1
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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024; 88:e0000624. [PMID: 38995044 PMCID: PMC11426024 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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2
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Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
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Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
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3
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Duan T, Xing C, Chu J, Deng X, Du Y, Liu X, Hu Y, Qian C, Yin B, Wang HY, Wang RF. ACE2-dependent and -independent SARS-CoV-2 entries dictate viral replication and inflammatory response during infection. Nat Cell Biol 2024; 26:628-644. [PMID: 38514841 DOI: 10.1038/s41556-024-01388-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Excessive inflammation is the primary cause of mortality in patients with severe COVID-19, yet the underlying mechanisms remain poorly understood. Our study reveals that ACE2-dependent and -independent entries of SARS-CoV-2 in epithelial cells versus myeloid cells dictate viral replication and inflammatory responses. Mechanistically, SARS-CoV-2 NSP14 potently enhances NF-κB signalling by promoting IKK phosphorylation, while SARS-CoV-2 ORF6 exerts an opposing effect. In epithelial cells, ACE2-dependent SARS-CoV-2 entry enables viral replication, with translated ORF6 suppressing NF-κB signalling. In contrast, in myeloid cells, ACE2-independent entry blocks the translation of ORF6 and other viral structural proteins due to inefficient subgenomic RNA transcription, but NSP14 could be directly translated from genomic RNA, resulting in an abortive replication but hyperactivation of the NF-κB signalling pathway for proinflammatory cytokine production. Importantly, we identified TLR1 as a critical factor responsible for viral entry and subsequent inflammatory response through interaction with E and M proteins, which could be blocked by the small-molecule inhibitor Cu-CPT22. Collectively, our findings provide molecular insights into the mechanisms by which strong viral replication but scarce inflammatory response during the early (ACE2-dependent) infection stage, followed by low viral replication and potent inflammatory response in the late (ACE2-independent) infection stage, may contribute to COVID-19 progression.
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Affiliation(s)
- Tianhao Duan
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Changsheng Xing
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Junjun Chu
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiangxue Deng
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yang Du
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Liu
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yuzhou Hu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chen Qian
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bingnan Yin
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Helen Y Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rong-Fu Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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4
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Huang X, Huang Y, Qin L, Xiao Q, Wang Q, Wang J, Wang W, Lu X, Wu Y. Maize DDK1 encoding an Importin-4 β protein is essential for seed development and grain filling by mediating nuclear exporting of eIF1A. THE NEW PHYTOLOGIST 2024; 241:2075-2089. [PMID: 38095260 DOI: 10.1111/nph.19475] [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: 09/01/2023] [Accepted: 11/27/2023] [Indexed: 02/09/2024]
Abstract
Nuclear-cytoplasmic trafficking is crucial for protein synthesis in eukaryotic cells due to the spatial separation of transcription and translation by the nuclear envelope. However, the mechanism underlying this process remains largely unknown in plants. In this study, we isolated a maize (Zea mays) mutant designated developmentally delayed kernel 1 (ddk1), which exhibits delayed seed development and slower filling. Ddk1 encodes a plant-specific protein known as Importin-4 β, and its mutation results in reduced 80S monosomes and suppressed protein synthesis. Through our investigations, we found that DDK1 interacts with eIF1A proteins in vivo. However, in vitro experiments revealed that this interaction exhibits low affinity in the absence of RanGTP. Additionally, while the eIF1A protein primarily localizes to the cytoplasm in the wild-type, it remains significantly retained within the nuclei of ddk1 mutants. These observations suggest that DDK1 functions as an exportin and collaborates with RanGTP to facilitate the nuclear export of eIF1A, consequently regulating endosperm development at the translational level. Importantly, both DDK1 and eIF1A are conserved among various plant species, implying the preservation of this regulatory module across diverse plants.
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Affiliation(s)
- Xing Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongcai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Li Qin
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Qiao Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenqin Wang
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai, 200233, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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5
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Liu HT, Gao ZX, Li F, Guo XY, Li CL, Zhang H, Zhao RN, Liu Y, Shi DB, Zhu WJ, Gao P. LncRNA LY6E-DT and its encoded metastatic-related protein play oncogenic roles via different pathways and promote breast cancer progression. Cell Death Differ 2024; 31:188-202. [PMID: 38114778 PMCID: PMC10850524 DOI: 10.1038/s41418-023-01247-5] [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: 03/25/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
Abnormal long noncoding RNA (lncRNA) expression plays an important role in tumor invasion and metastasis. Here, we show that lncRNA LY6E divergent transcript (LY6E-DT) levels are increased in breast cancer (BC) tissues. Transcription factor SP3 binds directly to the LY6E-DT promoter, activating its transcription. Moreover, LY6E-DT N6-methyladenosine modification by methyltransferase-like protein 14 (METTL14) promotes its expression, dependent on the "reader" insulin-like growth factor 2 mRNA binding protein 1(IGF2BP1)-dependent pathway. Notably, we discovered that the lncRNA LY6E-DT encodes a conserved 153-aa protein, "Metastatic-Related Protein" (MRP). Both LY6E-DT and MRP promote BC invasion and metastasis, and MRP expression could distinguish BC patients with lymph node metastasis from those without. Mechanistically, MRP binds heterogeneous nuclear ribonucleoproteins C1/C2 (HNRNPC), enhancing the interaction between HNRNPC and epidermal growth factor receptor (EGFR) mRNA, increasing EGFR mRNA stability and protein expression and subsequently activating the phosphatidylinositol 3‑kinase/protein kinase B signaling (PI3K) pathway. LncRNA LY6E-DT promotes the interaction between Y box binding protein 1 (YBX1) and importin α1 and increases YBX1 protein entry into the nucleus, where it transcriptionally activates zinc finger E-box-binding homeobox 1(ZEB1). Our findings uncover a novel regulatory mechanism underlying BC invasion orchestrated by LY6E-DT and its encoded MRP.
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Affiliation(s)
- Hai-Ting Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Zhao-Xin Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Feng Li
- Department of Pancreatic Surgery, General Surgery, Qi Lu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiang-Yu Guo
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Chun-Lan Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Han Zhang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Rui-Nan Zhao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Yuan Liu
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Duan-Bo Shi
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Wen-Jie Zhu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.
| | - Peng Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences and Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.
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6
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Dickson CF, Hertel S, Tuckwell AJ, Li N, Ruan J, Al-Izzi SC, Ariotti N, Sierecki E, Gambin Y, Morris RG, Towers GJ, Böcking T, Jacques DA. The HIV capsid mimics karyopherin engagement of FG-nucleoporins. Nature 2024; 626:836-842. [PMID: 38267582 PMCID: PMC10881392 DOI: 10.1038/s41586-023-06969-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024]
Abstract
HIV can infect non-dividing cells because the viral capsid can overcome the selective barrier of the nuclear pore complex and deliver the genome directly into the nucleus1,2. Remarkably, the intact HIV capsid is more than 1,000 times larger than the size limit prescribed by the diffusion barrier of the nuclear pore3. This barrier in the central channel of the nuclear pore is composed of intrinsically disordered nucleoporin domains enriched in phenylalanine-glycine (FG) dipeptides. Through multivalent FG interactions, cellular karyopherins and their bound cargoes solubilize in this phase to drive nucleocytoplasmic transport4. By performing an in vitro dissection of the nuclear pore complex, we show that a pocket on the surface of the HIV capsid similarly interacts with FG motifs from multiple nucleoporins and that this interaction licences capsids to penetrate FG-nucleoporin condensates. This karyopherin mimicry model addresses a key conceptual challenge for the role of the HIV capsid in nuclear entry and offers an explanation as to how an exogenous entity much larger than any known cellular cargo may be able to non-destructively breach the nuclear envelope.
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Affiliation(s)
- C F Dickson
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - S Hertel
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - A J Tuckwell
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - N Li
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - J Ruan
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - S C Al-Izzi
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - N Ariotti
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - E Sierecki
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Y Gambin
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - R G Morris
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - G J Towers
- Infection and Immunity, University College London, London, UK
| | - T Böcking
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - D A Jacques
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia.
