Gopal
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, CT, United States
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13
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Choudhary D, Mediani L, Avellaneda MJ, Bjarnason S, Alberti S, Boczek EE, Heidarsson PO, Mossa A, Carra S, Tans SJ, Cecconi C. Human Small Heat Shock Protein B8 Inhibits Protein Aggregation without Affecting the Native Folding Process. J Am Chem Soc 2023. [PMID: 37411010 PMCID: PMC10360156 DOI: 10.1021/jacs.3c02022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Small Heat Shock Proteins (sHSPs) are key components of our Protein Quality Control system and are thought to act as reservoirs that neutralize irreversible protein aggregation. Yet, sHSPs can also act as sequestrases, promoting protein sequestration into aggregates, thus challenging our understanding of their exact mechanisms of action. Here, we employ optical tweezers to explore the mechanisms of action of the human small heat shock protein HSPB8 and its pathogenic mutant K141E, which is associated with neuromuscular disease. Through single-molecule manipulation experiments, we studied how HSPB8 and its K141E mutant affect the refolding and aggregation processes of the maltose binding protein. Our data show that HSPB8 selectively suppresses protein aggregation without affecting the native folding process. This anti-aggregation mechanism is distinct from previous models that rely on the stabilization of unfolded polypeptide chains or partially folded structures, as has been reported for other chaperones. Rather, it appears that HSPB8 selectively recognizes and binds to aggregated species formed at the early stages of aggregation, preventing them from growing into larger aggregated structures. Consistently, the K141E mutation specifically targets the affinity for aggregated structures without impacting native folding, and hence impairs its anti-aggregation activity.
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Affiliation(s)
- Dhawal Choudhary
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Mario J Avellaneda
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Alessandro Mossa
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- INFN Firenze, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Sander J Tans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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14
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Vendruscolo M, Fuxreiter M. Towards sequence-based principles for protein phase separation predictions. Curr Opin Chem Biol 2023; 75:102317. [PMID: 37207400 DOI: 10.1016/j.cbpa.2023.102317] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, PD 35131, Italy; Department of Physics and Astronomy, University of Padova, PD 35131, Italy.
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15
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Kinger S, Dubey AR, Kumar P, Jagtap YA, Choudhary A, Kumar A, Prajapati VK, Dhiman R, Mishra A. Molecular Chaperones' Potential against Defective Proteostasis of Amyotrophic Lateral Sclerosis. Cells 2023; 12:cells12091302. [PMID: 37174703 PMCID: PMC10177248 DOI: 10.3390/cells12091302] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neuronal degenerative condition identified via a build-up of mutant aberrantly folded proteins. The native folding of polypeptides is mediated by molecular chaperones, preventing their pathogenic aggregation. The mutant protein expression in ALS is linked with the entrapment and depletion of chaperone capacity. The lack of a thorough understanding of chaperones' involvement in ALS pathogenesis presents a significant challenge in its treatment. Here, we review how the accumulation of the ALS-linked mutant FUS, TDP-43, SOD1, and C9orf72 proteins damage cellular homeostasis mechanisms leading to neuronal loss. Further, we discuss how the HSP70 and DNAJ family co-chaperones can act as potential targets for reducing misfolded protein accumulation in ALS. Moreover, small HSPB1 and HSPB8 chaperones can facilitate neuroprotection and prevent stress-associated misfolded protein apoptosis. Designing therapeutic strategies by pharmacologically enhancing cellular chaperone capacity to reduce mutant protein proteotoxic effects on ALS pathomechanisms can be a considerable advancement. Chaperones, apart from directly interacting with misfolded proteins for protein quality control, can also filter their toxicity by initiating strong stress-response pathways, modulating transcriptional expression profiles, and promoting anti-apoptotic functions. Overall, these properties of chaperones make them an attractive target for gaining fundamental insights into misfolded protein disorders and designing more effective therapies against ALS.
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Affiliation(s)
- Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
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16
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Protein-RNA interactions: from mass spectrometry to drug discovery. Essays Biochem 2023; 67:175-186. [PMID: 36866608 PMCID: PMC10070478 DOI: 10.1042/ebc20220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and RNAs form complexes and mutually affect their functions. In the present mini-review, we will first provide an overview of different mass spectrometry (MS)-based methods to study the RNA-binding proteome (RBPome), most of which are based on photochemical cross-linking. As we will show, some of these methods are also able to provide higher-resolution information about binding sites, which are important for the structural characterisation of protein-RNA interactions. In addition, classical structural biology techniques such as nuclear magnetic resonance (NMR) spectroscopy and biophysical methods such as electron paramagnetic resonance (EPR) spectroscopy and fluorescence-based methods contribute to a detailed understanding of the interactions between these two classes of biomolecules. We will discuss the relevance of such interactions in the context of the formation of membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes and their emerging importance as targets for drug discovery.
