1
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Fare CM, Rothstein JD. Nuclear pore dysfunction and disease: a complex opportunity. Nucleus 2024; 15:2314297. [PMID: 38383349 PMCID: PMC10883112 DOI: 10.1080/19491034.2024.2314297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.
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Affiliation(s)
- Charlotte M Fare
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
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2
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Stewart RA, Ding Z, Jeon US, Goodman LB, Tran JJ, Zientko JP, Sabu M, Cadigan KM. Wnt target gene activation requires β-catenin separation into biomolecular condensates. PLoS Biol 2024; 22:e3002368. [PMID: 39316611 DOI: 10.1371/journal.pbio.3002368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 08/30/2024] [Indexed: 09/26/2024] Open
Abstract
The Wnt/β-catenin signaling pathway plays numerous essential roles in animal development and tissue/stem cell maintenance. The activation of genes regulated by Wnt/β-catenin signaling requires the nuclear accumulation of β-catenin, a transcriptional co-activator. β-catenin is recruited to many Wnt-regulated enhancers through direct binding to T-cell factor/lymphoid enhancer factor (TCF/LEF) family transcription factors. β-catenin has previously been reported to form phase-separated biomolecular condensates (BMCs), which was implicated as a component of β-catenin's mechanism of action. This function required aromatic amino acid residues in the intrinsically disordered regions (IDRs) at the N- and C-termini of the protein. In this report, we further explore a role for β-catenin BMCs in Wnt target gene regulation. We find that β-catenin BMCs are miscible with LEF1 BMCs in vitro and in cultured cells. We characterized a panel of β-catenin mutants with different combinations of aromatic residue mutations in human cell culture and Drosophila melanogaster. Our data support a model in which aromatic residues across both IDRs contribute to BMC formation and signaling activity. Although different Wnt targets have different sensitivities to loss of β-catenin's aromatic residues, the activation of every target examined was compromised by aromatic substitution. These mutants are not defective in nuclear import or co-immunoprecipitation with several β-catenin binding partners. In addition, residues in the N-terminal IDR with no previously known role in signaling are clearly required for the activation of various Wnt readouts. Consistent with this, deletion of the N-terminal IDR results in a loss of signaling activity, which can be rescued by the addition of heterologous IDRs enriched in aromatic residues. Overall, our work supports a model in which the ability of β-catenin to form biomolecular condensates in the nucleus is tightly linked to its function as a transcriptional co-regulator.
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Affiliation(s)
- Richard A Stewart
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Zhihao Ding
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ung Seop Jeon
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lauren B Goodman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jeannine J Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John P Zientko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Malavika Sabu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ken M Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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3
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Sun YC, Hsieh TL, Lin CI, Shao WY, Lin YH, Huang JR. A Few Charged Residues in Galectin-3's Folded and Disordered Regions Regulate Phase Separation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402570. [PMID: 39248370 DOI: 10.1002/advs.202402570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/25/2024] [Indexed: 09/10/2024]
Abstract
Proteins with intrinsically disordered regions (IDRs) often undergo phase separation to control their functions spatiotemporally. Changing the pH alters the protonation levels of charged sidechains, which in turn affects the attractive or repulsive force for phase separation. In a cell, the rupture of membrane-bound compartments, such as lysosomes, creates an abrupt change in pH. However, how proteins' phase separation reacts to different pH environments remains largely unexplored. Here, using extensive mutagenesis, NMR spectroscopy, and biophysical techniques, it is shown that the assembly of galectin-3, a widely studied lysosomal damage marker, is driven by cation-π interactions between positively charged residues in its folded domain with aromatic residues in the IDR in addition to π-π interaction between IDRs. It is also found that the sole two negatively charged residues in its IDR sense pH changes for tuning the condensation tendency. Also, these two residues may prevent this prion-like IDR domain from forming rapid and extensive aggregates. These results demonstrate how cation-π, π-π, and electrostatic interactions can regulate protein condensation between disordered and structured domains and highlight the importance of sparse negatively charged residues in prion-like IDRs.
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Affiliation(s)
- Yung-Chen Sun
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Tsung-Lun Hsieh
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
| | - Chia-I Lin
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
| | - Wan-Yu Shao
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
| | - Yu-Hao Lin
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Taipei, 112304, Taiwan
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4
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Agarwal A, Chandran A, Raza F, Ungureanu IM, Hilcenko C, Stott K, Bright NA, Morone N, Warren AJ, Lautenschläger J. VAMP2 regulates phase separation of α-synuclein. Nat Cell Biol 2024; 26:1296-1308. [PMID: 38951707 PMCID: PMC11322000 DOI: 10.1038/s41556-024-01451-6] [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: 07/17/2023] [Accepted: 05/30/2024] [Indexed: 07/03/2024]
Abstract
α-Synuclein (αSYN), a pivotal synaptic protein implicated in synucleinopathies such as Parkinson's disease and Lewy body dementia, undergoes protein phase separation. We reveal that vesicle-associated membrane protein 2 (VAMP2) orchestrates αSYN phase separation both in vitro and in cells. Electrostatic interactions, specifically mediated by VAMP2 via its juxtamembrane domain and the αSYN C-terminal region, drive phase separation. Condensate formation is specific for R-SNARE VAMP2 and dependent on αSYN lipid membrane binding. Our results delineate a regulatory mechanism for αSYN phase separation in cells. Furthermore, we show that αSYN condensates sequester vesicles and attract complexin-1 and -2, thus supporting a role in synaptic physiology and pathophysiology.
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Affiliation(s)
- Aishwarya Agarwal
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Aswathy Chandran
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Farheen Raza
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Protein and Cellular Sciences, GSK, Stevenage, UK
| | - Irina-Maria Ungureanu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Christine Hilcenko
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Nicholas A Bright
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Alan J Warren
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Janin Lautenschläger
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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5
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Merigliano C, Ryu T, See CD, Caridi CP, Li X, Butova NL, Reynolds TW, Deng C, Chenoweth DM, Capelson M, Chiolo I. "Off-pore" nucleoporins relocalize heterochromatic breaks through phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.07.570729. [PMID: 39071440 PMCID: PMC11275802 DOI: 10.1101/2023.12.07.570729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Phase separation forms membraneless compartments in the nuclei, including by establishing heterochromatin "domains" and repair foci. Pericentromeric heterochromatin mostly comprises repeated sequences prone to aberrant recombination, and "safe" homologous recombination (HR) repair of these sequences requires the movement of repair sites to the nuclear periphery before Rad51 recruitment and strand invasion. How this mobilization initiates is unknown, and the contribution of phase separation to these dynamics is unclear. Here, we show that Nup98 nucleoporin is recruited to heterochromatic repair sites before relocalization through Sec13 or Nup88 nucleoporins, and downstream from the Smc5/6 complex and SUMOylation. Remarkably, the phase separation properties of Nup98 are required and sufficient to mobilize repair sites and exclude Rad51, thus preventing aberrant recombination while promoting HR repair. Disrupting this pathway results in heterochromatin repair defects and widespread chromosome rearrangements, revealing a novel "off-pore" role for nucleoporins and phase separation in nuclear dynamics and genome integrity in a multicellular eukaryote.
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Affiliation(s)
- Chiara Merigliano
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
| | - Taehyun Ryu
- Harvard Medical School, Department of Genetics, Boston, MA, USA
| | - Colby D. See
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
| | - Christopher P. Caridi
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
| | - Xiao Li
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
| | - Nadejda L. Butova
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
| | - Trevor W. Reynolds
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
| | - Changfeng Deng
- University of Pennsylvania, Department of Chemistry, School of Arts and Sciences, Philadelphia, PA, USA
| | - David M. Chenoweth
- University of Pennsylvania, Department of Chemistry, School of Arts and Sciences, Philadelphia, PA, USA
| | - Maya Capelson
- San Diego State University, Department of Biology, San Diego, CA, USA
| | - Irene Chiolo
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA, USA
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6
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Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos LE, Mariappan M, Lusk CP, Xiong Y, Lim RYH, Lin C. Channel width modulates the permeability of DNA origami based nuclear pore mimics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593438. [PMID: 38766144 PMCID: PMC11100828 DOI: 10.1101/2024.05.09.593438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importing substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.
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Affiliation(s)
- Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Chunxiang Wu
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Eason Cao
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | - Wei Zheng
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Amy Zhang
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Xia Li
- Department of Cell Biology, Yale School of Medicine, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biophysics and Biochemistry, Yale University, USA
| | | | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Yong Xiong
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biomedical Engineering, Yale University, USA
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7
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Zhang H, Guo H, Li D, Zhang Y, Zhang S, Kang W, Liu C, Le W, Wang L, Li D, Dai B. Halogen doped graphene quantum dots modulate TDP-43 phase separation and aggregation in the nucleus. Nat Commun 2024; 15:2980. [PMID: 38582774 PMCID: PMC10998863 DOI: 10.1038/s41467-024-47167-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
TDP-43 is implicated in the dynamic formation of nuclear bodies and stress granules through phase separation. In diseased states, it can further condense into pathological aggregates in the nucleus and cytoplasm, contributing to the onset of amyotrophic lateral sclerosis. In this study, we evaluate the effect of graphene quantum dots (GQDs) with different functional groups on TDP-43's phase separation and aggregation in various cellular locations. We find that halogen atom-doped GQDs (GQDs-Cl, Cl-GQDs-OH) penetrate the nuclear envelope, inhibiting the assembly of TDP-43 nuclear bodies and stress granules under oxidative stress or hyperosmotic environments, and reduce amyloid aggregates and disease-associated phosphorylation of TDP-43. Mechanistic analysis reveals GQDs-Cl and Cl-GQDs-OH modulate TDP-43 phase separation through hydrophobic and electrostatic interactions. Our findings highlight the potential of GQDs-Cl and Cl-GQDs-OH in modulating nuclear protein condensation and pathological aggregation, offering direction for the innovative design of GQDs to modulate protein phase separation and aggregation.