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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7
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Breckel CA, Johnson ZM, Hickey CM, Hochstrasser M. Yeast 26S proteasome nuclear import is coupled to nucleus-specific degradation of the karyopherin adaptor protein Sts1. Sci Rep 2024; 14:2048. [PMID: 38267508 PMCID: PMC10808114 DOI: 10.1038/s41598-024-52352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
In eukaryotes, the ubiquitin-proteasome system is an essential pathway for protein degradation and cellular homeostasis. 26S proteasomes concentrate in the nucleus of budding yeast Saccharomyces cerevisiae due to the essential import adaptor protein Sts1 and the karyopherin-α protein Srp1. Here, we show that Sts1 facilitates proteasome nuclear import by recruiting proteasomes to the karyopherin-α/β heterodimer. Following nuclear transport, the karyopherin proteins are likely separated from Sts1 through interaction with RanGTP in the nucleus. RanGTP-induced release of Sts1 from the karyopherin proteins initiates Sts1 proteasomal degradation in vitro. Sts1 undergoes karyopherin-mediated nuclear import in the absence of proteasome interaction, but Sts1 degradation in vivo is only observed when proteasomes successfully localize to the nucleus. Sts1 appears to function as a proteasome import factor during exponential growth only, as it is not found in proteasome storage granules (PSGs) during prolonged glucose starvation, nor does it appear to contribute to the rapid nuclear reimport of proteasomes following glucose refeeding and PSG dissipation. We propose that Sts1 acts as a single-turnover proteasome nuclear import factor by recruiting karyopherins for transport and undergoing subsequent RanGTP-initiated ubiquitin-independent proteasomal degradation in the nucleus.
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Affiliation(s)
- Carolyn Allain Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zane M Johnson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Arvinas, Inc., 5 Science Park, New Haven, CT, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
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8
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Khalil B, Linsenmeier M, Smith CL, Shorter J, Rossoll W. Nuclear-import receptors as gatekeepers of pathological phase transitions in ALS/FTD. Mol Neurodegener 2024; 19:8. [PMID: 38254150 PMCID: PMC10804745 DOI: 10.1186/s13024-023-00698-1] [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: 06/05/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders on a disease spectrum that are characterized by the cytoplasmic mislocalization and aberrant phase transitions of prion-like RNA-binding proteins (RBPs). The common accumulation of TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), and other nuclear RBPs in detergent-insoluble aggregates in the cytoplasm of degenerating neurons in ALS/FTD is connected to nuclear pore dysfunction and other defects in the nucleocytoplasmic transport machinery. Recent advances suggest that beyond their canonical role in the nuclear import of protein cargoes, nuclear-import receptors (NIRs) can prevent and reverse aberrant phase transitions of TDP-43, FUS, and related prion-like RBPs and restore their nuclear localization and function. Here, we showcase the NIR family and how they recognize cargo, drive nuclear import, and chaperone prion-like RBPs linked to ALS/FTD. We also discuss the promise of enhancing NIR levels and developing potentiated NIR variants as therapeutic strategies for ALS/FTD and related neurodegenerative proteinopathies.
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Affiliation(s)
- Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - Miriam Linsenmeier
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Neuroscience Track, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A..
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A..
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9
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Yang R, Ko YH, Li F, Lokareddy RK, Hou CFD, Kim C, Klein S, Antolínez S, Marín JF, Pérez-Segura C, Jarrold MF, Zlotnick A, Hadden-Perilla JA, Cingolani G. Structural basis for nuclear import of hepatitis B virus (HBV) nucleocapsid core. SCIENCE ADVANCES 2024; 10:eadi7606. [PMID: 38198557 PMCID: PMC10780889 DOI: 10.1126/sciadv.adi7606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an intact particle, hijacking human importins in a reaction stimulated by host kinases. This paper describes the mechanisms of HBV capsid recognition by importins. We found that importin α1 binds a nuclear localization signal (NLS) at the far end of the HBV coat protein Cp183 carboxyl-terminal domain (CTD). This NLS is exposed to the capsid surface through a pore at the icosahedral quasi-sixfold vertex. Phosphorylation at serine-155, serine-162, and serine-170 promotes CTD compaction but does not affect the affinity for importin α1. The binding of 30 importin α1/β1 augments HBV capsid diameter to ~620 angstroms, close to the maximum size trafficable through the NPC. We propose that phosphorylation favors CTD externalization and prompts its compaction at the capsid surface, exposing the NLS to importins.
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Affiliation(s)
- Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ravi K. Lokareddy
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Christine Kim
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | - Shelby Klein
- Department of Chemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | - Santiago Antolínez
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Juan F. Marín
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | | | - Gino Cingolani
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
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10
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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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11
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Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell 2023; 83:3283-3302.e5. [PMID: 37738963 PMCID: PMC10630966 DOI: 10.1016/j.molcel.2023.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/23/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution.
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Affiliation(s)
- Christopher W Akey
- Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christna Ouch
- Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
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12
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Chen G, Xu D, Liu Q, Yue Z, Dai B, Pan S, Chen Y, Feng X, Hu H. Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importin β SAD2. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2086-2106. [PMID: 37278318 DOI: 10.1111/jipb.13540] [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: 05/27/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
Flowering locus C (FLC) is a central transcriptional repressor that controls flowering time. However, how FLC is imported into the nucleus is unknown. Here, we report that Arabidopsis nucleoporins 62 (NUP62), NUP58, and NUP54 composed NUP62-subcomplex modulates FLC nuclear import during floral transition in an importin α-independent manner, via direct interaction. NUP62 recruits FLC to the cytoplasmic filaments and imports it into the nucleus through the NUP62-subcomplex composed central channel. Importin β supersensitive to ABA and drought 2 (SAD2), a carrier protein, is critical for FLC nuclear import and flower transition, which facilitates FLC import into the nucleus mainly through the NUP62-subcomplex. Proteomics, RNA-seq, and cell biological analyses indicate that the NUP62-subcomplex mainly mediates the nuclear import of cargos with unconventional nuclear localization sequences (NLSs), such as FLC. Our findings illustrate the mechanisms of the NUP62-subcomplex and SAD2 on FLC nuclear import process and floral transition, and provide insights into the role of NUP62-subcomplex and SAD2 in protein nucleocytoplasmic transport in plants.
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Affiliation(s)
- Gang Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Danyun Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhichuang Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Biao Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shujuan Pan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongqiang Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinhua Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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13
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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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14
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Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535055. [PMID: 37066338 PMCID: PMC10103940 DOI: 10.1101/2023.03.31.535055] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange of unsolicited material. However, key aspects of this gating mechanism remain controversial. To address this issue, we determined the nanoscopic behavior of the permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that the large intrinsically disordered domains of phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic fluctuations to create transient voids in the permeability barrier that continuously shape-shift and reseal, resembling a radial polymer brush. Together with cargo-carrying transport factors the FG domains form a feature called the central plug, which is also highly dynamic. Remarkably, NPC mutants with longer FG domains show interweaving meshwork-like behavior that attenuates nucleocytoplasmic transport in vivo. Importantly, the bona fide nanoscale NPC behaviors and morphologies are not recapitulated by in vitro FG domain hydrogels. NPCs also exclude self-assembling FG domain condensates in vivo, thereby indicating that the permeability barrier is not generated by a self-assembling phase condensate, but rather is largely a polymer brush, organized by the NPC scaffold, whose dynamic gating selectivity is strongly enhanced by the presence of transport factors.
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Affiliation(s)
- Toshiya Kozai
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | | | - Adam Mazur
- Biozentrum, University of Basel, Switzerland
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Jeremy Tempkin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Barak Raveh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
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15
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Jibiki K, Kodama TS, Yasuhara N. Importin alpha family NAAT/IBB domain: Functions of a pleiotropic long chameleon sequence. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:175-209. [PMID: 36858734 DOI: 10.1016/bs.apcsb.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nuclear transport is essential for eukaryotic cell survival and regulates the movement of functional molecules in and out of the nucleus via the nuclear pore. Transport is facilitated by protein-protein interactions between cargo and transport receptors, which contribute to the expression and regulation of downstream genetic information. This chapter focuses on the molecular basis of the multifunctional nature of the importin α family, the representative transport receptors that bring proteins into the nucleus. Importin α performs multiple functions during the nuclear transport cycle through interactions with multiple molecules by a single domain called the IBB domain. This domain is a long chameleon sequence, which can change its conformation and binding mode depending on the interaction partners. By considering the evolutionarily conserved biochemical/physicochemical propensities of the amino acids constituting the functional complex interfaces, together with their structural properties, the mechanisms of switching between multiple complexes formed via IBB and the regulation of downstream functions are examined in detail. The mechanism of regulation by IBB indicates that the time has come for a paradigm shift in the way we view the molecular mechanisms by which proteins regulate downstream functions through their interactions with other molecules.
