1
|
Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos LE, Mariappan M, Lusk CP, Xiong Y, Lim RYH, Lin C. Channel width modulates the permeability of DNA origami based nuclear pore mimics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593438. [PMID: 38766144 PMCID: PMC11100828 DOI: 10.1101/2024.05.09.593438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importing substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.
Collapse
Affiliation(s)
- Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Chunxiang Wu
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Eason Cao
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | - Wei Zheng
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Amy Zhang
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Xia Li
- Department of Cell Biology, Yale School of Medicine, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biophysics and Biochemistry, Yale University, USA
| | | | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Yong Xiong
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biomedical Engineering, Yale University, USA
| |
Collapse
|
2
|
Luo Y, Zhou L, Du L, Xie Y, Lou XY, Cai L, Tang BZ, Gong P, Zhang P. Malachite green: a long-buried water-soluble AIEgen with near-infrared fluorescence for living cell nucleus staining. Chem Commun (Camb) 2024; 60:1452-1455. [PMID: 38214095 DOI: 10.1039/d3cc05535c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Fluorescent imaging probes are crucial for exploring nucleus-related cellular events in live cells. Ideal probes should be photostable, small-sized, highly contrasted, and low in background. Here, we discovered that malachite green is a water-soluble near-infrared luminogen with aggregation-induced emission properties. Importantly, it can be used for living cell nucleus staining in a wash-free manner.
Collapse
Affiliation(s)
- Yuan Luo
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China.
| | - Lihua Zhou
- School of Applied Biology, Shenzhen Institute of Technology, No. 1 Jiangjunmao, Shenzhen, P. R. China
| | - Lili Du
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Yangzi Xie
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China.
| | - Xiang-Yang Lou
- GTS-UAB Research Group, Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lintao Cai
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China.
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, China
| | - Ping Gong
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China.
| | - Pengfei Zhang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China.
| |
Collapse
|
3
|
Keuenhof KS, Kohler V, Broeskamp F, Panagaki D, Speese SD, Büttner S, Höög JL. Nuclear envelope budding and its cellular functions. Nucleus 2023; 14:2178184. [PMID: 36814098 PMCID: PMC9980700 DOI: 10.1080/19491034.2023.2178184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
The nuclear pore complex (NPC) has long been assumed to be the sole route across the nuclear envelope, and under normal homeostatic conditions it is indeed the main mechanism of nucleo-cytoplasmic transport. However, it has also been known that e.g. herpesviruses cross the nuclear envelope utilizing a pathway entitled nuclear egress or envelopment/de-envelopment. Despite this, a thread of observations suggests that mechanisms similar to viral egress may be transiently used also in healthy cells. It has since been proposed that mechanisms like nuclear envelope budding (NEB) can facilitate the transport of RNA granules, aggregated proteins, inner nuclear membrane proteins, and mis-assembled NPCs. Herein, we will summarize the known roles of NEB as a physiological and intrinsic cellular feature and highlight the many unanswered questions surrounding these intriguing nuclear events.
Collapse
Affiliation(s)
| | - Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Filomena Broeskamp
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| | - Dimitra Panagaki
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| | - Sean D. Speese
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S Moody Ave, Portland, OR, 97201, USA
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Johanna L. Höög
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| |
Collapse
|
4
|
Fichtman B, Harel A. The magnified view: from ancient trinkets to single nuclear pore complexes. FEBS Lett 2023; 597:2590-2596. [PMID: 37777820 DOI: 10.1002/1873-3468.14746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023]
Abstract
A journey from the earliest known use of lenses and magnifying glasses in ancient times, through the development of microscopes and towards modern electron microscopy techniques. The evolving technology and improved microscopes enabled the discovery of intracellular organelles, the nucleus and nuclear pore complexes (NPCs). Current advances have led to composite three-dimensional models showing NPC structure in unprecedented detail but relying on the averaging of many images. A complementary approach is field emission scanning electron microscopy providing topographic surface images that are easily and intuitively interpreted by our brain. Recent advances in this technique have made it possible to expose nuclei from human cells and to focus on individual NPCs and their architectural features.