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Affiliation(s)
- Hong Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huazhang Guo
- Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Baoshan District, Shanghai, 200444, PR China
| | - Danni Li
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiling Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Wenyan Kang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Department of Neurology, Ruijin Hainan Hospital, Shanghai Jiao Tong University School of Medicine (Boao Research Hospital), Hainan, 571434, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Weidong Le
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, 201318, China
- Center for Clinical and Translational Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Liang Wang
- Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Baoshan District, Shanghai, 200444, PR China.
| | - Dan Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bin Dai
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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8
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Zhou Y, Panhale A, Shvedunova M, Balan M, Gomez-Auli A, Holz H, Seyfferth J, Helmstädter M, Kayser S, Zhao Y, Erdogdu NU, Grzadzielewska I, Mittler G, Manke T, Akhtar A. RNA damage compartmentalization by DHX9 stress granules. Cell 2024; 187:1701-1718.e28. [PMID: 38503283 DOI: 10.1016/j.cell.2024.02.028] [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: 07/05/2023] [Revised: 10/24/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Biomolecules incur damage during stress conditions, and damage partitioning represents a vital survival strategy for cells. Here, we identified a distinct stress granule (SG), marked by dsRNA helicase DHX9, which compartmentalizes ultraviolet (UV)-induced RNA, but not DNA, damage. Our FANCI technology revealed that DHX9 SGs are enriched in damaged intron RNA, in contrast to classical SGs that are composed of mature mRNA. UV exposure causes RNA crosslinking damage, impedes intron splicing and decay, and triggers DHX9 SGs within daughter cells. DHX9 SGs promote cell survival and induce dsRNA-related immune response and translation shutdown, differentiating them from classical SGs that assemble downstream of translation arrest. DHX9 modulates dsRNA abundance in the DHX9 SGs and promotes cell viability. Autophagy receptor p62 is activated and important for DHX9 SG disassembly. Our findings establish non-canonical DHX9 SGs as a dedicated non-membrane-bound cytoplasmic compartment that safeguards daughter cells from parental RNA damage.
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Affiliation(s)
- Yilong Zhou
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Amol Panhale
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Mirela Balan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Martin Helmstädter
- EMcore, Renal Division, Department of Medicine, University Freiburg, Hospital Freiburg, University Faculty of Medicine, Freiburg, Germany
| | - Séverine Kayser
- EMcore, Renal Division, Department of Medicine, University Freiburg, Hospital Freiburg, University Faculty of Medicine, Freiburg, Germany
| | - Yuling Zhao
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Iga Grzadzielewska
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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9
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Hirano A, Wada M, Sato TK, Kameda T. N-acetyl amino acid amide solubility in aqueous 1,6-hexanediol solutions: Insights into the protein droplet deformation mechanism. Int J Biol Macromol 2024; 261:129724. [PMID: 38272403 DOI: 10.1016/j.ijbiomac.2024.129724] [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: 10/11/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Proteinaceous liquid droplets, generated by liquid-liquid phase separation, function as membraneless compartments that are essential for diverse biological functions. Studies addressing droplet generation have used 1,6-hexanediol (1,6-HD) as a droplet-discerning agent owing to its capacity to induce droplet deformation. Despite the empirical utility of 1,6-HD, the mechanism underlying 1,6-HD-induced droplet deformation remains unknown. In this study, the solubilities of N-acetyl amino acid amides, which correspond to proteinogenic amino acid residues, were examined in the presence of 1,6-HD at 25 °C. Other solvents included ethanol, 1-propanol, and amides. Remarkably, 1,6-HD effectively solubilized hydrophobic species (particularly aromatic species) and exhibited reduced efficacy in solubilizing hydrophilic species and peptide bond moieties. These solubilizing effects are reflected in changes in protein solubility and structure. Specifically, 1,6-HD primarily targets the hydrophobic regions of a protein, increasing protein solubility without causing substantial structural changes. This solubilization mechanism is essential for elucidating the role of 1,6-HD as a droplet-discerning agent and recognizing its potential limitations.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takehiro K Sato
- Spiber, Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
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10
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Sipko EL, Chappell GF, Berlow RB. Multivalency emerges as a common feature of intrinsically disordered protein interactions. Curr Opin Struct Biol 2024; 84:102742. [PMID: 38096754 DOI: 10.1016/j.sbi.2023.102742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Intrinsically disordered proteins (IDPs) use their unique molecular properties and conformational plasticity to interact with cellular partners in a wide variety of biological contexts. Multivalency is an important feature of IDPs that allows for utilization of an expanded toolkit for interactions with other macromolecules and confers additional complexity to molecular recognition processes. Recent studies have offered insights into how multivalent interactions of IDPs enable responsive and sensitive regulation in the context of transcription and cellular signaling. Multivalency is also widely recognized as an important feature of IDP interactions that mediate formation of biomolecular condensates. We highlight recent examples of multivalent interactions of IDPs across diverse contexts to illustrate the breadth of biological processes that utilize multivalency in molecular interactions.
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Affiliation(s)
- Emily L Sipko
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett F Chappell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca B Berlow
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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11
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Oishi A, Nakagawa S, Tamura K. Nucleoporin 50 proteins affect longevity and salinity stress tolerance in seeds. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:60-72. [PMID: 37849222 DOI: 10.1093/jxb/erad396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023]
Abstract
Nucleoporin 50 (Nup50) is an evolutionarily conserved protein that is a constituent of the nuclear pore complex (NPC); however, its physiological role in plants is unclear. Arabidopsis has two Nup50 proteins, Nup50a and Nup50b, which are highly expressed in developing seeds. Green fluoresceent protein (GFP)-fused Nup50a and Nup50b are localized exclusively in the nucleopolasm, implying an additional function beyond the NPC in the nuclear envelope. To investigate the function of Nup50s, we employed the CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] system to generate a nup50a nup50b double mutant, which exhibited premature translation termination of both Nup50 proteins. While the mutant showed no significant abnormal phenotype during vegetative growth, the nup50a nup50b seeds had an abnormal shape compared with the wild type. Comparative transcriptomics using immature seeds revealed that Nup50s regulate the expression of various genes, including cell wall-related genes. The nup50a nup50b seeds exhibited reduced seed longevity and salinity stress tolerance. Tetrazolium uptake and mucilage release assays implied that the nup50a nup50b seeds had greater water permeability than the wild type. Taken together, our results imply that Nup50s play a critical role in seed formation by regulating gene expression.
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Affiliation(s)
- Ayumi Oishi
- School of Food and Nutritional Sciences, Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Shitomi Nakagawa
- School of Food and Nutritional Sciences, Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kentaro Tamura
- School of Food and Nutritional Sciences, Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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12
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Patel MK, Chakrabarti B, Panwar AS. Emergence of selectivity and specificity in a coarse-grained model of the nuclear pore complex with sequence-agnostic FG-Nups. Phys Chem Chem Phys 2023; 25:32824-32836. [PMID: 38018404 DOI: 10.1039/d3cp03746k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining the transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Furthermore, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 ≤ f ≤ 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the central role of the FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of the FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion, which resulted in enhanced translocation probability for 0.05 ≤ f ≤ 0.20. Extended brush configurations outside the pore resulted in entropic repulsion and exclusion of inert cargo in this range. Thus, our minimal NPC model exhibited a hybrid cargo translocation mechanism, with aspects of both virtual gate and selective-phase models, in this range of FG-hydrophobic fraction.
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Affiliation(s)
- Manoj K Patel
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | | | - Ajay S Panwar
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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13
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Barrientos ECR, Otto TA, Mouton SN, Steen A, Veenhoff LM. A survey of the specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport. Nucleus 2023; 14:2240139. [PMID: 37498221 PMCID: PMC10376917 DOI: 10.1080/19491034.2023.2240139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of FG-repeat containing nucleoporins, the FG-nups, with each other and with Karyopherins (Kaps). Here, we assessed the specificity and mechanism by which the aliphatic alcohol 1,6-hexanediol (1,6HD) disrupts the permeability barrier of NPCs in live baker's yeast cells. After a 10-minute exposure to 5% 1,6HD, no notable changes were observed in cell growth, cytosolic pH and ATP levels, or the appearance of organelles. However, effects on the cytoskeleton and Hsp104 were noted. 1,6HD clearly affected the NPC permeability barrier, allowing passive nuclear entry of a 177kDa reporter protein that is normally confined to the cytosol. Moreover, multiple Kaps were displaced from NPCs, and the displacement of Kap122-GFP correlated with the observed passive permeability changes. 1,6HD thus temporarily permeates NPCs, and in line with Kap-centric models, the mechanism includes the release of numerous Kaps from the NPCs.