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Affiliation(s)
- Kazuya Jibiki
- Graduate School of Integrated Basic Sciences, Nihon University, Setagaya-ku, Tokyo, Japan
| | - Takashi S Kodama
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Noriko Yasuhara
- Graduate School of Integrated Basic Sciences, Nihon University, Setagaya-ku, Tokyo, Japan.
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16
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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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17
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Fare CM, Rhine K, Lam A, Myong S, Shorter J. A minimal construct of nuclear-import receptor Karyopherin-β2 defines the regions critical for chaperone and disaggregation activity. J Biol Chem 2023; 299:102806. [PMID: 36529289 PMCID: PMC9860449 DOI: 10.1016/j.jbc.2022.102806] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Karyopherin-β2 (Kapβ2) is a nuclear-import receptor that recognizes proline-tyrosine nuclear localization signals of diverse cytoplasmic cargo for transport to the nucleus. Kapβ2 cargo includes several disease-linked RNA-binding proteins with prion-like domains, such as FUS, TAF15, EWSR1, hnRNPA1, and hnRNPA2. These RNA-binding proteins with prion-like domains are linked via pathology and genetics to debilitating degenerative disorders, including amyotrophic lateral sclerosis, frontotemporal dementia, and multisystem proteinopathy. Remarkably, Kapβ2 prevents and reverses aberrant phase transitions of these cargoes, which is cytoprotective. However, the molecular determinants of Kapβ2 that enable these activities remain poorly understood, particularly from the standpoint of nuclear-import receptor architecture. Kapβ2 is a super-helical protein comprised of 20 HEAT repeats. Here, we design truncated variants of Kapβ2 and assess their ability to antagonize FUS aggregation and toxicity in yeast and FUS condensation at the pure protein level and in human cells. We find that HEAT repeats 8 to 20 of Kapβ2 recapitulate all salient features of Kapβ2 activity. By contrast, Kapβ2 truncations lacking even a single cargo-binding HEAT repeat display reduced activity. Thus, we define a minimal Kapβ2 construct for delivery in adeno-associated viruses as a potential therapeutic for amyotrophic lateral sclerosis/frontotemporal dementia, multisystem proteinopathy, and related disorders.
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Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Lam
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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18
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Jafarinia H, Van der Giessen E, Onck PR. Molecular basis of C9orf72 poly-PR interference with the β-karyopherin family of nuclear transport receptors. Sci Rep 2022; 12:21324. [PMID: 36494425 PMCID: PMC9734553 DOI: 10.1038/s41598-022-25732-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Nucleocytoplasmic transport (NCT) is affected in several neurodegenerative diseases including C9orf72-ALS. It has recently been found that arginine-containing dipeptide repeat proteins (R-DPRs), translated from C9orf72 repeat expansions, directly bind to several importins. To gain insight into how this can affect nucleocytoplasmic transport, we use coarse-grained molecular dynamics simulations to study the molecular interaction of poly-PR, the most toxic DPR, with several Kapβs (importins and exportins). We show that poly-PR-Kapβ binding depends on the net charge per residue (NCPR) of the Kapβ, salt concentration of the solvent, and poly-PR length. Poly-PR makes contact with the inner surface of most importins, which strongly interferes with Kapβ binding to cargo-NLS, IBB, and RanGTP in a poly-PR length-dependent manner. Longer poly-PRs at higher concentrations are also able to make contact with the outer surface of importins that contain several binding sites to FG-Nups. We also show that poly-PR binds to exportins, especially at lower salt concentrations, interacting with several RanGTP and FG-Nup binding sites. Overall, our results suggest that poly-PR might cause length-dependent defects in cargo loading, cargo release, Kapβ transport and Ran gradient across the nuclear envelope.
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Affiliation(s)
- Hamidreza Jafarinia
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Erik Van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.
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19
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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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20
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Madheshiya PK, Shukla E, Singh J, Bawaria S, Ansari MY, Chauhan R. Insights into the role of Nup62 and Nup93 in assembling cytoplasmic ring and central transport channel of the nuclear pore complex. Mol Biol Cell 2022; 33:ar139. [PMID: 36222862 PMCID: PMC9727814 DOI: 10.1091/mbc.e22-01-0027] [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] [Indexed: 02/04/2023] Open
Abstract
The nuclear pore complex (NPC) is a highly modular assembly of 34 distinct nucleoporins (Nups) to form a versatile transport channel between the nucleus and the cytoplasm. Among them, Nup62 is known as an essential component for nuclear transport, Nup93 for proper nuclear envelope assembly. These Nups constitute various NPC subcomplexes such as the central transport channel (CTC), the cytoplasmic ring (CR), and the inner ring (IR). However, how they play their roles in NPC assembly and transport activity is not clear. Here we delineated the interacting regions and conducted biochemical reconstitution and structural characterization of the mammalian CR complex to reveal its intrinsic dynamic behavior and a distinct "4"-shaped architecture resembling the CTC complex. Our in vitro reconstitution data demonstrate that the Nup62 coiled-coil domain is critical to form both Nup62322-525 •Nup88517-742 and Nup62322-525•Nup88517-742•Nup214693-926 heterotrimers and both can bind to Nup931-150. We therefore propose that Nup93 acts as a "sensor" to bind to Nup62 shared heterotrimers including the Nup62•Nup54 heterotrimer of the CTC, which was not shown previously to be an interacting partner. Altogether, our biochemical study suggests that Nup62 via its coiled-coil domain is central to form compositionally distinct yet structurally similar heterotrimers and Nup93 binds these diverse heterotrimers nonselectively.
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Affiliation(s)
| | - Ekta Shukla
- National Centre for Cell Science, Pune 411007, Maharashtra, India
| | - Jyotsana Singh
- National Centre for Cell Science, Pune 411007, Maharashtra, India
| | | | | | - Radha Chauhan
- National Centre for Cell Science, Pune 411007, Maharashtra, India,*Address correspondence to: Radha Chauhan ()
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Spittler D, Indorato RL, Boeri Erba E, Delaforge E, Signor L, Harris SJ, Garcia-Saez I, Palencia A, Gabel F, Blackledge M, Noirclerc-Savoye M, Petosa C. Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex. Life Sci Alliance 2022; 5:5/10/e202201431. [PMID: 35995566 PMCID: PMC9396022 DOI: 10.26508/lsa.202201431] [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: 02/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos.
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Affiliation(s)
- Didier Spittler
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Rose-Laure Indorato
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elise Delaforge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Luca Signor
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Simon J Harris
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Isabel Garcia-Saez
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences, Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Marjolaine Noirclerc-Savoye
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
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22
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Gao X, Tian H, Zhu K, Li Q, Hao W, Wang L, Qin B, Deng H, Cui S. Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport. Nat Commun 2022; 13:4782. [PMID: 35970938 PMCID: PMC9376891 DOI: 10.1038/s41467-022-32489-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
The emergence of heavily mutated SARS-CoV-2 variants of concern (VOCs) place the international community on high alert. In addition to numerous mutations that map in the spike protein of VOCs, expression of the viral accessory proteins ORF6 and ORF9b also elevate; both are potent interferon antagonists. Here, we present the crystal structures of Rae1-Nup98 in complex with the C-terminal tails (CTT) of SARS-CoV-2 and SARS-CoV ORF6 to 2.85 Å and 2.39 Å resolution, respectively. An invariant methionine (M) 58 residue of ORF6 CTT extends its side chain into a hydrophobic cavity in the Rae1 mRNA binding groove, resembling a bolt-fitting-hole; acidic residues flanking M58 form salt-bridges with Rae1. Our mutagenesis studies identify key residues of ORF6 important for its interaction with Rae1-Nup98 in vitro and in cells, of which M58 is irreplaceable. Furthermore, we show that ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport correlate with the binding affinity between ORF6 and Rae1-Nup98. Finally, binding of ORF6 to Rae1-Nup98 is linked to ORF6-induced interferon antagonism. Taken together, this study reveals the molecular basis for the antagonistic function of Sarbecovirus ORF6, and implies a strategy of using ORF6 CTT-derived peptides for immunosuppressive drug development. Sarbecovirus ORF6 binds to the Rae1-Nup98 complex, a component of the cytoplasmic face of the nuclear pore complex, and has been shown to suppress interferon responses. Here, the authors provide structures of Rae1-Nup98 in complex with the C-terminal tails of SARS-CoV-2 and SARS-CoV ORF6 and provide insights into ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Huabin Tian
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Qing Li
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Hao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China. .,Sanming Project of Medicine in Shenzhen, National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
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23
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Choi J, Kim R, Koh J. Quantitative Frameworks for Multivalent Macromolecular Interactions in Biological Linear Lattice Systems. Mol Cells 2022; 45:444-453. [PMID: 35754369 PMCID: PMC9260134 DOI: 10.14348/molcells.2022.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.