Collapse
Affiliation(s)
- Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Nie Y, Li Y, Liu M, Ma B, Sui X, Chen J, Yu Y, Dong CH. The nucleoporin NUP160 and NUP96 regulate nucleocytoplasmic export of mRNAs and participate in ethylene signaling and response in Arabidopsis. PLANT CELL REPORTS 2023; 42:549-559. [PMID: 36598573 DOI: 10.1007/s00299-022-02976-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis nucleoporin involved in the regulation of ethylene signaling via controlling of nucleocytoplasmic transport of mRNAs. The two-way transport of mRNAs between the nucleus and cytoplasm are controlled by the nuclear pore complex (NPC). In higher plants, the NPC contains at least 30 nucleoporins. The Arabidopsis nucleoporins are involved in various biological processes such as pathogen interaction, nodulation, cold response, flowering, and hormone signaling. However, little is known about the regulatory functions of the nucleoporin NUP160 and NUP96 in ethylene signaling pathway. In the present study, we provided data showing that the Arabidopsis nucleoporin NUP160 and NUP96 participate in ethylene signaling-related mRNAs nucleocytoplasmic transport. The Arabidopsis nucleoporin mutants (nup160, nup96-1, nup96-2) exhibited enhanced ethylene sensitivity. Nuclear qRT-PCR analysis and poly(A)-mRNA in situ hybridization showed that the nucleoporin mutants affected the nucleocytoplasmic transport of all the examined mRNAs, including the ethylene signaling-related mRNAs such as ETR2, ERS1, ERS2, EIN4, CTR1, EIN2, and EIN3. Transcriptome analysis of the nucleoporin mutants provided clues suggesting that the nucleoporin NUP160 and NUP96 may participate in ethylene signaling via various molecular mechanisms. These observations significantly advance our understanding of the regulatory mechanisms of nucleoporin proteins in ethylene signaling and ethylene response.
Collapse
Affiliation(s)
- Yuanyuan Nie
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yang Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Menghui Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Binran Ma
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinying Sui
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiacai Chen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanchong Yu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chun-Hai Dong
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
7
|
Dubey AK, Kumar P, Mandal D, Ravichandiran V, Singh SK. An introduction to dynamic nucleoporins in Leishmania species: Novel targets for tropical-therapeutics. J Parasit Dis 2022; 46:1176-1191. [PMID: 36457769 PMCID: PMC9606170 DOI: 10.1007/s12639-022-01515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/20/2022] [Indexed: 11/28/2022] Open
Abstract
As an ailment, leishmaniasis is still an incessant challenge in neglected tropical diseases and neglected infections of poverty worldwide. At present, the diagnosis and treatment to combat Leishmania tropical infections are not substantial remedies and require advanced & specific research. Therefore, there is a need for a potential novel target to overcome established medicament modalities' limitations in pathogenicity. In this review, we proposed a few ab initio findings in nucleoporins of nuclear pore complex in Leishmania sp. concerning other infectious protists. So, through structural analysis and dynamics studies, we hypothesize the nuclear pore molecular machinery & functionality. The gatekeepers Nups, export of mRNA, mitotic spindle formation are salient features in cellular mechanics and this is regulated by dynamic nucleoporins. Here, diverse studies suggest that Nup93/NIC96, Nup155/Nup144, Mlp1/Mlp2/Tpr of Leishmania Species can be a picked out marker for diagnostic, immune-modulation, and novel drug targets. In silico prediction of nucleoporin-functional interactors such as NUP54/57, RNA helicase, Ubiquitin-protein ligase, Exportin 1, putative T-lymphocyte triggering factor, and 9 uncharacterized proteins suggest few more noble targets. The novel drug targeting to importins/exportins of Leishmania sp. and defining mechanism of Leptomycin-B, SINE compounds, Curcumins, Selinexor can be an arc-light in therapeutics. The essence of the review in Leishmania's nucleoporins is to refocus our research on noble molecular targets for tropical therapeutics. Supplementary Information The online version contains supplementary material available at 10.1007/s12639-022-01515-0.