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Affiliation(s)
- Elizabeth C Riquelme Barrientos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Tegan A Otto
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
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14
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Varol HS, Herberger T, Kirsch M, Mikolei J, Veith L, Kannan-Sampathkumar V, Brand RD, Synatschke CV, Weil T, Andrieu-Brunsen A. Electropolymerization of Polydopamine at Electrode-Supported Insulating Mesoporous Films. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:9192-9207. [PMID: 38027541 PMCID: PMC10653081 DOI: 10.1021/acs.chemmater.3c01890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Bioinspired, stimuli-responsive, polymer-functionalized mesoporous films are promising platforms for precisely regulating nanopore transport toward applications in water management, iontronics, catalysis, sensing, drug delivery, or energy conversion. Nanopore technologies still require new, facile, and effective nanopore functionalization with multi- and stimuli-responsive polymers to reach these complicated application targets. In recent years, zwitterionic and multifunctional polydopamine (PDA) films deposited on planar surfaces by electropolymerization have helped surfaces respond to various external stimuli such as light, temperature, moisture, and pH. However, PDA has not been used to functionalize nanoporous films, where the PDA-coating could locally regulate the ionic nanopore transport. This study investigates the electropolymerization of homogeneous thin PDA films to functionalize nanopores of mesoporous silica films. We investigate the effect of different mesoporous film structures and the number of electropolymerization cycles on the presence of PDA at mesopores and mesoporous film surfaces. Our spectroscopic, microscopic, and electrochemical analysis reveals that the amount and location (pores and surface) of deposited PDA at mesoporous films is related to the combination of the number of electropolymerization cycles and the mesoporous film thickness and pore size. In view of the application of the proposed PDA-functionalized mesoporous films in areas requiring ion transport control, we studied the ion nanopore transport of the films by cyclic voltammetry. We realized that the amount of PDA in the nanopores helps to limit the overall ionic transport, while the pH-dependent transport mechanism of pristine silica films remains unchanged. It was found that (i) the pH-dependent deprotonation of PDA and silica walls and (ii) the insulation of the indium-tin oxide (ITO) surface by increasing the amount of PDA within the mesoporous silica film affect the ionic nanopore transport.
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Affiliation(s)
- H. Samet Varol
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
- Department
of Chemistry “Giacomo Ciamician″, Università degli Studi di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Tilmann Herberger
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marius Kirsch
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Joanna Mikolei
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Lothar Veith
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Raoul D. Brand
- Institute
of Physical Chemistry, Justus-Liebig University, 35392 Giessen, Germany
| | | | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Annette Andrieu-Brunsen
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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15
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Foressi NN, Rodríguez LC, Celej MS. Heterotypic liquid-liquid phase separation of tau and α-synuclein: Implications for overlapping neuropathologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140950. [PMID: 37574035 DOI: 10.1016/j.bbapap.2023.140950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Tauopathies and synucleinopathies are characterized by the aggregation of Tau and α-synuclein (AS) into amyloid structures, respectively. Individuals with these neuropathies have an elevated risk of developing subsequent neurodegenerative or comorbid disorders. Intriguingly, post-mortem brain examinations have revealed co-localization of Tau and AS aggregates, suggesting a synergistic pathological relationship with an adverse prognosis. The role of liquid-liquid phase separation (LLPS) in the development of neurodegenerative diseases is currently receiving significant attention, as it can contribute to the aggregation and co-deposition of amyloidogenic proteins. In this study, we investigated the phase separation behavior of Tau and AS under various insults, some of which are implicated in disease progression. Our findings demonstrate the formation of heterotypic droplets composed of Tau and AS at physiologically relevant mole ratios that mimic neurons' soma and terminal buttons. Importantly, these heterotypic droplets exhibit increased resistance to electrostatic screening compared to homotypic condensates. Moreover, we observed that biologically relevant biomolecules, known to be dysregulated in disease, exert different effects on these droplets. Additionally, we provide evidence that phase separation itself influences the amyloid aggregation of Tau and AS, underscoring the significance of this process in the development of aggregopathies.
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Affiliation(s)
- Nahuel N Foressi
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Leandro Cruz Rodríguez
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
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16
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Rush C, Jiang Z, Tingey M, Feng F, Yang W. Unveiling the complexity: assessing models describing the structure and function of the nuclear pore complex. Front Cell Dev Biol 2023; 11:1245939. [PMID: 37876551 PMCID: PMC10591098 DOI: 10.3389/fcell.2023.1245939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
The nuclear pore complex (NPC) serves as a pivotal subcellular structure, acting as a gateway that orchestrates nucleocytoplasmic transport through a selectively permeable barrier. Nucleoporins (Nups), particularly those containing phenylalanine-glycine (FG) motifs, play indispensable roles within this barrier. Recent advancements in technology have significantly deepened our understanding of the NPC's architecture and operational intricacies, owing to comprehensive investigations. Nevertheless, the conspicuous presence of intrinsically disordered regions within FG-Nups continues to present a formidable challenge to conventional static characterization techniques. Historically, a multitude of strategies have been employed to unravel the intricate organization and behavior of FG-Nups within the NPC. These endeavors have given rise to multiple models that strive to elucidate the structural layout and functional significance of FG-Nups. Within this exhaustive review, we present a comprehensive overview of these prominent models, underscoring their proposed dynamic and structural attributes, supported by pertinent research. Through a comparative analysis, we endeavor to shed light on the distinct characteristics and contributions inherent in each model. Simultaneously, it remains crucial to acknowledge the scarcity of unequivocal validation for any of these models, as substantiated by empirical evidence.
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Affiliation(s)
| | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, United States
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17
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Cristi AC, Rapuri S, Coyne AN. Nuclear pore complex and nucleocytoplasmic transport disruption in neurodegeneration. FEBS Lett 2023; 597:2546-2566. [PMID: 37657945 PMCID: PMC10612469 DOI: 10.1002/1873-3468.14729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/29/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Nuclear pore complexes (NPCs) play a critical role in maintaining the equilibrium between the nucleus and cytoplasm, enabling bidirectional transport across the nuclear envelope, and are essential for proper nuclear organization and gene regulation. Perturbations in the regulatory mechanisms governing NPCs and nuclear envelope homeostasis have been implicated in the pathogenesis of several neurodegenerative diseases. The ESCRT-III pathway emerges as a critical player in the surveillance and preservation of well-assembled, functional NPCs, as well as nuclear envelope sealing. Recent studies have provided insights into the involvement of nuclear ESCRT-III in the selective reduction of specific nucleoporins associated with neurodegenerative pathologies. Thus, maintaining quality control of the nuclear envelope and NPCs represents a pivotal element in the pathological cascade leading to neurodegenerative diseases. This review describes the constituents of the nuclear-cytoplasmic transport machinery, encompassing the nuclear envelope, NPC, and ESCRT proteins, and how their structural and functional alterations contribute to the development of neurodegenerative diseases.
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Affiliation(s)
- América Chandía Cristi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Sampath Rapuri
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
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18
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Kuiper EFE, Prophet SM, Schlieker C. Coordinating nucleoporin condensation and nuclear pore complex assembly. FEBS Lett 2023; 597:2534-2545. [PMID: 37620293 DOI: 10.1002/1873-3468.14725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
The nuclear pore complex (NPC) is among the most elaborate protein complexes in eukaryotes. While ribosomes and proteasomes are known to require dedicated assembly machinery, our understanding of NPC assembly is at a relatively early stage. Defects in NPC assembly or homeostasis are tied to movement disorders, including dystonia and amyotrophic lateral sclerosis (ALS), as well as aging, requiring a better understanding of these processes to enable therapeutic intervention. Here, we discuss recent progress in the understanding of NPC assembly and highlight how related defects in human disorders can shed light on NPC biogenesis. We propose that the condensation of phenylalanine-glycine repeat nucleoporins needs to be carefully controlled during NPC assembly to prevent aberrant condensation, aggregation, or amyloid formation.
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Affiliation(s)
- E F Elsiena Kuiper
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Sarah M Prophet
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
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19
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Williamson I, Boyle S, Grimes GR, Friman ET, Bickmore WA. Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loops. Life Sci Alliance 2023; 6:e202302101. [PMID: 37487640 PMCID: PMC10366532 DOI: 10.26508/lsa.202302101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) strongly influences 3D genome organization, mediating local chromatin compaction and clustering of target loci. Several PRC1 subunits have the capacity to form biomolecular condensates through liquid-liquid phase separation in vitro and when tagged and over-expressed in cells. Here, we use 1,6-hexanediol, which can disrupt liquid-like condensates, to examine the role of endogenous PRC1 biomolecular condensates on local and chromosome-wide clustering of PRC1-bound loci. Using imaging and chromatin immunoprecipitation, we show that PRC1-mediated chromatin compaction and clustering of targeted genomic loci-at different length scales-can be reversibly disrupted by the addition and subsequent removal of 1,6-hexanediol to mouse embryonic stem cells. Decompaction and dispersal of polycomb domains and clusters cannot be solely attributable to reduced PRC1 occupancy detected by chromatin immunoprecipitation following 1,6-hexanediol treatment as the addition of 2,5-hexanediol has similar effects on binding despite this alcohol not perturbing PRC1-mediated 3D clustering, at least at the sub-megabase and megabase scales. These results suggest that weak hydrophobic interactions between PRC1 molecules may have a role in polycomb-mediated genome organization.