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Affiliation(s)
- Jaejun Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ryeonghyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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KPNB1 modulates the Machado-Joseph disease protein ataxin-3 through activation of the mitochondrial protease CLPP. Cell Mol Life Sci 2022; 79:401. [PMID: 35794401 PMCID: PMC9259533 DOI: 10.1007/s00018-022-04372-5] [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: 12/20/2021] [Revised: 04/25/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022]
Abstract
Machado–Joseph disease (MJD) is characterized by a pathological expansion of the polyglutamine (polyQ) tract within the ataxin-3 protein. Despite its primarily cytoplasmic localization, polyQ-expanded ataxin-3 accumulates in the nucleus and forms intranuclear aggregates in the affected neurons. Due to these histopathological hallmarks, the nucleocytoplasmic transport machinery has garnered attention as an important disease relevant mechanism. Here, we report on MJD cell model-based analysis of the nuclear transport receptor karyopherin subunit beta-1 (KPNB1) and its implications in the molecular pathogenesis of MJD. Although directly interacting with both wild-type and polyQ-expanded ataxin-3, modulating KPNB1 did not alter the intracellular localization of ataxin-3. Instead, overexpression of KPNB1 reduced ataxin-3 protein levels and the aggregate load, thereby improving cell viability. On the other hand, its knockdown and inhibition resulted in the accumulation of soluble and insoluble ataxin-3. Interestingly, the reduction of ataxin-3 was apparently based on protein fragmentation independent of the classical MJD-associated proteolytic pathways. Label-free quantitative proteomics and knockdown experiments identified mitochondrial protease CLPP as a potential mediator of the ataxin-3-degrading effect induced by KPNB1. We confirmed reduction of KPNB1 protein levels in MJD by analyzing two MJD transgenic mouse models and induced pluripotent stem cells (iPSCs) derived from MJD patients. Our results reveal a yet undescribed regulatory function of KPNB1 in controlling the turnover of ataxin-3, thereby highlighting a new potential target of therapeutic value for MJD.
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25
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Pei F, Wang M, Wang Y, Pan X, Cen X, Huang X, Jin Y, Zhao Z. Quantitative proteomic analysis of gingival crevicular fluids to identify novel biomarkers of gingival recession in orthodontic patients. J Proteomics 2022; 266:104647. [PMID: 35779762 DOI: 10.1016/j.jprot.2022.104647] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/23/2022] [Accepted: 06/04/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To identify gingival recession-related biomarkers in orthodontic patients, we compared the proteome of gingival crevicular fluids (GCF) from healthy gingiva without orthodontic treatment (GH), healthy gingiva undergoing orthodontic treatment (OGH), and recessed gingiva undergoing orthodontic treatment (OGR). METHODS GCF samples were obtained from the anterior teeth of 15 volunteers (n = 5/group). Quantitative proteomic analysis was performed using DIA-based liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were used to annotate differentially expressed proteins (DEPs). Receiver-operating characteristic (ROC) analysis was performed to detect and filter biomarker candidates, while Protein-Protein Interaction (PPI) Networks were utilized to determine the interactions between these DEPs. RESULTS A total of 253, 238, and 101 DEPs were found in OGR vs. OGH, OGR vs. GH, and OGH vs. GH groups, respectively. Based on the Venn diagram of three groups, 128 DEPs in OGR vs. OGH group were identified as specific proteins associated with progressive gingival recession (GR) during orthodontic treatment. Molecular function analysis showed that 128 DEPs were enriched in "molecular binding", including antigen binding, RNA binding, double-stranded RNA binding, cadherin binding involved in cell-cell adhesion, vinculin binding, S100 protein binding, and Ral GTPase binding. The majority of these DEPs were also involved in cytoskeletal regulation. In addition, biological process analysis showed an enrichment in translation, while cellular component analysis indicated that 128 DEPs were related to extracellular exosome. Furthermore, Ribosome and Phagosome were the top two terms in KEGG analysis. The results of ROC analysis demonstrated that 26 proteins could be potential biomarker candidates for GR. PPI networks analysis predicted that IQGAP1, ACTN1, TLN1, VASP, FN1, FERMT3, MYO1C, RALA, RPL35, SEC61G, KPNB1, and NPM1 could be involved in the development of GR via cytoskeletal regulation. CONCLUSIONS In summary, we identified several GCF proteins associated with GR after orthodontic treatment. These findings could contribute to the prevention of GR in susceptible patients before the initiation of orthodontic treatment. SIGNIFICANCE Orthodontic patients with GR often report esthetic defects or root hypersensitivity during orthodontic treatment, especially at the anterior teeth site. GCF, rich in protein, is an easily accessible source of potential biomarkers for the diagnosis of periodontal diseases; however, little is known about the changes in GCF proteome associated with GR in orthodontic patients. In this study we firstly used DIA-based LC-MS/MS to evaluate the proteome and to identify the biomarker candidates for GR in orthodontic patients. These findings will improve our understanding of GR during orthodontic treatment, and could contribute to an earlier diagnosis, or even prevention, of GR in susceptible populations before orthodontic treatment.
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Affiliation(s)
- Fang Pei
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Mengjiao Wang
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yifan Wang
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xuefeng Pan
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xiao Cen
- Department of Temporomandibular Joint, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Xinqi Huang
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Ying Jin
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Zhihe Zhao
- Department of Orthodontics, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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Biophysical characterization of the interaction of Atg8 with a disordered region of Nup159 involved in selective autophagy of the nuclear pore complex. Biochem Biophys Res Commun 2022; 604:172-178. [DOI: 10.1016/j.bbrc.2022.03.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022]
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Basu S, Rajendra KC, Alagar S, Bahadur RP. Impaired nuclear transport induced by juvenile ALS causing P525L mutation in NLS domain of FUS: A molecular mechanistic study. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140766. [PMID: 35134572 DOI: 10.1016/j.bbapap.2022.140766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/15/2022] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration (FTLD) are progressive neurological disorders affecting motor neurons. Cellular aggregates of fused in sarcoma (FUS) protein are found in cytoplasm of ALS and FTLD patients. Nuclear localisation signal (NLS) domain of FUS binds to Karyopherin β2 (Kapβ2), which drives nuclear transport of FUS from cytoplasm. Several pathogenic mutations are reported in FUS NLS, which are associated with its impaired nuclear transport and cytoplasmic mis-localisation. P525L mutation in NLS is most commonly found in cases of juvenile ALS (jALS), which affects individuals below 25 years of age. jALS progresses aggressively causing death within a year of its onset. This study elucidates the molecular mechanism behind jALS-causing P525L mutation hindering nuclear transport of FUS. We perform multiple molecular dynamics simulations in aqueous and hydrophobic solvent to understand the effect of the mutation at molecular level. Dynamics of Kapβ2-FUS complex is better captured in hydrophobic solvent compared to aqueous solvent. P525 and Y526 (PY-motif) of NLS exhibit fine-tuned stereochemical arrangement, which is essential for optimum Kapβ2 binding. P525L causes loss of several native contacts at interface leading to weaker binding, which promotes self-aggregation of FUS in cytoplasm. Native complex samples closed conformation, while mutant complex exhibits open conformation exposing hydrophilic residues of Kapβ2 to hydrophobic solvent. Mutant complex also fails to exhibit spring-like motion essential for its transport through nuclear pore complex. This study provides a mechanistic insight of binding affinity between NLS and Kapβ2 that inhibits self-aggregation of FUS preventing the disease condition.