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17
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Li Y, Chen T, You K, Peng T, Li T. Sequence determinants and solution conditions underlying liquid to solid phase transition. Am J Physiol Cell Physiol 2023; 324:C236-C246. [PMID: 36503242 DOI: 10.1152/ajpcell.00280.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Life consists of numberless functional biomolecules that exist in various states. Besides well-dissolved phases, biomolecules especially proteins and nucleic acids can form liquid droplets through liquid-liquid phase separation (LLPS). Stronger interactions promote a solid-like state of biomolecular condensates, which are also formerly referred to as detergent-insoluble aggregates. Solid-like condensates exist in vivo physiologically and pathologically, and their formation has not been fully understood. Recently, more and more research has proven that liquid to solid phase transition (LST) is an essential way to form solid condensates. In this review, we summarized the regions in the sequence that have different impacts on phase transition and emphasized that the LST is affected by its sequence characteristics. Moreover, increasing evidence unveiled that LST is affected by various solution conditions. We discussed solution conditions like protein concentration, pH, ATP, ions, and small molecules in a solution. Methods have been established to study these solid phase components. Here, we summarized low-throughput experimental techniques and high-throughput omics methods in the study of the LST.
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Affiliation(s)
- Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Kaiqing You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Happy Life Technology, Beijing, China
| | - Tao Peng
- Happy Life Technology, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
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18
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Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation. Commun Biol 2023; 6:121. [PMID: 36717706 PMCID: PMC9887055 DOI: 10.1038/s42003-023-04512-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Small heat shock proteins (sHSPs) are chaperones with well-characterized roles in heat stress, but potential roles for sHSPs in desiccation tolerance have not been as thoroughly explored. We identified nine sHSPs from the tardigrade Hypsibius exemplaris, each containing a conserved alpha-crystallin domain flanked by disordered regions. Many of these sHSPs are highly expressed. Multiple tardigrade and human sHSPs could improve desiccation tolerance of E. coli, suggesting that the capacity to contribute to desicco-protection is a conserved property of some sHSPs. Purification and subsequent analysis of two tardigrade sHSPs, HSP21 and HSP24.6, revealed that these proteins can oligomerize in vitro. These proteins limited heat-induced aggregation of the model enzyme citrate synthase. Heterologous expression of HSP24.6 improved bacterial heat shock survival, and the protein significantly reduced heat-induced aggregation of soluble bacterial protein. Thus, HSP24.6 likely chaperones against protein aggregation to promote heat tolerance. Furthermore, HSP21 and HSP24.6 limited desiccation-induced aggregation and loss of function of citrate synthase. This suggests a mechanism by which tardigrade sHSPs promote desiccation tolerance, by limiting desiccation-induced protein aggregation, thereby maintaining proteostasis and supporting survival. These results suggest that sHSPs provide a mechanism of general stress resistance that can also be deployed to support survival during anhydrobiosis.
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19
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Félix SS, Laurents DV, Oroz J, Cabrita EJ. Fused in sarcoma undergoes cold denaturation: Implications for phase separation. Protein Sci 2023; 32:e4521. [PMID: 36453011 PMCID: PMC9793971 DOI: 10.1002/pro.4521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.
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Affiliation(s)
- Sara S. Félix
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | | | - Javier Oroz
- Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | - Eurico J. Cabrita
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal
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20
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Tibble RW, Gross JD. A call to order: Examining structured domains in biomolecular condensates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107318. [PMID: 36657879 PMCID: PMC10878105 DOI: 10.1016/j.jmr.2022.107318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Diverse cellular processes have been observed or predicted to occur in biomolecular condensates, which are comprised of proteins and nucleic acids that undergo liquid-liquid phase separation (LLPS). Protein-driven LLPS often involves weak, multivalent interactions between intrinsically disordered regions (IDRs). Due to their inherent lack of defined tertiary structures, NMR has been a powerful resource for studying the behavior and interactions of IDRs in condensates. While IDRs in proteins are necessary for phase separation, core proteins enriched in condensates often contain structured domains that are essential for their function and contribute to phase separation. How phase separation can affect the structure and conformational dynamics of structured domains is critical for understanding how biochemical reactions can be effectively regulated in cellular condensates. In this perspective, we discuss the consequences phase separation can have on structured domains and outline NMR observables we believe are useful for assessing protein structure and dynamics in condensates.