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Affiliation(s)
- Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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20
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Huang Y, Wen J, Ramirez LM, Gümüşdil E, Pokhrel P, Man VH, Ye H, Han Y, Liu Y, Li P, Su Z, Wang J, Mao H, Zweckstetter M, Perrett S, Wu S, Gao M. Methylene blue accelerates liquid-to-gel transition of tau condensates impacting tau function and pathology. Nat Commun 2023; 14:5444. [PMID: 37673952 PMCID: PMC10482834 DOI: 10.1038/s41467-023-41241-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
Preventing tau aggregation is a potential therapeutic strategy in Alzheimer's disease and other tauopathies. Recently, liquid-liquid phase separation has been found to facilitate the formation of pathogenic tau conformations and fibrillar aggregates, although many aspects of the conformational transitions of tau during the phase transition process remain unknown. Here, we demonstrate that the tau aggregation inhibitor methylene blue promotes tau liquid-liquid phase separation and accelerates the liquid-to-gel transition of tau droplets independent of the redox activity of methylene blue. We further show that methylene blue inhibits the conversion of tau droplets into fibrils and reduces the cytotoxicity of tau aggregates. Although gelation slows down the mobility of tau and tubulin, it does not impair microtubule assembly within tau droplets. These findings suggest that methylene blue inhibits tau amyloid fibrillization and accelerates tau droplet gelation via distinct mechanisms, thus providing insights into the activity of tau aggregation inhibitors in the context of phase transition.
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Affiliation(s)
- Yongqi Huang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China.
| | - Jitao Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Lisa-Marie Ramirez
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Eymen Gümüşdil
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze Çayirova, Kocaeli, Turkey
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Advanced Materials and Liquid Crystal Institute, Department of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Viet H Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Haiqiong Ye
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China
| | - Yue Han
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China
| | - Yunfei Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China
| | - Ping Li
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China
| | - Zhengding Su
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Advanced Materials and Liquid Crystal Institute, Department of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of the Chinese Academy of Sciences, 100049, Beijing, China.
| | - Meng Gao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, 430068, Wuhan, China.
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21
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Liu Q, Yi D, Ding J, Mao Y, Wang S, Ma L, Li Q, Wang J, Zhang Y, Zhao J, Guo S, Liu Z, Guo F, Zhao D, Liang C, Li X, Peng X, Cen S. MOV10 recruits DCP2 to decap human LINE-1 RNA by forming large cytoplasmic granules with phase separation properties. EMBO Rep 2023; 24:e56512. [PMID: 37437058 PMCID: PMC10481665 DOI: 10.15252/embr.202256512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Long interspersed element 1 (LINE-1) is the only active autonomous mobile element in the human genome. Its transposition can exert deleterious effects on the structure and function of the host genome and cause sporadic genetic diseases. Tight control of LINE-1 mobilization by the host is crucial for genetic stability. In this study, we report that MOV10 recruits the main decapping enzyme DCP2 to LINE-1 RNA and forms a complex of MOV10, DCP2, and LINE-1 RNP, exhibiting liquid-liquid phase separation (LLPS) properties. DCP2 cooperates with MOV10 to decap LINE-1 RNA, which causes degradation of LINE-1 RNA and thus reduces LINE-1 retrotransposition. We here identify DCP2 as one of the key effector proteins determining LINE-1 replication, and elucidate an LLPS mechanism that facilitates the anti-LINE-1 action of MOV10 and DCP2.
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Affiliation(s)
- Qian Liu
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Dongrong Yi
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Jiwei Ding
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Yang Mao
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Shujie Wang
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Ling Ma
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Quanjie Li
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Jing Wang
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Yongxin Zhang
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Jianyuan Zhao
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Saisai Guo
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Zhenlong Liu
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontrealQCCanada
| | - Fei Guo
- Institute of Pathogen BiologyChinese Academy of Medical ScienceBeijingChina
| | - Dongbing Zhao
- National Cancer CenterChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Chen Liang
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontrealQCCanada
| | - Xiaoyu Li
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Shan Cen
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
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22
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Pérez‐Berlanga M, Wiersma VI, Zbinden A, De Vos L, Wagner U, Foglieni C, Mallona I, Betz KM, Cléry A, Weber J, Guo Z, Rigort R, de Rossi P, Manglunia R, Tantardini E, Sahadevan S, Stach O, Hruska‐Plochan M, Allain FH, Paganetti P, Polymenidou M. Loss of TDP-43 oligomerization or RNA binding elicits distinct aggregation patterns. EMBO J 2023; 42:e111719. [PMID: 37431963 PMCID: PMC10476175 DOI: 10.15252/embj.2022111719] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023] Open
Abstract
Aggregation of the RNA-binding protein TAR DNA-binding protein 43 (TDP-43) is the key neuropathological feature of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). In physiological conditions, TDP-43 is predominantly nuclear, forms oligomers, and is contained in biomolecular condensates assembled by liquid-liquid phase separation (LLPS). In disease, TDP-43 forms cytoplasmic or intranuclear inclusions. How TDP-43 transitions from physiological to pathological states remains poorly understood. Using a variety of cellular systems to express structure-based TDP-43 variants, including human neurons and cell lines with near-physiological expression levels, we show that oligomerization and RNA binding govern TDP-43 stability, splicing functionality, LLPS, and subcellular localization. Importantly, our data reveal that TDP-43 oligomerization is modulated by RNA binding. By mimicking the impaired proteasomal activity observed in ALS/FTLD patients, we found that monomeric TDP-43 forms inclusions in the cytoplasm, whereas its RNA binding-deficient counterpart aggregated in the nucleus. These differentially localized aggregates emerged via distinct pathways: LLPS-driven aggregation in the nucleus and aggresome-dependent inclusion formation in the cytoplasm. Therefore, our work unravels the origins of heterogeneous pathological species reminiscent of those occurring in TDP-43 proteinopathy patients.
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Affiliation(s)
| | - Vera I Wiersma
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Aurélie Zbinden
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Laura De Vos
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Ulrich Wagner
- Department of Pathology and Molecular Pathology, University Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Chiara Foglieni
- Neurodegeneration Research Group, Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Ente Ospedaliero CantonaleBellinzonaSwitzerland
| | - Izaskun Mallona
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Katharina M Betz
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Antoine Cléry
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Julien Weber
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Zhongning Guo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Ruben Rigort
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Pierre de Rossi
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Ruchi Manglunia
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Elena Tantardini
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Sonu Sahadevan
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Oliver Stach
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | | | | | - Paolo Paganetti
- Neurodegeneration Research Group, Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Ente Ospedaliero CantonaleBellinzonaSwitzerland
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23
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Zhu P, Hou C, Liu M, Chen T, Li T, Wang L. Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol. BMC Genomics 2023; 24:493. [PMID: 37641002 PMCID: PMC10464338 DOI: 10.1186/s12864-023-09600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid-liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are still based on low-throughput experiments, which consume time and could not be used to explore protein LLPS properties in bulk. RESULTS By combining gradient 1,6-hexanediol (1,6-HD) elution and quantitative proteomics, we developed chromatin enriching hexanediol separation coupled with liquid chromatography-mass spectrometry (CHS-MS) to explore the LLPS properties of different chromatin-associated proteins (CAPs). First, we found that CAPs were enriched more effectively in the 1,6-HD treatment group than in the isotonic solution treatment group. Further analysis showed that the 1,6-HD treatment group could effectively enrich CAPs prone to LLPS. Finally, we compared the representative proteins eluted by different gradients of 1,6-HD and found that the representative proteins of the 2% 1,6-HD treatment group had the highest percentage of IDRs and LCDs, whereas the 10% 1,6-HD treatment group had the opposite trend. CONCLUSION This study provides a convenient high-throughput experimental method called CHS-MS. This method can efficiently enrich proteins prone to LLPS and can be extended to explore LLPS properties of CAPs in different biological systems.
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Affiliation(s)
- Peiyu Zhu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chao Hou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Manlin Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - 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
| | - Tingting Li
- 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.
| | - Likun Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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24
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Jones CE, Forsburg SL. Impact of 1,6-hexanediol on Schizosaccharomyces pombe genome stability. G3 (BETHESDA, MD.) 2023; 13:jkad123. [PMID: 37284815 PMCID: PMC10411564 DOI: 10.1093/g3journal/jkad123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 06/08/2023]
Abstract
Phase separation is a major mechanism of macromolecular condensation within cells. A frequently chosen tool for global disruption of phase separation via weak hydrophobic interactions is treatment with 1,6-hexanediol. This study evaluates the cytotoxic and genotoxic effects of treating live fission yeast with 1,6-hexanediol. We find that 1,6-hexanediol causes a drastic decrease in cell survival and growth rate. We also see a reduction in HP1 protein foci and increase in DNA damage foci. However, there is no evidence for increased genomic instability in two classically phase-separated domains, the heterochromatic pericentromere and the nucleolar rDNA repeats. This study reveals that 1,6-hexanediol is a blunt tool for phase separation inhibition and its secondary effects must be taken into consideration during its in vivo use.