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Affiliation(s)
- Sushmita Basu
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - K C Rajendra
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Suresh Alagar
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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Diez L, Kapinos LE, Hochmair J, Huebschmann S, Dominguez-Baquero A, Vogt A, Rankovic M, Zweckstetter M, Lim RYH, Wegmann S. Phosphorylation but Not Oligomerization Drives the Accumulation of Tau with Nucleoporin Nup98. Int J Mol Sci 2022; 23:3495. [PMID: 35408855 PMCID: PMC8998617 DOI: 10.3390/ijms23073495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Tau is a neuronal protein that stabilizes axonal microtubules (MTs) in the central nervous system. In Alzheimer's disease (AD) and other tauopathies, phosphorylated Tau accumulates in intracellular aggregates, a pathological hallmark of these diseases. However, the chronological order of pathological changes in Tau prior to its cytosolic aggregation remains unresolved. These include its phosphorylation and detachment from MTs, mislocalization into the somatodendritic compartment, and oligomerization in the cytosol. Recently, we showed that Tau can interact with phenylalanine-glycine (FG)-rich nucleoporins (Nups), including Nup98, that form a diffusion barrier inside nuclear pore complexes (NPCs), leading to defects in nucleocytoplasmic transport. Here, we used surface plasmon resonance (SPR) and bio-layer interferometry (BLI) to investigate the molecular details of Tau:Nup98 interactions and determined how Tau phosphorylation and oligomerization impact the interactions. Importantly, phosphorylation, but not acetylation, strongly facilitates the accumulation of Tau with Nup98. Oligomerization, however, seems to inhibit Tau:Nup98 interactions, suggesting that Tau-FG Nup interactions occur prior to oligomerization. Overall, these results provide fundamental insights into the molecular mechanisms of Tau-FG Nup interactions within NPCs, which might explain how stress-and disease-associated posttranslational modifications (PTMs) may lead to Tau-induced nucleocytoplasmic transport (NCT) failure. Intervention strategies that could rescue Tau-induced NCT failure in AD and tauopathies will be further discussed.
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Affiliation(s)
- Lisa Diez
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Larisa E. Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland; (L.E.K.); (R.Y.H.L.)
| | - Janine Hochmair
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Sabrina Huebschmann
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Alvaro Dominguez-Baquero
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Amelie Vogt
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, Germany; (M.R.); (M.Z.)
| | - Markus Zweckstetter
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, Germany; (M.R.); (M.Z.)
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Goettingen, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland; (L.E.K.); (R.Y.H.L.)
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
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Li Z, Chen S, Zhao L, Huang G, Pi X, Sun S, Wang P, Sui SF. Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex. Cell Res 2022; 32:437-450. [PMID: 35301440 PMCID: PMC9061825 DOI: 10.1038/s41422-022-00632-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188–Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR.
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Affiliation(s)
- Zongqiang Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuaijiabin Chen
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Liang Zhao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiong Pi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peiyi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.,Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China. .,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China. .,Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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30
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Kalita J, Kapinos LE, Zheng T, Rencurel C, Zilman A, Lim RY. Karyopherin enrichment and compensation fortifies the nuclear pore complex against nucleocytoplasmic leakage. J Cell Biol 2022; 221:e202108107. [PMID: 35089308 PMCID: PMC8932525 DOI: 10.1083/jcb.202108107] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
Nuclear pore complexes (NPCs) discriminate nonspecific macromolecules from importin and exportin receptors, collectively termed "karyopherins" (Kaps), that mediate nucleocytoplasmic transport. This selective barrier function is attributed to the behavior of intrinsically disordered phenylalanine-glycine nucleoporins (FG Nups) that guard the NPC channel. However, NPCs in vivo are typically enriched with different Kaps, and how they impact the NPC barrier remains unknown. Here, we show that two major Kaps, importinβ1/karyopherinβ1 (Kapβ1) and exportin 1/chromosomal maintenance 1 (CRM1), are required to fortify NPC barrier function in vivo. Their enrichment at the NPC is sustained by promiscuous binding interactions with the FG Nups, which enable CRM1 to compensate for the loss of Kapβ1 as a means to maintain NPC barrier function. However, such a compensatory mechanism is constrained by the cellular abundances and different binding kinetics for each respective Kap, as evidenced for importin-5. Consequently, we find that NPC malfunction and nucleocytoplasmic leakage result from poor Kap enrichment.
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Affiliation(s)
- Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Larisa E. Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Chantal Rencurel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Roderick Y.H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
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31
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Kinoshita K, Tsubota Y, Tane S, Aizawa Y, Sakata R, Takeuchi K, Shintomi K, Nishiyama T, Hirano T. A loop extrusion-independent mechanism contributes to condensin I-mediated chromosome shaping. J Cell Biol 2022; 221:212966. [PMID: 35045152 PMCID: PMC8932526 DOI: 10.1083/jcb.202109016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/16/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Condensin I is a five-subunit protein complex that is central to mitotic chromosome assembly in eukaryotic cells. Despite recent progress, its molecular mechanisms of action remain to be fully elucidated. By using Xenopus egg extracts as a functional assay, we find that condensin I complexes harboring mutations in its kleisin subunit CAP-H produce chromosomes with confined axes in the presence of topoisomerase IIα (topo IIα) and highly compact structures (termed “beans”) with condensin-positive central cores in its absence. The bean phenotype depends on the SMC ATPase cycle and can be reversed by subsequent addition of topo IIα. The HEAT repeat subunit CAP-D2, but not CAP-G, is essential for the bean formation. Notably, loop extrusion activities of the mutant complexes cannot explain the chromosomal defects they exhibit in Xenopus egg extracts, implying that a loop extrusion–independent mechanism contributes to condensin I–mediated chromosome assembly and shaping. We provide evidence that condensin–condensin interactions underlie these processes.
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Affiliation(s)
| | - Yuko Tsubota
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shoji Tane
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
| | - Yuuki Aizawa
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
| | - Ryota Sakata
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kozo Takeuchi
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
| | | | - Tomoko Nishiyama
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
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32
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Raices M, D'Angelo MA. Structure, Maintenance, and Regulation of Nuclear Pore Complexes: The Gatekeepers of the Eukaryotic Genome. Cold Spring Harb Perspect Biol 2022; 14:a040691. [PMID: 34312247 PMCID: PMC8789946 DOI: 10.1101/cshperspect.a040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the genetic material is segregated inside the nucleus. This compartmentalization of the genome requires a transport system that allows cells to move molecules across the nuclear envelope, the membrane-based barrier that surrounds the chromosomes. Nuclear pore complexes (NPCs) are the central component of the nuclear transport machinery. These large protein channels penetrate the nuclear envelope, creating a passage between the nucleus and the cytoplasm through which nucleocytoplasmic molecule exchange occurs. NPCs are one of the largest protein assemblies of eukaryotic cells and, in addition to their critical function in nuclear transport, these structures also play key roles in many cellular processes in a transport-independent manner. Here we will review the current knowledge of the NPC structure, the cellular mechanisms that regulate their formation and maintenance, and we will provide a brief description of a variety of processes that NPCs regulate.
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Affiliation(s)
- Marcela Raices
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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33
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Stewart M. Function of the Nuclear Transport Machinery in Maintaining the Distinctive Compositions of the Nucleus and Cytoplasm. Int J Mol Sci 2022; 23:2578. [PMID: 35269721 PMCID: PMC8910404 DOI: 10.3390/ijms23052578] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/13/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Although the separation of transcription and translation, mediated by the nuclear envelope, is the defining characteristic of Eukaryotes, the barrier between the nuclear and cytoplasmic compartments needs to be semipermeable to enable material to be moved between them. Moreover, each compartment needs to have a distinctive complement of macromolecules to mediate specific functions and so movement between them needs to be controlled. This is achieved through the selective active transport of macromolecules through the nuclear pores that stud the nuclear envelope, and which serve as a conduit between these compartments. Nuclear pores are huge cylindrical macromolecular assemblies and are constructed from the order of 30 different proteins called nucleoporins. Nuclear pores have a central transport channel that is filled with a dense network of natively unfolded portions of many different nuclear pore proteins (nucleoporins or nups). This network generates a barrier that impedes, but does not entirely prevent, the diffusion of many macromolecules through the pores. The rapid movement of a range of proteins and RNAs through the pores is mediated by a range of transport factors that bind their cargo in one compartment and release it in the other. However, although as their size increases the diffusion of macromolecules through nuclear pores is progressively impaired, additional mechanisms, including the binding of some macromolecules to immobile components of each compartment and also the active removal of macromolecules from the inappropriate compartment, are needed to fully maintain the distinctive compositions of each compartment.