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Affiliation(s)
- Ryan W Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States.
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21
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Ubbiali D, Fratini M, Piersimoni L, Ihling CH, Kipping M, Heilmann I, Iacobucci C, Sinz A. Direct Observation of "Elongated" Conformational States in α-Synuclein upon Liquid-Liquid Phase Separation. Angew Chem Int Ed Engl 2022; 61:e202205726. [PMID: 36115020 PMCID: PMC9828221 DOI: 10.1002/anie.202205726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 01/12/2023]
Abstract
α-Synuclein (α-syn) is an intrinsically disordered protein (IDP) that undergoes liquid-liquid phase separation (LLPS), fibrillation, and forms insoluble intracellular Lewy bodies in neurons, which are the hallmark of Parkinson's Disease (PD). Neurotoxicity precedes the formation of aggregates and might be related to α-syn LLPS. The molecular mechanisms underlying the early stages of LLPS are still elusive. To obtain structural insights into α-syn upon LLPS, we take advantage of cross-linking/mass spectrometry (XL-MS) and introduce an innovative approach, termed COMPASS (COMPetitive PAiring StatisticS). In this work, we show that the conformational ensemble of α-syn shifts from a "hairpin-like" structure towards more "elongated" conformational states upon LLPS. We obtain insights into the critical initial stages of LLPS and establish a novel mass spectrometry-based approach that will aid to solve open questions in LLPS structural biology.
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Affiliation(s)
- Daniele Ubbiali
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Marta Fratini
- Department of Plant BiochemistryCharles Tanford Protein CenterInstitute for Biochemistry and BiotechnologyMartin-Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Lolita Piersimoni
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Marc Kipping
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Ingo Heilmann
- Department of Plant BiochemistryCharles Tanford Protein CenterInstitute for Biochemistry and BiotechnologyMartin-Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Department of Physical and Chemical SciencesUniversity of L'AquilaVia Vetoio, Coppito67100L'AquilaItaly
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
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22
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Mukherjee P, Panda P, Kasturi P. A comparative meta-analysis of membraneless organelle-associated proteins with age related proteome of C. elegans. Cell Stress Chaperones 2022; 27:619-631. [PMID: 36169889 PMCID: PMC9672229 DOI: 10.1007/s12192-022-01299-5] [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: 04/18/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 01/25/2023] Open
Abstract
Proteome imbalance can lead to protein misfolding and aggregation which is associated with pathologies. Protein aggregation can also be an active, organized process and can be exploited by cells as a survival strategy. In adverse conditions, it is beneficial to deposit the proteins in a condensate rather degrading and resynthesizing. Membraneless organelles (MLOs) are biological condensates formed through liquid-liquid phase separation (LLPS), involving cellular components such as nucleic acids and proteins. LLPS is a regulated process, which when perturbed, can undergo a transition from a physiological liquid condensate to pathological solid-like protein aggregates. To understand how the MLO-associated proteins (MLO-APs) behave during aging, we performed a comparative meta-analysis with age-related proteome of C. elegans. We found that the MLO-APs are highly abundant throughout the lifespan in wild-type and long-lived daf-2 mutant animals. Interestingly, they are aggregating more in long-lived mutant animals compared to the age matched wild-type and short-lived daf-16 and hsf-1 mutant animals. GO term analysis revealed that the cell cycle and embryonic development are among the top enriched processes in addition to RNP components in aggregated proteome. Considering antagonistic pleotropic nature of these developmental genes and post mitotic status of C. elegans, we assume that these proteins phase transit during post development. As the organism ages, these MLO-APs either mature to become more insoluble or dissolve in uncontrolled manner. However, in the long-lived daf-2 mutant animals, the MLOs may attain protective states due to extended availability and association of molecular chaperones.
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Affiliation(s)
- Pritam Mukherjee
- BioX Centre, School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Prajnadipta Panda
- BioX Centre, School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Prasad Kasturi
- BioX Centre, School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India.