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Affiliation(s)
- Chance E Jones
- Section of Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Susan L Forsburg
- Section of Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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25
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Sahoo R, Chakrabarti R. Structure and dynamics of an active polymer chain inside a nanochannel grafted with polymers. SOFT MATTER 2023; 19:5978-5988. [PMID: 37497754 DOI: 10.1039/d3sm00618b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
We use computer simulations to investigate the complex dynamics of a polymer, made of active Brownian particles, inside a channel grafted internally with passive polymer chains. Our simulations reveal that this probe-polymer, if passive, exhibits a compact structure when its interaction is repulsive with the grafted chains as it tends to stay within the hollow space created along the axis of the channel. On increasing the attractive interaction, the passive probe-polymer is pulled towards the grafted polymeric region and adopts an extended structure. By contrast, switching on the activity helps the probe-polymer to escape from the local traps caused by the sticky grafted chains. The interplay between the activity of the probe-polymer and its sticky interaction with the grafted chains results in shrinking, followed by swelling as the activity is increased. To elucidate the dynamics we compute the mean square displacement (MSD) of the center of mass of the probe-polymer, which increases monotonically with activity and displays superdiffusive behavior at an intermediate time and enhanced diffusion at a long time period. In addition, compared with the attractive interaction, the active probe-polymer shows faster dynamics when the interaction is repulsive to the grafted polymers. We believe that our current study will provide insights into the structural changes and dynamics of active polymers in heterogeneous media and will be useful in designing polymer-based drug delivery vehicles.
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Affiliation(s)
- Rajiblochan Sahoo
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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26
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Kehlenbach RH, Neumann P, Ficner R, Dickmanns A. Interaction of nucleoporins with nuclear transport receptors: a structural perspective. Biol Chem 2023; 404:791-805. [PMID: 37210735 DOI: 10.1515/hsz-2023-0155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/04/2023] [Indexed: 05/23/2023]
Abstract
Soluble nuclear transport receptors and stationary nucleoporins are at the heart of the nucleocytoplasmic transport machinery. A subset of nucleoporins contains characteristic and repetitive FG (phenylalanine-glycine) motifs, which are the basis for the permeability barrier of the nuclear pore complex (NPC) that controls transport of macromolecules between the nucleus and the cytoplasm. FG-motifs can interact with each other and/or with transport receptors, mediating their translocation across the NPC. The molecular details of homotypic and heterotypic FG-interactions have been analyzed at the structural level. In this review, we focus on the interactions of nucleoporins with nuclear transport receptors. Besides the conventional FG-motifs as interaction spots, a thorough structural analysis led us to identify additional similar motifs at the binding interface between nucleoporins and transport receptors. A detailed analysis of all known human nucleoporins revealed a large number of such phenylalanine-containing motifs that are not buried in the predicted 3D-structure of the respective protein but constitute part of the solvent-accessible surface area. Only nucleoporins that are rich in conventional FG-repeats are also enriched for these motifs. This additional layer of potential low-affinity binding sites on nucleoporins for transport receptors may have a strong impact on the interaction of transport complexes with the nuclear pore and, thus, the efficiency of nucleocytoplasmic transport.
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Affiliation(s)
- Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Piotr Neumann
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
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27
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Yu W, Rush C, Tingey M, Junod S, Yang W. Application of Super-resolution SPEED Microscopy in the Study of Cellular Dynamics. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:356-371. [PMID: 37501792 PMCID: PMC10369678 DOI: 10.1021/cbmi.3c00036] [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: 03/23/2023] [Revised: 05/11/2023] [Accepted: 06/08/2023] [Indexed: 07/29/2023]
Abstract
Super-resolution imaging techniques have broken the diffraction-limited resolution of light microscopy. However, acquiring three-dimensional (3D) super-resolution information about structures and dynamic processes in live cells at high speed remains challenging. Recently, the development of high-speed single-point edge-excitation subdiffraction (SPEED) microscopy, along with its 2D-to-3D transformation algorithm, provides a practical and effective approach to achieving 3D subdiffraction-limit information in subcellular structures and organelles with rotational symmetry. One of the major benefits of SPEED microscopy is that it does not rely on complex optical components and can be implemented on a standard, inverted epifluorescence microscope, simplifying the process of sample preparation and the expertise requirement. SPEED microscopy is specifically designed to obtain 2D spatial locations of individual immobile or moving fluorescent molecules inside submicrometer biological channels or cavities at high spatiotemporal resolution. The collected data are then subjected to postlocalization 2D-to-3D transformation to obtain 3D super-resolution structural and dynamic information. In recent years, SPEED microscopy has provided significant insights into nucleocytoplasmic transport across the nuclear pore complex (NPC) and cytoplasm-cilium trafficking through the ciliary transition zone. This Review focuses on the applications of SPEED microscopy in studying the structure and function of nuclear pores.
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Affiliation(s)
- Wenlan Yu
- Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coby Rush
- Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Samuel Junod
- Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
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28
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Liashkovich I, Stefanello ST, Vidyadharan R, Haufe G, Erofeev A, Gorelkin PV, Kolmogorov V, Mizdal CR, Dulebo A, Bulk E, Kouzel IU, Shahin V. Pitstop-2 and its novel derivative RVD-127 disrupt global cell dynamics and nuclear pores integrity by direct interaction with small GTPases. Bioeng Transl Med 2023; 8:e10425. [PMID: 37476059 PMCID: PMC10354767 DOI: 10.1002/btm2.10425] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 07/22/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is an essential cell physiological process of broad biomedical relevance. Since the recent introduction of Pitstop-2 as a potent CME inhibitor, we and others have reported on substantial clathrin-independent inhibitory effects. Herein, we developed and experimentally validated a novel fluorescent derivative of Pitstop-2, termed RVD-127, to clarify Pitstop-2 diverse effects. Using RVD-127, we were able to trace additional protein targets of Pitstop-2. Besides inhibiting CME, Pitstop-2 and RVD-127 proved to directly and reversibly bind to at least two members of the small GTPase superfamily Ran and Rac1 with particularly high efficacy. Binding locks the GTPases in a guanosine diphosphate (GDP)-like conformation disabling their interaction with their downstream effectors. Consequently, overall cell motility, mechanics and nucleocytoplasmic transport integrity are rapidly disrupted at inhibitor concentrations well below those required to significantly reduce CME. We conclude that Pitstop-2 is a highly potent, reversible inhibitor of small GTPases. The inhibition of these molecular switches of diverse crucial signaling pathways, including nucleocytoplasmic transport and overall cell dynamics and motility, clarifies the diversity of Pitstop-2 activities. Moreover, considering the fundamental importance and broad implications of small GTPases in physiology, pathophysiology and drug development, Pitstop-2 and RVD-127 open up novel avenues.
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Affiliation(s)
| | | | | | - Günter Haufe
- Organic Chemistry Institute, University of MünsterMünsterGermany
| | - Alexander Erofeev
- National University of Science and Technology «MISiS»MoscowRussia
- Department of ChemistryLomonosov Moscow State UniversityMoscowRussia
| | | | | | | | | | - Etmar Bulk
- Institute of Physiology II, University of MünsterMünsterGermany
| | | | - Victor Shahin
- Institute of Physiology II, University of MünsterMünsterGermany
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29
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Thomas L, Taleb Ismail B, Askjaer P, Seydoux G. Nucleoporin foci are stress-sensitive condensates dispensable for C. elegans nuclear pore assembly. EMBO J 2023:e112987. [PMID: 37254647 DOI: 10.15252/embj.2022112987] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Nucleoporins (Nups) assemble nuclear pores that form the permeability barrier between nucleoplasm and cytoplasm. Nucleoporins also localize in cytoplasmic foci proposed to function as pore pre-assembly intermediates. Here, we characterize the composition and incidence of cytoplasmic Nup foci in an intact animal, C. elegans. We find that, in young non-stressed animals, Nup foci only appear in developing sperm, oocytes and embryos, tissues that express high levels of nucleoporins. The foci are condensates of highly cohesive FG repeat-containing nucleoporins (FG-Nups), which are maintained near their solubility limit in the cytoplasm by posttranslational modifications and chaperone activity. Only a minor fraction of FG-Nup molecules concentrate in Nup foci, which dissolve during M phase and are dispensable for nuclear pore assembly. Nucleoporin condensation is enhanced by stress and advancing age, and overexpression of a single FG-Nup in post-mitotic neurons is sufficient to induce ectopic condensation and organismal paralysis. We speculate that Nup foci are non-essential and potentially toxic condensates whose assembly is actively suppressed in healthy cells.
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Affiliation(s)
- Laura Thomas
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Basma Taleb Ismail
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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30
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Lee S, Abini-Agbomson S, Perry DS, Goodman A, Rao B, Huang MY, Diedrich JK, Moresco JJ, Yates JR, Armache KJ, Madhani HD. Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity. Nat Struct Mol Biol 2023:10.1038/s41594-023-01000-z. [PMID: 37217653 DOI: 10.1038/s41594-023-01000-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Little is understood about how the two major types of heterochromatin domains (HP1 and Polycomb) are kept separate. In the yeast Cryptococcus neoformans, the Polycomb-like protein Ccc1 prevents deposition of H3K27me3 at HP1 domains. Here we show that phase separation propensity underpins Ccc1 function. Mutations of the two basic clusters in the intrinsically disordered region or deletion of the coiled-coil dimerization domain alter phase separation behavior of Ccc1 in vitro and have commensurate effects on formation of Ccc1 condensates in vivo, which are enriched for PRC2. Notably, mutations that alter phase separation trigger ectopic H3K27me3 at HP1 domains. Supporting a direct condensate-driven mechanism for fidelity, Ccc1 droplets efficiently concentrate recombinant C. neoformans PRC2 in vitro whereas HP1 droplets do so only weakly. These studies establish a biochemical basis for chromatin regulation in which mesoscale biophysical properties play a key functional role.