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Affiliation(s)
- Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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34
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Nachmias B, Khan DH, Voisin V, Mer AS, Thomas GE, Segev N, St-Germain J, Hurren R, Gronda M, Botham A, Wang X, Maclean N, Seneviratne AK, Duong N, Xu C, Arruda A, Orouji E, Algouneh A, Hakem R, Shlush L, Minden MD, Raught B, Bader GD, Schimmer AD. IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells. Leukemia 2022; 36:1283-1295. [PMID: 35152270 PMCID: PMC9061300 DOI: 10.1038/s41375-022-01513-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 01/06/2022] [Accepted: 01/26/2022] [Indexed: 12/24/2022]
Abstract
AML cells are arranged in a hierarchy with stem/progenitor cells giving rise to more differentiated bulk cells. Despite the importance of stem/progenitors in the pathogenesis of AML, the determinants of the AML stem/progenitor state are not fully understood. Through a comparison of genes that are significant for growth and viability of AML cells by way of a CRISPR screen, with genes that are differentially expressed in leukemia stem cells (LSC), we identified importin 11 (IPO11) as a novel target in AML. Importin 11 (IPO11) is a member of the importin β family of proteins that mediate transport of proteins across the nuclear membrane. In AML, knockdown of IPO11 decreased growth, reduced engraftment potential of LSC, and induced differentiation. Mechanistically, we identified the transcription factors BZW1 and BZW2 as novel cargo of IPO11. We further show that BZW1/2 mediate a transcriptional signature that promotes stemness and survival of LSC. Thus, we demonstrate for the first time how specific cytoplasmic-nuclear regulation supports stem-like transcriptional signature in relapsed AML.
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35
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Naudi-Fabra S, Blackledge M, Milles S. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins. Biomolecules 2021; 12:biom12010027. [PMID: 35053175 PMCID: PMC8773649 DOI: 10.3390/biom12010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
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36
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Fang Y, Gu Y. Regulation of Plant Immunity by Nuclear Membrane-Associated Mechanisms. Front Immunol 2021; 12:771065. [PMID: 34938291 PMCID: PMC8685260 DOI: 10.3389/fimmu.2021.771065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/18/2021] [Indexed: 12/25/2022] Open
Abstract
Unlike animals, plants do not have specialized immune cells and lack an adaptive immune system. Instead, plant cells rely on their unique innate immune system to defend against pathogens and coordinate beneficial interactions with commensal and symbiotic microbes. One of the major convergent points for plant immune signaling is the nucleus, where transcriptome reprogramming is initiated to orchestrate defense responses. Mechanisms that regulate selective transport of nuclear signaling cargo and chromatin activity at the nuclear boundary play a pivotal role in immune activation. This review summarizes the current knowledge of how nuclear membrane-associated core protein and protein complexes, including the nuclear pore complex, nuclear transport receptors, and the nucleoskeleton participate in plant innate immune activation and pathogen resistance. We also discuss the role of their functional counterparts in regulating innate immunity in animals and highlight potential common mechanisms that contribute to nuclear membrane-centered immune regulation in higher eukaryotes.
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Affiliation(s)
- Yiling Fang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, CA, United States
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, CA, United States
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37
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Ubiquitin Ligase Redundancy and Nuclear-Cytoplasmic Localization in Yeast Protein Quality Control. Biomolecules 2021; 11:biom11121821. [PMID: 34944465 PMCID: PMC8698790 DOI: 10.3390/biom11121821] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
The diverse functions of proteins depend on their proper three-dimensional folding and assembly. Misfolded cellular proteins can potentially harm cells by forming aggregates in their resident compartments that can interfere with vital cellular processes or sequester important factors. Protein quality control (PQC) pathways are responsible for the repair or destruction of these abnormal proteins. Most commonly, the ubiquitin-proteasome system (UPS) is employed to recognize and degrade those proteins that cannot be refolded by molecular chaperones. Misfolded substrates are ubiquitylated by a subset of ubiquitin ligases (also called E3s) that operate in different cellular compartments. Recent research in Saccharomyces cerevisiae has shown that the most prominent ligases mediating cytoplasmic and nuclear PQC have overlapping yet distinct substrate specificities. Many substrates have been characterized that can be targeted by more than one ubiquitin ligase depending on their localization, and cytoplasmic PQC substrates can be directed to the nucleus for ubiquitylation and degradation. Here, we review some of the major yeast PQC ubiquitin ligases operating in the nucleus and cytoplasm, as well as current evidence indicating how these ligases can often function redundantly toward substrates in these compartments.
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38
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Teratake Y, Kimura Y, Ishizaka Y. Role of karyopherin nuclear transport receptors in nuclear transport by nuclear trafficking peptide. Exp Cell Res 2021; 409:112893. [PMID: 34695436 DOI: 10.1016/j.yexcr.2021.112893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/17/2021] [Accepted: 10/18/2021] [Indexed: 11/15/2022]
Abstract
Nuclear trafficking peptide (NTP), a cell-penetrating peptide (CPP) composed of 10 amino acids (aa) (RIFIHFRIGC), has potent nuclear trafficking activity. Recently, we established a protein-based cell engineering system by using NTP, but it remained elusive how NTP functions as a CPP with nuclear orientation. In the present study, we identified importin subunit β1 (IMB1) and transportin 1 (TNPO1) as cellular proteins underlying the activity of NTP. These karyopherin nuclear transport receptors were identified as candidate molecules by liquid chromatography/mass spectrometry analysis, and downregulation of each protein by small interfering RNA significantly reduced NTP activity (P < 0.01). Biochemical analyses revealed that NTP bound directly to both molecules, and the forced expression of an IMB1 fragment (296-516 aa) or TNPO1 fragment (1-297 aa), which both contain binding sites to NTP, reduced nuclear NTP-green fluorescent protein (GFP) levels when it was added to cell culture medium. NTP is derived from viral protein R (Vpr) of human immunodeficiency virus-1, and Vpr enters the nucleus and exerts pleiotropic functions. Notably, Vpr bound directly to IMB1 and TNPO1, and its function was significantly impaired by the forced expression of the 296-516-aa fragment of IMB1 and 1-297-aa fragment of TNPO1. Interestingly, NTP completely blocked the physical association of Vpr with IMB1 and TNPO1. Although the nuclear localization mechanism of Vpr remains unknown, our data suggest that NTP functions as a novel nuclear localization signal of Vpr.
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Affiliation(s)
- Yoichi Teratake
- Department of Intractable Diseases, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, 3-9 Fukuura, Knazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yukihito Ishizaka
- Department of Intractable Diseases, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan.
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39
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Pasha T, Zatorska A, Sharipov D, Rogelj B, Hortobágyi T, Hirth F. Karyopherin abnormalities in neurodegenerative proteinopathies. Brain 2021; 144:2915-2932. [PMID: 34019093 PMCID: PMC8194669 DOI: 10.1093/brain/awab201] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/08/2021] [Accepted: 05/11/2021] [Indexed: 11/12/2022] Open
Abstract
Neurodegenerative proteinopathies are characterized by progressive cell loss that is preceded by the mislocalization and aberrant accumulation of proteins prone to aggregation. Despite their different physiological functions, disease-related proteins like tau, α-synuclein, TAR DNA binding protein-43, fused in sarcoma and mutant huntingtin, all share low complexity regions that can mediate their liquid-liquid phase transitions. The proteins' phase transitions can range from native monomers to soluble oligomers, liquid droplets and further to irreversible, often-mislocalized aggregates that characterize the stages and severity of neurodegenerative diseases. Recent advances into the underlying pathogenic mechanisms have associated mislocalization and aberrant accumulation of disease-related proteins with defective nucleocytoplasmic transport and its mediators called karyopherins. These studies identify karyopherin abnormalities in amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer's disease, and synucleinopathies including Parkinson's disease and dementia with Lewy bodies, that range from altered expression levels to the subcellular mislocalization and aggregation of karyopherin α and β proteins. The reported findings reveal that in addition to their classical function in nuclear import and export, karyopherins can also act as chaperones by shielding aggregation-prone proteins against misfolding, accumulation and irreversible phase-transition into insoluble aggregates. Karyopherin abnormalities can, therefore, be both the cause and consequence of protein mislocalization and aggregate formation in degenerative proteinopathies. The resulting vicious feedback cycle of karyopherin pathology and proteinopathy identifies karyopherin abnormalities as a common denominator of onset and progression of neurodegenerative disease. Pharmacological targeting of karyopherins, already in clinical trials as therapeutic intervention targeting cancers such as glioblastoma and viral infections like COVID-19, may therefore represent a promising new avenue for disease-modifying treatments in neurodegenerative proteinopathies.