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23
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Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 PMCID: PMC11331907 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
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24
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Abstract
Condensed states of proteins, including liquid-like membraneless organelles and solid-like aggregates, contribute in fundamental ways to the organisation and function of the cell. Perturbations of these states can lead to a variety of diseases through mechanisms that we are now beginning to understand. We define protein condensation diseases as conditions caused by the disruption of the normal behaviour of the condensed states of proteins. We analyze the problem of the identification of targets for pharmacological interventions for these diseases and explore opportunities for the regulation of the formation and organisation of aberrant condensed states of proteins. In this review, the authors define protein condensation diseases as conditions caused by aberrant liquid-like or solid-like states of proteins, and describe opportunities for therapeutic interventions to restore the normal phase behaviour of proteins. The review accompanies the related collection of articles published in Nature Communications focusing on possible therapeutic approaches involving liquid-liquid phase separation.
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25
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Hou C, Wang X, Xie H, Chen T, Zhu P, Xu X, You K, Li T. PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information. Nucleic Acids Res 2022; 51:D460-D465. [PMID: 36124686 PMCID: PMC9825587 DOI: 10.1093/nar/gkac783] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 01/29/2023] Open
Abstract
Phase separation (PS) proteins form droplets to regulate myriad membraneless organelles (MLOs) and cellular pathways such as transcription, signaling transduction and protein degeneration. PS droplets are usually liquid-like and can convert to hydrogel/solid-like under certain conditions. The PS behavior of proteins is regulated by co-PS partners and mutations, modifications, oligomerizations, repeat regions and alternative splicing of the proteins. With growing interest in PS condensates and associated proteins, we established PhaSepDB 1.0, which provided experimentally verified PS proteins and MLO-related proteins. The past few years witnessed a surge in PS-related research works; thus, we kept updating PhaSepDB. The current PhaSepDB contains 1419 PS entries, 770 low-throughput MLO-related entries and 7303 high-throughput MLO-related entries. We provided more detailed annotations of PS proteins, including PS verification experiments, regions used in experiments, phase diagrams of different experimental conditions, droplet states, co-PS partners and PS regulatory information. We believe that researchers can go further in studying PS proteins with the updated PhaSepDB (http://db.phasep.pro/).
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Affiliation(s)
| | | | | | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China
| | - Peiyu Zhu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China
| | - Xiaofeng Xu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China
| | - Tingting Li
- To whom correspondence should be addressed. Tel: +86 13810582006;
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26
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Lu S, Hu J, Arogundade OA, Goginashvili A, Vazquez-Sanchez S, Diedrich JK, Gu J, Blum J, Oung S, Ye Q, Yu H, Ravits J, Liu C, Yates JR, Cleveland DW. Heat-shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition. Nat Cell Biol 2022; 24:1378-1393. [PMID: 36075972 PMCID: PMC9872726 DOI: 10.1038/s41556-022-00988-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 07/28/2022] [Indexed: 01/27/2023]
Abstract
While acetylated, RNA-binding-deficient TDP-43 reversibly phase separates within nuclei into complex droplets (anisosomes) comprised of TDP-43-containing liquid outer shells and liquid centres of HSP70-family chaperones, cytoplasmic aggregates of TDP-43 are hallmarks of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Here we show that transient oxidative stress, proteasome inhibition or inhibition of the ATP-dependent chaperone activity of HSP70 provokes reversible cytoplasmic TDP-43 de-mixing and transition from liquid to gel/solid, independently of RNA binding or stress granules. Isotope labelling mass spectrometry was used to identify that phase-separated cytoplasmic TDP-43 is bound by the small heat-shock protein HSPB1. Binding is direct, mediated through TDP-43's RNA binding and low-complexity domains. HSPB1 partitions into TDP-43 droplets, inhibits TDP-43 assembly into fibrils, and is essential for disassembly of stress-induced TDP-43 droplets. A decrease in HSPB1 promotes cytoplasmic TDP-43 de-mixing and mislocalization. HSPB1 depletion was identified in spinal motor neurons of patients with ALS containing aggregated TDP-43. These findings identify HSPB1 to be a regulator of cytoplasmic TDP-43 phase separation and aggregation.
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Affiliation(s)
- Shan Lu
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
- Ludwig Institute for Cancer Research, San Diego, CA, USA
| | - Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Alexander Goginashvili
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
- Ludwig Institute for Cancer Research, San Diego, CA, USA
| | - Sonia Vazquez-Sanchez
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
- Ludwig Institute for Cancer Research, San Diego, CA, USA
| | | | - Jinge Gu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jacob Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Spencer Oung
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
- Ludwig Institute for Cancer Research, San Diego, CA, USA
| | - Qiaozhen Ye
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Haiyang Yu
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John Ravits
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - John R Yates
- The Scripps Research Institute, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA.