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Affiliation(s)
- Sujin Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniela S Perry
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Allen Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Manning Y Huang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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31
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Pan L, Song XW, Song JC, Shi CY, Wang ZK, Huang SQ, Guo ZF, Li SH, Zhao XX, Ge JB. Downregulation of NUP93 aggravates hypoxia-induced death of cardiomyocytes in vitro through abnormal regulation of gene transcription. Acta Pharmacol Sin 2023; 44:969-983. [PMID: 36807413 PMCID: PMC10104817 DOI: 10.1038/s41401-022-01036-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/27/2022] [Indexed: 02/22/2023] Open
Abstract
Nuclear pore complex in the nuclear envelope plays an important role in controlling the transportation of RNAs, proteins and other macromolecules between the nucleus and cytoplasm. The relationship between abnormal expression of nucleoporins and cardiovascular diseases is unclear. In this study we investigated how myocardial infarction affected the expression and function of nucleoporins in cardiomyocytes. We separately knocked down 27 nucleoporins in rat primary myocardial cells. Among 27 nucleoporins, knockdown of Nup93, Nup210 and Nup214 markedly increased the expression of ANP and BNP, two molecular markers of cardiomyocyte function. We showed that Nup93 was significantly downregulated in hypoxic cardiomyocytes. Knockdown of Nup93 aggravated hypoxia-induced injury and cell death of cardiomyocytes, whereas overexpression of Nup93 led to the opposite effects. RNA-seq and bioinformatics analysis revealed that knockdown of Nup93 did not affect the overall transportation of mRNAs from the nucleus to the cytoplasm, but regulated the transcription of a large number of mRNAs in cardiomyocytes, which are mainly involved in oxidative phosphorylation and ribosome subunits. Most of the down-regulated genes by Nup93 knockdown overlapped with the genes whose promoters could be directly bound by Nup93. Among these genes, we demonstrated that Nup93 knockdown significantly down-regulated the expression of YAP1. Overexpression of YAP1 partially rescued the function of Nup93 knockdown and attenuated the effects of hypoxia on cell injury and cardiomyocyte death. We conclude that down-regulation of Nup93, at least partially, contributes to hypoxia-induced injury and cardiomyocyte death through abnormal interaction with the genome to dynamically regulate the transcription of YAP1 and other genes. These results reveal a new mechanism of Nup93 and might provide new therapeutic targets for the treatment of ischemia-induced heart failure.
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Affiliation(s)
- Lei Pan
- Department of Cardiology, Zhongshan Hospital of Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Xiao-Wei Song
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Jin-Chao Song
- Department of Anesthesiology, Shidong Hospital of Shanghai, University of Shanghai for Science and Technology, Shanghai, 200433, China
| | - Cheng-Yong Shi
- Department of Cardiology, No. 903 Hospital of Chinese People's Liberation Army, Hangzhou, 310013, China
| | - Zhong-Kai Wang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Song-Qun Huang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Zhi-Fu Guo
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Song-Hua Li
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
| | - Xian-Xian Zhao
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
| | - Jun-Bo Ge
- Department of Cardiology, Zhongshan Hospital of Fudan University, Shanghai Institute of Cardiovascular Diseases, National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
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32
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Guo C, Zhang Y, Shuai S, Sigbessia A, Hao S, Xie P, Jiang X, Luo Z, Lin C. The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release. EMBO Rep 2023; 24:e55699. [PMID: 36629390 PMCID: PMC9986819 DOI: 10.15252/embr.202255699] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Release of promoter-proximally paused RNA Pol II into elongation is a tightly regulated and rate-limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease-associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC-mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.
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Affiliation(s)
- Chenghao Guo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
| | - Yadi Zhang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Shimin Shuai
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Abire Sigbessia
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Shaohua Hao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Peng Xie
- Southeast University‐Allen Institute Joint Center, Institute for Brain and IntelligenceSoutheast UniversityNanjingChina
| | - Xu Jiang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Zhuojuan Luo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
- Shenzhen Research InstituteSoutheast UniversityShenzhenChina
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Chengqi Lin
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
- Shenzhen Research InstituteSoutheast UniversityShenzhenChina
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Key Laboratory of Technical Evaluation of Fertility Regulation of Non‐human primate, Fujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
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33
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Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nat Struct Mol Biol 2023; 30:425-435. [PMID: 36807645 PMCID: PMC10121901 DOI: 10.1038/s41594-023-00925-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
Delivering the virus genome into the host nucleus through the nuclear pore complex (NPC) is pivotal in human immunodeficiency virus 1 (HIV-1) infection. The mechanism of this process remains mysterious owing to the NPC complexity and the labyrinth of molecular interactions involved. Here we built a suite of NPC mimics-DNA-origami-corralled nucleoporins with programmable arrangements-to model HIV-1 nuclear entry. Using this system, we determined that multiple cytoplasm-facing Nup358 molecules provide avid binding for capsid docking to the NPC. The nucleoplasm-facing Nup153 preferentially attaches to high-curvature regions of the capsid, positioning it for tip-leading NPC insertion. Differential capsid binding strengths of Nup358 and Nup153 constitute an affinity gradient that drives capsid penetration. Nup62 in the NPC central channel forms a barrier that viruses must overcome during nuclear import. Our study thus provides a wealth of mechanistic insight and a transformative toolset for elucidating how viruses like HIV-1 enter the nucleus.
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34
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Ng SC, Biswas A, Huyton T, Schünemann J, Reber S, Görlich D. Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length. Nat Commun 2023; 14:747. [PMID: 36765044 PMCID: PMC9918544 DOI: 10.1038/s41467-023-36331-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
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Affiliation(s)
- Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abin Biswas
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Biological Optomechanics, Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Simone Reber
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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35
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Shen Q, Xiong Q, Zhou K, Feng Q, Liu L, Tian T, Wu C, Xiong Y, Melia TJ, Lusk CP, Lin C. Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity. J Am Chem Soc 2023; 145:1292-1300. [PMID: 36577119 PMCID: PMC9852090 DOI: 10.1021/jacs.2c11226] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The DNA-origami technique has enabled the engineering of transmembrane nanopores with programmable size and functionality, showing promise in building biosensors and synthetic cells. However, it remains challenging to build large (>10 nm), functionalizable nanopores that spontaneously perforate lipid membranes. Here, we take advantage of pneumolysin (PLY), a bacterial toxin that potently forms wide ring-like channels on cell membranes, to construct hybrid DNA-protein nanopores. This PLY-DNA-origami complex, in which a DNA-origami ring corrals up to 48 copies of PLY, targets the cholesterol-rich membranes of liposomes and red blood cells, readily forming uniformly sized pores with an average inner diameter of ∼22 nm. Such hybrid nanopores facilitate the exchange of macromolecules between perforated liposomes and their environment, with the exchange rate negatively correlating with the macromolecule size (diameters of gyration: 8-22 nm). Additionally, the DNA ring can be decorated with intrinsically disordered nucleoporins to further restrict the diffusion of traversing molecules, highlighting the programmability of the hybrid nanopores. PLY-DNA pores provide an enabling biophysical tool for studying the cross-membrane translocation of ultralarge molecules and open new opportunities for analytical chemistry, synthetic biology, and nanomedicine.
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Affiliation(s)
- Qi Shen
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Qiancheng Xiong
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Kaifeng Zhou
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Longfei Liu
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Taoran Tian
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department of Biomedical Engineering, Yale University, 17 Hillhouse Ave, New Haven, Connecticut 06511, United States
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36
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Morphology of Polymer Brushes in the Presence of Attractive Nanoparticles: Effects of Temperature. Int J Mol Sci 2023; 24:ijms24010832. [PMID: 36614298 PMCID: PMC9821464 DOI: 10.3390/ijms24010832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
We study the role of temperature on the structure of pure polymer brushes and their mixture with attractive nanoparticles in flat and cylindrical geometries. It has previously been established that the addition of such nanoparticles causes the polymer brush to collapse and the intensity of the collapse depends on the attraction strength, the nanoparticle diameter, and the grafting density. In this work, we carry out molecular dynamics simulation under good solvent conditions to show how the collapse transition is affected by the temperature, for both plane grafted and inside-cylinder grafted brushes. We first examine the pure brush morphology and verify that the brush height is insensitive to temperature changes in both planar and cylindrical geometries, as expected for a polymer brush in a good solvent. On the other hand, for both system geometries, the brush structure in the presence of attractive nanoparticles is quite responsive to temperature changes. Generally speaking, for a given nanoparticle concentration, increasing the temperature causes the brush height to increase. A brush which contracts when nanoparticles are added eventually swells beyond its pure brush height as the system temperature is increased. The combination of two easily controlled external parameters, namely, concentration of nanoparticles in solution and temperature, allows for sensitive and reversible adjustment of the polymer brush height, a feature which could be exploited in designing smart polymer devices.