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Affiliation(s)
- Terouz Pasha
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London SE5 9RT, UK
| | - Anna Zatorska
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London SE5 9RT, UK
| | - Daulet Sharipov
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London SE5 9RT, UK
| | - Boris Rogelj
- Jozef Stefan Institute, Department of Biotechnology, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 1000 Ljubljana, Slovenia
| | - Tibor Hortobágyi
- ELKH-DE Cerebrovascular and Neurodegenerative Research Group, Department of Neurology, University of Debrecen, 4032 Debrecen, Hungary
- King's College London, Department of Old Age Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | - Frank Hirth
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London SE5 9RT, UK
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40
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Tian Y, Zhu Q, Sun Z, Geng D, Lin B, Su X, He J, Guo M, Xu H, Zhao Y, Qin W, Wang PG, Wen L, Yi W. One‐Step Enzymatic Labeling Reveals a Critical Role of O‐GlcNAcylation in Cell‐Cycle Progression and DNA Damage Response. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yinping Tian
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Qiang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Jiahui He
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Weijie Qin
- National Center for Protein Sciences Beijing State Key Laboratory of Proteomics, Beijing Proteome Research Center Beijing Institute of Lifeomics Beijing China
| | - Peng George Wang
- School of Medicine Southern University of Science and Technology Shenzhen China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai China
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
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41
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Lennon KM, Soheilypour M, Peyro M, Wakefield DL, Choo GE, Mofrad MRK, Jovanovic-Talisman T. Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex. Int J Mol Sci 2021; 22:10898. [PMID: 34639238 PMCID: PMC8509584 DOI: 10.3390/ijms221910898] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of proteins help maintain the selective NPC barrier. To interrogate their binding interactions in vitro, we deployed an NPC barrier mimic. We created the stationary phase by covalently attaching fragments of a yeast FG Nup called Nsp1 to glass coverslips. We used a tunable mobile phase containing NTR, nuclear transport factor 2 (NTF2). In the stationary phase, three main factors affected binding: the number of FG repeats, the charge of fragments, and the fragment density. We also identified three main factors affecting binding in the mobile phase: the avidity of the NTF2 variant for Nsp1, the presence of nonspecific proteins, and the presence of additional NTRs. We used both experimentally determined binding parameters and molecular dynamics simulations of Nsp1FG fragments to create an agent-based model. The results suggest that NTF2 binding is negatively cooperative and dependent on the density of Nsp1FG molecules. Our results demonstrate the strengths of combining experimental and physical modeling approaches to study NPC-mediated transport.
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Affiliation(s)
- Kathleen M. Lennon
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| | - Mohammad Soheilypour
- Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA; (M.S.); (M.P.)
| | - Mohaddeseh Peyro
- Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA; (M.S.); (M.P.)
| | - Devin L. Wakefield
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| | - Grace E. Choo
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| | - Mohammad R. K. Mofrad
- Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA; (M.S.); (M.P.)
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
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42
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Tian Y, Zhu Q, Sun Z, Geng D, Lin B, Su X, He J, Guo M, Xu H, Zhao Y, Qin W, Wang PG, Wen L, Yi W. One-Step Enzymatic Labeling Reveals a Critical Role of O-GlcNAcylation in Cell-Cycle Progression and DNA Damage Response. Angew Chem Int Ed Engl 2021; 60:26128-26135. [PMID: 34590401 DOI: 10.1002/anie.202110053] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 12/26/2022]
Abstract
O-linked N-acetylglucosamine (O-GlcNAcylation) is a ubiquitous post-translational modification of proteins that is essential for cell function. Perturbation of O-GlcNAcylation leads to altered cell-cycle progression and DNA damage response. However, the underlying mechanisms are poorly understood. Here, we develop a highly sensitive one-step enzymatic strategy for capture and profiling O-GlcNAcylated proteins in cells. Using this strategy, we discover that flap endonuclease 1 (FEN1), an essential enzyme in DNA synthesis, is a novel substrate for O-GlcNAcylation. FEN1 O-GlcNAcylation is dynamically regulated during the cell cycle. O-GlcNAcylation at the serine 352 of FEN1 disrupts its interaction with Proliferating Cell Nuclear Antigen (PCNA) at the replication foci, and leads to altered cell cycle, defects in DNA replication, accumulation of DNA damage, and enhanced sensitivity to DNA damage agents. Thus, our study provides a sensitive method for profiling O-GlcNAcylated proteins, and reveals an unknown mechanism of O-GlcNAcylation in regulating cell cycle progression and DNA damage response.
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Affiliation(s)
- Yinping Tian
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiahui He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Peng George Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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43
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Cho B, Choi J, Kim R, Yun JN, Choi Y, Lee HH, Koh J. Thermodynamic Models for Assembly of Intrinsically Disordered Protein Hubs with Multiple Interaction Partners. J Am Chem Soc 2021; 143:12509-12523. [PMID: 34362249 DOI: 10.1021/jacs.1c00811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prevalent in diverse protein interactomes, intrinsically disordered proteins or regions (IDPs or IDRs) often drive assembly of higher-order macromolecular complexes, using multiple target-binding motifs. Such IDP hubs are suggested to process various cellular signals and coordinate relevant biological processes. However, the mechanism of assembly and functional regulation of IDP hubs remains elusive due to the challenges in dissecting their intricate protein-protein interaction networks. Here we present basic thermodynamic models for the assembly of simple IDP hubs with multiple target proteins, constructing partition functions from fundamental binding parameters. We combined these basic functions to develop advanced thermodynamic models to analyze the assembly of the Nup153 hubs interacting with multiple karyopherin β1 (Kap) molecules, critical components of nucleocytoplasmic transport. The thermodynamic analysis revealed a complex organization of the Kap binding sites within the C-terminal IDR of Nup153 including a high-affinity 1:1 interaction site and a series of low-affinity sites for binding of multiple Kaps with negative cooperativity. The negative cooperativity arises from the overlapping nature of the low-affinity sites where Kap occupies multiple dipeptide motifs. The quantitative dissection culminated in construction of the Nup153 hub ensemble, elucidating how distribution among various Kap-bound states is modulated by Kap concentration and competing nuclear proteins. In particular, the Kap occupancy of the IDR can be fine-tuned by varying the location of competition within the overlapping sites, suggesting coupling of specific nuclear processes to distinct transport activities. In general, our results demonstrate the feasibility and a potential mechanism for manifold regulation of IDP functions by diverse cellular signals.
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Affiliation(s)
- ByeongJin Cho
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaejun Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - RyeongHyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jean Nyoung Yun
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yuri Choi
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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44
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Hoogenboom BW, Hough LE, Lemke EA, Lim RYH, Onck PR, Zilman A. Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment. PHYSICS REPORTS 2021; 921:1-53. [PMID: 35892075 PMCID: PMC9306291 DOI: 10.1016/j.physrep.2021.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.