- Ludwig Institute for Cancer Research, San Diego, CA, USA.
- Department of Neurosciences, University of California, San Diego, CA, USA.
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27
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Krokowski D, Jobava R, Szkop KJ, Chen CW, Fu X, Venus S, Guan BJ, Wu J, Gao Z, Banaszuk W, Tchorzewski M, Mu T, Ropelewski P, Merrick WC, Mao Y, Sevval AI, Miranda H, Qian SB, Manifava M, Ktistakis NT, Vourekas A, Jankowsky E, Topisirovic I, Larsson O, Hatzoglou M. Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR. Cell Rep 2022; 40:111092. [PMID: 35858571 PMCID: PMC9491157 DOI: 10.1016/j.celrep.2022.111092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 12/23/2022] Open
Abstract
The integrated stress response (ISR) plays a pivotal role in adaptation of translation machinery to cellular stress. Here, we demonstrate an ISR-independent osmoadaptation mechanism involving reprogramming of translation via coordinated but independent actions of mTOR and plasma membrane amino acid transporter SNAT2. This biphasic response entails reduced global protein synthesis and mTOR signaling followed by translation of SNAT2. Induction of SNAT2 leads to accumulation of amino acids and reactivation of mTOR and global protein synthesis, paralleled by partial reversal of the early-phase, stress-induced translatome. We propose SNAT2 functions as a molecular switch between inhibition of protein synthesis and establishment of an osmoadaptive translation program involving the formation of cytoplasmic condensates of SNAT2-regulated RNA-binding proteins DDX3X and FUS. In summary, we define key roles of SNAT2 in osmotolerance.
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Affiliation(s)
- Dawid Krokowski
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Raul Jobava
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xu Fu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wioleta Banaszuk
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchorzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland; EcoTech-Complex Centre, Maria Curie-Skłodowska University, Lublin, Poland
| | - Tingwei Mu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Phil Ropelewski
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Aksoylu Inci Sevval
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Helen Miranda
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Anastasios Vourekas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ivan Topisirovic
- The Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada; Department of Biochemistry and Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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28
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Nickerson JA. The ribonucleoprotein network of the nucleus: a historical perspective. Curr Opin Genet Dev 2022; 75:101940. [PMID: 35777349 DOI: 10.1016/j.gde.2022.101940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
Abstract
There is a long experimental history supporting the principle that RNA is essential for normal nuclear and chromatin architecture. Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. In the nucleus, most non-coding RNA, packaged in proteins, is bound into structures including chromatin and a non-chromatin scaffolding, the nuclear matrix, which was first observed by electron microscopy. Removing nuclear RNA or inhibiting its transcription causes the condensation of chromatin, showing the importance of RNA in spatially and functionally organizing the genome. Today, powerful techniques for the molecular characterization of RNA and for mapping its spatial organization in the nucleus have provided molecular detail to these principles.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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29
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Carey JL, Guo L. Liquid-Liquid Phase Separation of TDP-43 and FUS in Physiology and Pathology of Neurodegenerative Diseases. Front Mol Biosci 2022; 9:826719. [PMID: 35187086 PMCID: PMC8847598 DOI: 10.3389/fmolb.2022.826719] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid phase separation of RNA-binding proteins mediates the formation of numerous membraneless organelles with essential cellular function. However, aberrant phase transition of these proteins leads to the formation of insoluble protein aggregates, which are pathological hallmarks of neurodegenerative diseases including ALS and FTD. TDP-43 and FUS are two such RNA-binding proteins that mislocalize and aggregate in patients of ALS and FTD. They have similar domain structures that provide multivalent interactions driving their phase separation in vitro and in the cellular environment. In this article, we review the factors that mediate and regulate phase separation of TDP-43 and FUS. We also review evidences that connect the phase separation property of TDP-43 and FUS to their functional roles in cells. Aberrant phase transition of TDP-43 and FUS leads to protein aggregation and disrupts their regular cell function. Therefore, restoration of functional protein phase of TDP-43 and FUS could be beneficial for neuronal cells. We discuss possible mechanisms for TDP-43 and FUS aberrant phase transition and aggregation while reviewing the methods that are currently being explored as potential therapeutic strategies to mitigate aberrant phase transition and aggregation of TDP-43 and FUS.