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37
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Wu M, Zhang J, Xiong Y, Zhao Y, Zheng M, Huang X, Huang F, Wu X, Li X, Fan W, Hu L, Zeng Y, Cheng X, Yue J, Du J, Chen N, Wei W, Yao Q, Lu X, Huang C, Deng J, Chang Z, Liu H, Zhao TC, Chinn YE. Promotion of Lung Cancer Metastasis by SIRT2-Mediated Extracellular Protein Deacetylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205462. [PMID: 36453571 PMCID: PMC9875677 DOI: 10.1002/advs.202205462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Acetylation of extracellular proteins has been observed in many independent studies where particular attention has been given to the dynamic change of the microenvironmental protein post-translational modifications. While extracellular proteins can be acetylated within the cells prior to their micro-environmental distribution, their deacetylation in a tumor microenvironment remains elusive. Here it is described that multiple acetyl-vWA domain-carrying proteins including integrin β3 (ITGB3) and collagen 6A (COL6A) are deacetylated by Sirtuin family member SIRT2 in extracellular space. SIRT2 is secreted by macrophages following toll-like receptor (TLR) family member TLR4 or TLR2 activation. TLR-activated SIRT2 undergoes autophagosome translocation. TNF receptor associated factor 6 (TRAF6)-mediated autophagy flux in response to TLR2/4 activation can then pump SIRT2 into the microenvironment to function as extracellular SIRT2 (eSIRT2). In the extracellular space, eSIRT2 deacetylates ITGB3 on aK416 involved in cell attachment and migration, leading to a promotion of cancer cell metastasis. In lung cancer patients, significantly increased serum eSIRT2 level correlates with dramatically decreased ITGB3-K416 acetylation in cancer cells. Thus, the extracellular space is a subcellular organelle-like arena where eSIRT2 promotes cancer cell metastasis via catalyzing extracellular protein deacetylation.
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38
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Obtaining 3D super-resolution images by utilizing rotationally symmetric structures and 2D-to-3D transformation. Comput Struct Biotechnol J 2023; 21:1424-1432. [PMID: 36824228 PMCID: PMC9941874 DOI: 10.1016/j.csbj.2023.02.008] [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: 10/20/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Super-resolution imaging techniques have provided unprecedentedly detailed information by surpassing the diffraction-limited resolution of light microscopy. However, in order to derive high quality spatial resolution, many of these techniques require high laser power, extended imaging time, dedicated sample preparation, or some combination of the three. These constraints are particularly evident when considering three-dimensional (3D) super-resolution imaging. As a result, high-speed capture of 3D super-resolution information of structures and dynamic processes within live cells remains both desirable and challenging. Recently, a highly effective approach to obtain 3D super-resolution information was developed that can be employed in commonly available laboratory microscopes. This development makes it both scientifically possible and financially feasible to obtain super-resolution 3D information under certain conditions. This is accomplished by converting 2D single-molecule localization data captured at high speed within subcellular structures and rotationally symmetric organelles. Here, a high-speed 2D single-molecule tracking and post-localization technique, known as single-point edge-excitation sub-diffraction (SPEED) microcopy, along with its 2D-to-3D transformation algorithm is detailed with special emphasis on the mathematical principles and Monte Carlo simulation validation of the technique.
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39
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Regulation of cell size and Wee1 kinase by elevated levels of the cell cycle regulatory protein kinase Cdr2. J Biol Chem 2022; 299:102831. [PMID: 36574843 PMCID: PMC9860436 DOI: 10.1016/j.jbc.2022.102831] [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: 11/07/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Many cell cycle regulatory proteins catalyze cell cycle progression in a concentration-dependent manner. In the fission yeast Schizosaccharomyces pombe, the protein kinase Cdr2 promotes mitotic entry by organizing cortical oligomeric nodes that lead to inhibition of Wee1, which itself inhibits the cyclin-dependent kinase Cdk1. cdr2Δ cells lack nodes and divide at increased size due to overactive Wee1, but it has not been known how increased Cdr2 levels might impact Wee1 and cell size. It also has not been clear if and how Cdr2 might regulate Wee1 in the absence of the related kinase Cdr1/Nim1. Using a tetracycline-inducible expression system, we found that a 6× increase in Cdr2 expression caused hyperphosphorylation of Wee1 and reduction in cell size even in the absence of Cdr1/Nim1. This overexpressed Cdr2 formed clusters that sequestered Wee1 adjacent to the nuclear envelope. Cdr2 mutants that disrupt either kinase activity or clustering ability failed to sequester Wee1 and to reduce cell size. We propose that Cdr2 acts as a dosage-dependent regulator of cell size by sequestering its substrate Wee1 in cytoplasmic clusters, away from Cdk1 in the nucleus. This mechanism has implications for other clustered kinases, which may act similarly by sequestering substrates.
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40
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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41
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Li H, Ernst C, Kolonko-Adamska M, Greb-Markiewicz B, Man J, Parissi V, Ng BWL. Phase separation in viral infections. Trends Microbiol 2022; 30:1217-1231. [PMID: 35902318 DOI: 10.1016/j.tim.2022.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Viruses rely on the reprogramming of cellular processes to enable efficient viral replication; this often requires subcompartmentalization within the host cell. Liquid-liquid phase separation (LLPS) has emerged as a fundamental principle to organize and subdivide cellular processes, and plays an important role in viral life cycles. Despite substantial advances in the field, elucidating the exact organization and function of these organelles remains a major challenge. In this review, we summarize the biochemical basis of condensate formation, the role of LLPS during viral infection, and interplay of LLPS with innate immune responses. Finally, we discuss possible strategies and molecules to modulate LLPS during viral infections.
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Affiliation(s)
- Haohua Li
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christina Ernst
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marta Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jackie Man
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; Faculty of Medicine, Imperial College, London, UK
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MPF), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, Bordeaux, France
| | - Billy Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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42
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Tingey M, Li Y, Yu W, Young A, Yang W. Spelling out the roles of individual nucleoporins in nuclear export of mRNA. Nucleus 2022; 13:170-193. [PMID: 35593254 PMCID: PMC9132428 DOI: 10.1080/19491034.2022.2076965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/01/2022] Open
Abstract
The Nuclear Pore Complex (NPC) represents a critical passage through the nuclear envelope for nuclear import and export that impacts nearly every cellular process at some level. Recent technological advances in the form of Auxin Inducible Degron (AID) strategies and Single-Point Edge-Excitation sub-Diffraction (SPEED) microscopy have enabled us to provide new insight into the distinct functions and roles of nuclear basket nucleoporins (Nups) upon nuclear docking and export for mRNAs. In this paper, we provide a review of our recent findings as well as an assessment of new techniques, updated models, and future perspectives in the studies of mRNA's nuclear export.
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Affiliation(s)
- Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Yichen Li
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Wenlan Yu
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Albert Young
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
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43
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Andersson J, Svirelis J, Medin J, Järlebark J, Hailes R, Dahlin A. Pore performance: artificial nanoscale constructs that mimic the biomolecular transport of the nuclear pore complex. NANOSCALE ADVANCES 2022; 4:4925-4937. [PMID: 36504753 PMCID: PMC9680827 DOI: 10.1039/d2na00389a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/12/2022] [Indexed: 06/17/2023]
Abstract
The nuclear pore complex is a nanoscale assembly that achieves shuttle-cargo transport of biomolecules: a certain cargo molecule can only pass the barrier if it is attached to a shuttle molecule. In this review we summarize the most important efforts aiming to reproduce this feature in artificial settings. This can be achieved by solid state nanopores that have been functionalized with the most important proteins found in the biological system. Alternatively, the nanopores are chemically modified with synthetic polymers. However, only a few studies have demonstrated a shuttle-cargo transport mechanism and due to cargo leakage, the selectivity is not comparable to that of the biological system. Other recent approaches are based on DNA origami, though biomolecule transport has not yet been studied with these. The highest selectivity has been achieved with macroscopic gels, but they are yet to be scaled down to nano-dimensions. It is concluded that although several interesting studies exist, we are still far from achieving selective and efficient artificial shuttle-cargo transport of biomolecules. Besides being of fundamental interest, such a system could be potentially useful in bioanalytical devices.
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Affiliation(s)
- John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Rebekah Hailes
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
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Yang J, Griffin A, Qiang Z, Ren J. Organelle-targeted therapies: a comprehensive review on system design for enabling precision oncology. Signal Transduct Target Ther 2022; 7:379. [PMID: 36402753 PMCID: PMC9675787 DOI: 10.1038/s41392-022-01243-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
Abstract
Cancer is a major threat to human health. Among various treatment methods, precision therapy has received significant attention since the inception, due to its ability to efficiently inhibit tumor growth, while curtailing common shortcomings from conventional cancer treatment, leading towards enhanced survival rates. Particularly, organelle-targeted strategies enable precise accumulation of therapeutic agents in organelles, locally triggering organelle-mediated cell death signals which can greatly reduce the therapeutic threshold dosage and minimize side-effects. In this review, we comprehensively discuss history and recent advances in targeted therapies on organelles, specifically including nucleus, mitochondria, lysosomes and endoplasmic reticulum, while focusing on organelle structures, organelle-mediated cell death signal pathways, and design guidelines of organelle-targeted nanomedicines based on intervention mechanisms. Furthermore, a perspective on future research and clinical opportunities and potential challenges in precision oncology is presented. Through demonstrating recent developments in organelle-targeted therapies, we believe this article can further stimulate broader interests in multidisciplinary research and technology development for enabling advanced organelle-targeted nanomedicines and their corresponding clinic translations.