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Affiliation(s)
- Bart W. Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado, Boulder CO 80309, United States of America
| | - Edward A. Lemke
- Biocenter Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University and Institute of Molecular Biology, 55128 Mainz, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Anton Zilman
- Department of Physics and Institute for Biomedical Engineering (IBME), University of Toronto, Toronto, ON M5S 1A7, Canada
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45
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Clerc I, Sagar A, Barducci A, Sibille N, Bernadó P, Cortés J. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Comput Struct Biotechnol J 2021; 19:3817-3828. [PMID: 34285781 PMCID: PMC8273358 DOI: 10.1016/j.csbj.2021.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/15/2023] Open
Abstract
Intrinsically Disordered Proteins and Regions (IDPs/IDRs) are key components of a multitude of biological processes. Conformational malleability enables IDPs/IDRs to perform very specialized functions that cannot be accomplished by globular proteins. The functional role for most of these proteins is related to the recognition of other biomolecules to regulate biological processes or as a part of signaling pathways. Depending on the extent of disorder, the number of interacting sites and the type of partner, very different architectures for the resulting assemblies are possible. More recently, molecular condensates with liquid-like properties composed of multiple copies of IDPs and nucleic acids have been proven to regulate key processes in eukaryotic cells. The structural and kinetic details of disordered biomolecular complexes are difficult to unveil experimentally due to their inherent conformational heterogeneity. Computational approaches, alone or in combination with experimental data, have emerged as unavoidable tools to understand the functional mechanisms of this elusive type of assemblies. The level of description used, all-atom or coarse-grained, strongly depends on the size of the molecular systems and on the timescale of the investigated mechanism. In this mini-review, we describe the most relevant architectures found for molecular interactions involving IDPs/IDRs and the computational strategies applied for their investigation.
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Affiliation(s)
- Ilinka Clerc
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
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Yoshizawa T, Guo L. Karyopherin-βs play a key role as a phase separation regulator. J Biochem 2021; 170:15-23. [PMID: 34223614 DOI: 10.1093/jb/mvab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Recent studies have revealed that cells utilize liquid-liquid phase separation (LLPS) as a mechanism in assembly of membrane-less organelles, such as RNP granules. The nucleus is a well-known membrane-bound organelle surrounded by the nuclear envelope; the nuclear pore complex on the nuclear envelope likely applies LLPS in the central channel to facilitate selective biological macromolecule exchange. Karyopherin-β family proteins exclusively pass through the central channel with cargos by dissolving the phase separated hydrogel formed by the phenylalanine-glycine (FG) repeats-containing nucleoporins. Karyopherin-βs also exhibit dissolution activity for the phase separation of cargo proteins. Many cargos, including RNA-binding proteins containing intrinsically disordered regions (IDRs), undergo phase separation; however, aberrant phase separation is linked to fatal neurodegenerative diseases. Multiple weak interactions between karyopherin-βs and phase separation-prone proteins, such as FG repeats-containing nucleoporins or IDR-containing karyopherin-β cargos, are likely to be important for passing through the nuclear pore complex and maintaining the soluble state of cargo, respectively. In this review, we discuss how karyopherin-βs regulate phase separation to function.
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Affiliation(s)
- Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu-shi, Shiga 525-8577, Japan
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
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Sajidah ES, Lim K, Wong RW. How SARS-CoV-2 and Other Viruses Build an Invasion Route to Hijack the Host Nucleocytoplasmic Trafficking System. Cells 2021; 10:1424. [PMID: 34200500 PMCID: PMC8230057 DOI: 10.3390/cells10061424] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The host nucleocytoplasmic trafficking system is often hijacked by viruses to accomplish their replication and to suppress the host immune response. Viruses encode many factors that interact with the host nuclear transport receptors (NTRs) and the nucleoporins of the nuclear pore complex (NPC) to access the host nucleus. In this review, we discuss the viral factors and the host factors involved in the nuclear import and export of viral components. As nucleocytoplasmic shuttling is vital for the replication of many viruses, we also review several drugs that target the host nuclear transport machinery and discuss their feasibility for use in antiviral treatment.
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Affiliation(s)
- Elma Sakinatus Sajidah
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan;
| | - Keesiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Richard W. Wong
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan;
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
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48
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Amemiya S. Nanoelectrochemical Study of Molecular Transport through the Nuclear Pore Complex. CHEM REC 2021; 21:1430-1441. [PMID: 33502100 PMCID: PMC8217113 DOI: 10.1002/tcr.202000175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 11/10/2022]
Abstract
The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates the transport of both small molecules and macromolecules between the nucleus and cytoplasm of a eukaryotic cell to regulate gene expression. In this personal account, we introduce recent progress in our nanoelectrochemical study of molecular transport through the NPC. Our work represents the importance of chemistry in understanding and controlling of NPC-mediated molecular transport to enable the efficient and safe delivery of genetic therapeutics into the nucleus, thereby fundamentally contributing to human health. Specifically, we employ nanoscale scanning electrochemical microscopy to test our hypothesis that the nanopore of the NPC is divided by transport barriers concentrically into peripheral and central routes to efficiently mediate the bimodal traffic of protein transport and RNA export, respectively, through cooperative hydrophobic and electrostatic interactions.
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Affiliation(s)
- Shigeru Amemiya
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, 15260, PA
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49
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Xu F, Jia M, Li X, Tang Y, Jiang K, Bao J, Gu Y. Exportin-4 coordinates nuclear shuttling of TOPLESS family transcription corepressors to regulate plant immunity. THE PLANT CELL 2021; 33:697-713. [PMID: 33955481 PMCID: PMC8136914 DOI: 10.1093/plcell/koaa047] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 05/03/2023]
Abstract
The regulated nucleocytoplasmic exchange of macromolecules is essential for the eukaryotic cell. However, nuclear transport pathways defined by different nuclear transport receptors (NTRs), including importins and exportins, and their significance in activating distinct stress responses are poorly understood in plants. Here, we exploited a CRISPR/Cas9-based genetic screen to search for modifiers of CONSTITUTIVE EXPRESSION OF PATHOGENESIS-RELATED GENE 5 (cpr5), an Arabidopsis thaliana nucleoporin mutant that activates autoimmune responses that partially mimic effector-triggered immunity (ETI). We identified an NTR gene, Exportin-4 (XPO4), as a genetic interactor of CPR5. The xpo4 cpr5 double mutant activates catastrophic immune responses, which leads to seedling lethality. By leveraging the newly developed proximity-labeling proteomics, we profiled XPO4 substrates and identified TOPLESS (TPL) and TPL-related (TPR) transcription corepressors as XPO4-specific cargo. TPL/TPRs target negative regulators of immunity and are redundantly required for ETI induction. We found that loss-of-XPO4 promotes the nuclear accumulation of TPL/TPRs in the presence of elevated salicylic acid (SA), which contributes to the SA-mediated defense amplification and potentiates immune induction in the cpr5 mutant. We showed that TPL and TPRs are required for the enhanced immune activation observed in xpo4 cpr5 but not for the cpr5 single-mutant phenotype, underscoring the functional interplay between XPO4 and TPL/TPRs and its importance in cpr5-dependent immune induction. We propose that XPO4 coordinates the nuclear accumulation of TPL/TPRs, which plays a role in regulating SA-mediated defense feedback to modulate immune strength downstream of CPR5 during ETI induction.
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Affiliation(s)
- Feifei Xu
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Min Jia
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Xin Li
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Keni Jiang
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
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50
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Kalita J, Kapinos LE, Lim RYH. On the asymmetric partitioning of nucleocytoplasmic transport - recent insights and open questions. J Cell Sci 2021; 134:239102. [PMID: 33912945 DOI: 10.1242/jcs.240382] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macromolecular cargoes are asymmetrically partitioned in the nucleus or cytoplasm by nucleocytoplasmic transport (NCT). At the center of this activity lies the nuclear pore complex (NPC), through which soluble factors circulate to orchestrate NCT. These include cargo-carrying importin and exportin receptors from the β-karyopherin (Kapβ) family and the small GTPase Ran, which switches between guanosine triphosphate (GTP)- and guanosine diphosphate (GDP)-bound forms to regulate cargo delivery and compartmentalization. Ongoing efforts have shed considerable light on how these soluble factors traverse the NPC permeability barrier to sustain NCT. However, this does not explain how importins and exportins are partitioned in the cytoplasm and nucleus, respectively, nor how a steep RanGTP-RanGDP gradient is maintained across the nuclear envelope. In this Review, we peel away the multiple layers of control that regulate NCT and juxtapose unresolved features against known aspects of NPC function. Finally, we discuss how NPCs might function synergistically with Kapβs, cargoes and Ran to establish the asymmetry of NCT.
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Affiliation(s)
- Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
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