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30
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Wang Z, Collier M, Benesch J. Aggregation in the spotlight. eLife 2021; 10:73586. [PMID: 34636721 PMCID: PMC8510577 DOI: 10.7554/elife.73586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022] Open
Abstract
New findings clarify apparently conflicting results about how molecular agents that preserve protein integrity prevent harmful, dense aggregates from forming.
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Affiliation(s)
- Zihao Wang
- Department of Chemistry, Oxford University, Oxford, United Kingdom
| | - Miranda Collier
- Department of Biology, Stanford University, Stanford, United States
| | - Justin Benesch
- Department of Chemistry, Oxford University, Oxford, United Kingdom
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31
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Fürsch J, Voormann C, Kammer KM, Stengel F. Structural Probing of Hsp26 Activation and Client Binding by Quantitative Cross-Linking Mass Spectrometry. Anal Chem 2021; 93:13226-13234. [PMID: 34542282 DOI: 10.1021/acs.analchem.1c02282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small heat-shock proteins (sHSPs) are important members of the cellular stress response in all species. Their best-described function is the binding of early unfolding states and the resulting prevention of protein aggregation. Many sHSPs exist as a polydisperse composition of oligomers, which undergoes changes in subunit composition, folding status, and relative distribution upon heat activation. To date, only an incomplete picture of the mechanism of sHSP activation exists; in particular, the molecular basis of how sHSPs bind client proteins and mediate client specificity is not fully understood. In this study, we have applied cross-linking mass spectrometry (XL-MS) to obtain detailed structural information on sHSP activation and client binding for yeast Hsp26. Our cross-linking data reveals the middle domain of Hsp26 as a client-independent interface in multiple Hsp26::client complexes and indicates that client specificity is likely mediated via additional binding sites within its α-crystallin domain and C-terminal extension. Our quantitative XL-MS data underpins the middle domain as the main driver of heat-induced activation and client binding but shows that global rearrangements spanning all domains of Hsp26 take place simultaneously. We also investigated a Hsp26::client complex in the presence of Ssa1 (Hsp70) and Ydj1(Hsp40) at the initial stage of refolding and observe that the interaction between refolding chaperones is altered by the presence of a client protein, pointing to a mechanism where the interaction of Ydj1 with the HSP::client complex initiates the assembly of the active refolding machinery.
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Affiliation(s)
- Julius Fürsch
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Carsten Voormann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Kai-Michael Kammer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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32
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Boczek EE, Fürsch J, Niedermeier ML, Jawerth L, Jahnel M, Ruer-Gruß M, Kammer KM, Heid P, Mediani L, Wang J, Yan X, Pozniakovski A, Poser I, Mateju D, Hubatsch L, Carra S, Alberti S, Hyman AA, Stengel F. HspB8 prevents aberrant phase transitions of FUS by chaperoning its folded RNA-binding domain. eLife 2021; 10:69377. [PMID: 34487489 PMCID: PMC8510580 DOI: 10.7554/elife.69377] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Aberrant liquid-to-solid phase transitions of biomolecular condensates have been linked to various neurodegenerative diseases. However, the underlying molecular interactions that drive aging remain enigmatic. Here, we develop quantitative time-resolved crosslinking mass spectrometry to monitor protein interactions and dynamics inside condensates formed by the protein fused in sarcoma (FUS). We identify misfolding of the RNA recognition motif of FUS as a key driver of condensate aging. We demonstrate that the small heat shock protein HspB8 partitions into FUS condensates via its intrinsically disordered domain and prevents condensate hardening via condensate-specific interactions that are mediated by its α-crystallin domain (αCD). These αCD-mediated interactions are altered in a disease-associated mutant of HspB8, which abrogates the ability of HspB8 to prevent condensate hardening. We propose that stabilizing aggregation-prone folded RNA-binding domains inside condensates by molecular chaperones may be a general mechanism to prevent aberrant phase transitions.
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Affiliation(s)
- Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Dewpoint Therapeutics GmbH, Dresden, Germany
| | - Julius Fürsch
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie Laura Niedermeier
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Louise Jawerth
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Martine Ruer-Gruß
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai-Michael Kammer
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Peter Heid
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jie Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrej Pozniakovski
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Dewpoint Therapeutics GmbH, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lars Hubatsch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Florian Stengel
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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