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Affiliation(s)
- Jingjing Yang
- grid.24516.340000000123704535Institute of Nano and Biopolymeric Materials, School of Materials Science and Engineering, Tongji University, 201804 Shanghai, China
| | - Anthony Griffin
- grid.267193.80000 0001 2295 628XSchool of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, MS 39406 USA
| | - Zhe Qiang
- grid.267193.80000 0001 2295 628XSchool of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, MS 39406 USA
| | - Jie Ren
- grid.24516.340000000123704535Institute of Nano and Biopolymeric Materials, School of Materials Science and Engineering, Tongji University, 201804 Shanghai, China
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A simple thermodynamic description of phase separation of Nup98 FG domains. Nat Commun 2022; 13:6172. [PMID: 36257947 PMCID: PMC9579204 DOI: 10.1038/s41467-022-33697-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls nucleocytoplasmic transport. It retains inert macromolecules but allows facilitated passage of nuclear transport receptors that shuttle cargoes into or out of nuclei. The barrier can be described as a condensed phase assembled from cohesive FG repeat domains, including foremost the charge-depleted FG domain of Nup98. We found that Nup98 FG domains show an LCST-type phase separation, and we provide comprehensive and orthogonal experimental datasets for a quantitative description of this behaviour. A derived thermodynamic model correlates saturation concentration with repeat number, temperature, and ionic strength. It allows estimating the enthalpy, entropy, and ΔG (0.2 kJ/mol, 0.1 kB·T) contributions per repeat to phase separation and inter-repeat cohesion. While changing the cohesion strength strongly impacts the strictness of barrier, these numbers provide boundary conditions for in-depth modelling not only of barrier assembly but also of NPC passage.
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Imoto Y, Raychaudhuri S, Ma Y, Fenske P, Sandoval E, Itoh K, Blumrich EM, Matsubayashi HT, Mamer L, Zarebidaki F, Söhl-Kielczynski B, Trimbuch T, Nayak S, Iwasa JH, Liu J, Wu B, Ha T, Inoue T, Jorgensen EM, Cousin MA, Rosenmund C, Watanabe S. Dynamin is primed at endocytic sites for ultrafast endocytosis. Neuron 2022; 110:2815-2835.e13. [PMID: 35809574 PMCID: PMC9464723 DOI: 10.1016/j.neuron.2022.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023]
Abstract
Dynamin mediates fission of vesicles from the plasma membrane during endocytosis. Typically, dynamin is recruited from the cytosol to endocytic sites, requiring seconds to tens of seconds. However, ultrafast endocytosis in neurons internalizes vesicles as quickly as 50 ms during synaptic vesicle recycling. Here, we demonstrate that Dynamin 1 is pre-recruited to endocytic sites for ultrafast endocytosis. Specifically, Dynamin 1xA, a splice variant of Dynamin 1, interacts with Syndapin 1 to form molecular condensates on the plasma membrane. Single-particle tracking of Dynamin 1xA molecules confirms the liquid-like property of condensates in vivo. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1, the condensates do not form, and consequently, ultrafast endocytosis slows down by 100-fold. Mechanistically, Syndapin 1 acts as an adaptor by binding the plasma membrane and stores Dynamin 1xA at endocytic sites. This cache bypasses the recruitment step and accelerates endocytosis at synapses.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pascal Fenske
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Eduardo Sandoval
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eva-Maria Blumrich
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; Simons Initiatives for the Developing Brain, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Hideaki T Matsubayashi
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lauren Mamer
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Fereshteh Zarebidaki
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Thorsten Trimbuch
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Jian Liu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Bin Wu
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Takanari Inoue
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Erik M Jorgensen
- HHMI, Department of Biology, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; Simons Initiatives for the Developing Brain, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Christian Rosenmund
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA.
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47
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Winogradoff D, Chou HY, Maffeo C, Aksimentiev A. Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex. Nat Commun 2022; 13:5138. [PMID: 36050301 PMCID: PMC9437005 DOI: 10.1038/s41467-022-32857-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/18/2022] [Indexed: 11/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) control biomolecular transport in and out of the nucleus. Disordered nucleoporins in the complex's pore form a permeation barrier, preventing unassisted transport of large biomolecules. Here, we combine coarse-grained simulations of experimentally derived NPC structures with a theoretical model to determine the microscopic mechanism of passive transport. Brute-force simulations of protein transport reveal telegraph-like behavior, where prolonged diffusion on one side of the NPC is interrupted by rapid crossings to the other. We rationalize this behavior using a theoretical model that reproduces the energetics and kinetics of permeation solely from statistics of transient voids within the disordered mesh. As the protein size increases, the mesh transforms from a soft to a hard barrier, enabling orders-of-magnitude reduction in permeation rate for proteins beyond the percolation size threshold. Our model enables exploration of alternative NPC architectures and sets the stage for uncovering molecular mechanisms of facilitated nuclear transport.
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Affiliation(s)
- David Winogradoff
- grid.35403.310000 0004 1936 9991Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Han-Yi Chou
- grid.35403.310000 0004 1936 9991Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Christopher Maffeo
- grid.35403.310000 0004 1936 9991Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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48
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Lin Z, Li Y, Hang Y, Wang C, Liu B, Li J, Yin L, Jiang X, Du X, Qiao Z, Zhu F, Zhang Z, Zhang Q, Zhou Z. Tuning the Size of Large Dense-Core Vesicles and Quantal Neurotransmitter Release via Secretogranin II Liquid-Liquid Phase Separation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202263. [PMID: 35896896 PMCID: PMC9507364 DOI: 10.1002/advs.202202263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Large dense-core vesicles (LDCVs) are larger in volume than synaptic vesicles, and are filled with multiple neuropeptides, hormones, and neurotransmitters that participate in various physiological processes. However, little is known about the mechanism determining the size of LDCVs. Here, it is reported that secretogranin II (SgII), a vesicle matrix protein, contributes to LDCV size regulation through its liquid-liquid phase separation in neuroendocrine cells. First, SgII undergoes pH-dependent polymerization and the polymerized SgII forms phase droplets with Ca2+ in vitro and in vivo. Further, the Ca2+ -induced SgII droplets recruit reconstituted bio-lipids, mimicking the LDCVs biogenesis. In addition, SgII knockdown leads to significant decrease of the quantal neurotransmitter release by affecting LDCV size, which is differently rescued by SgII truncations with different degrees of phase separation. In conclusion, it is shown that SgII is a unique intravesicular matrix protein undergoing liquid-liquid phase separation, and present novel insights into how SgII determines LDCV size and the quantal neurotransmitter release.
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Affiliation(s)
- Zhaohan Lin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Yinglin Li
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Yuqi Hang
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Changhe Wang
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Bing Liu
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Jie Li
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Lili Yin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Xiaohan Jiang
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Xingyu Du
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Zhongjun Qiao
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Feipeng Zhu
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Zhe Zhang
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Quanfeng Zhang
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
| | - Zhuan Zhou
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking‐Tsinghua Center for Life Sciences, and PKU‐IDG/McGovern Institute for Brain ResearchPeking UniversityBeijing100871China
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49
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Elaswad MT, Watkins BM, Sharp KG, Munderloh C, Schisa JA. Large RNP granules in Caenorhabditis elegans oocytes have distinct phases of RNA-binding proteins. G3 GENES|GENOMES|GENETICS 2022; 12:6639704. [PMID: 35816006 PMCID: PMC9434171 DOI: 10.1093/g3journal/jkac173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 11/14/2022]
Abstract
The germ line provides an excellent in vivo system to study the regulation and function of RNP granules. Germ granules are conserved germ line-specific RNP granules that are positioned in the Caenorhabditis elegans adult gonad to function in RNA maintenance, regulation, and surveillance. In Caenorhabditis elegans, when oogenesis undergoes extended meiotic arrest, germ granule proteins and other RNA-binding proteins assemble into much larger RNP granules whose hypothesized function is to regulate RNA metabolism and maintain oocyte quality. To gain insight into the function of oocyte RNP granules, in this report, we characterize distinct phases for four protein components of RNP granules in arrested oocytes. We find that the RNA-binding protein PGL-1 is dynamic and has liquid-like properties, while the intrinsically disordered protein MEG-3 has gel-like properties, similar to the properties of the two proteins in small germ granules of embryos. We find that MEX-3 exhibits several gel-like properties but is more dynamic than MEG-3, while CGH-1 is dynamic but does not consistently exhibit liquid-like characteristics and may be an intermediate phase within RNP granules. These distinct phases of RNA-binding proteins correspond to, and may underlie, differential responses to stress. Interestingly, in oocyte RNP granules, MEG-3 is not required for the condensation of PGL-1 or other RNA-binding proteins, which differs from the role of MEG-3 in small, embryonic germ granules. Lastly, we show that the PUF-5 translational repressor appears to promote MEX-3 and MEG-3 condensation into large RNP granules; however, this role may be associated with regulation of oogenesis.
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Affiliation(s)
- Mohamed T Elaswad
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
| | - Brooklynne M Watkins
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
| | - Katherine G Sharp
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
| | - Chloe Munderloh
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
| | - Jennifer A Schisa
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
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50
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Gamliel A, Meluzzi D, Oh S, Jiang N, Destici E, Rosenfeld MG, Nair SJ. Long-distance association of topological boundaries through nuclear condensates. Proc Natl Acad Sci U S A 2022; 119:e2206216119. [PMID: 35914133 PMCID: PMC9371644 DOI: 10.1073/pnas.2206216119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/24/2022] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.
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Affiliation(s)
- Amir Gamliel
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Soohwan Oh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Nan Jiang
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Eugin Destici
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Sreejith J Nair
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
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