Collapse
Affiliation(s)
- Amit Kumar Dubey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
- Parasite Immunology Lab, Microbiology Department, Indian Council of Medical Research (ICMR)-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar 800007 India
| | - Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
| | - V. Ravichandiran
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
| | - Shubhankar Kumar Singh
- Parasite Immunology Lab, Microbiology Department, Indian Council of Medical Research (ICMR)-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar 800007 India
| |
Collapse
|
8
|
Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119205. [PMID: 34995711 DOI: 10.1016/j.bbamcr.2021.119205] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the nucleus and the cytoplasm. The interior of NPCs contains densely packed intrinsically disordered FG-nucleoporins (FG-Nups), consequently forming a permeability barrier. This barrier facilitates the selection and specificity of the cargoes that are imported, exported, or shuttled through the NPCs. Recent studies have revealed that FG-Nups undergo the process of liquid-liquid phase separation into liquid droplets. Moreover, these liquid droplets mimic the permeability barrier observed in the interior of NPCs. This review highlights the phase separation of FG-Nups occurring inside the NPCs rooted in the NE. We discuss the phase separation of FG-Nups and compare the different aspects contributing to their phase separation. Furthermore, several diseases caused by the aberrant phase separation of the proteins are examined with respect to NEs. By understanding the fundamental process of phase separation at the nuclear membrane, the review seeks to explore the parameters influencing this phenomenon as well as its importance, ultimately paving the way for better research on the structure-function relationship of biomolecular condensates.
Collapse
Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
| |
Collapse
|
9
|
Chen J, Sui X, Ma B, Li Y, Li N, Qiao L, Yu Y, Dong CH. Arabidopsis CPR5 plays a role in regulating nucleocytoplasmic transport of mRNAs in ethylene signaling pathway. PLANT CELL REPORTS 2022; 41:1075-1085. [PMID: 35201411 DOI: 10.1007/s00299-022-02838-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis CPR5 is involved in regulation of ethylene signaling via two different ways: interacting with the ETR1 N-terminal domains, and controlling nucleocytoplasmic transport of ethylene-related mRNAs. The ETR1 receptor plays a predominant role in ethylene signaling in Arabidopsis thaliana. Previous studies showed that both RTE1 and CPR5 can directly bind to the ETR1 receptor and regulate ethylene signaling. RTE1 was suggested to promote the ETR1 receptor signaling by influencing its conformation, but little is known about the regulatory mechanism of CPR5 in ethylene signaling. In this study, we presented the data showing that both RTE1 and CPR5 bound to the N-terminal domains of ETR1, and regulated ethylene signaling via the ethylene receptor. On the other hand, the research provided evidence indicating that CPR5 could act as a nucleoporin to regulate the ethylene-related mRNAs export out of the nucleus, while RTE1 or its homolog (RTH) had no effect on the nucleocytoplasmic transport of mRNAs. Nuclear qRT-PCR analysis and poly(A)-mRNA in situ hybridization showed that defect of CPR5 restricted nucleocytoplasmic transport of mRNAs. These results advance our understanding of the regulatory mechanism of CPR5 in ethylene signaling.
Collapse
Affiliation(s)
- Jiacai Chen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinying Sui
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Binran Ma
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuetong Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Na Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Longfei Qiao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanchong Yu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chun-Hai Dong
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
10
|
Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell 2022; 185:361-378.e25. [PMID: 34982960 PMCID: PMC8928745 DOI: 10.1016/j.cell.2021.12.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/26/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.
Collapse
Affiliation(s)
- Christopher W Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Christna Ouch
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, San Francisco, San Francisco, CA 94158, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | | | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fei Fang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Daniel Salzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kangkang Song
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Chen Xu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sergey Suslov
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, 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
| | | | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA.
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
11
|
Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore. Proc Natl Acad Sci U S A 2021; 118:2015621118. [PMID: 34504007 DOI: 10.1073/pnas.2015621118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
The in vivo characterization of the exact copy number and the specific function of each composite protein within the nuclear pore complex (NPC) remains both desirable and challenging. Through the implementation of live-cell high-speed super-resolution single-molecule microscopy, we first quantified the native copies of nuclear basket (BSK) proteins (Nup153, Nup50, and Tpr) prior to knocking them down in a highly specific manner via an auxin-inducible degron strategy. Second, we determined the specific roles that BSK proteins play in the nuclear export kinetics of model messenger RNA (mRNA) substrates. Finally, the three-dimensional (3D) nuclear export routes of these mRNA substrates through native NPCs in the absence of specific BSK proteins were obtained and further validated via postlocalization computational simulations. We found that these BSK proteins possess the stoichiometric ratio of 1:1:1 and play distinct roles in the nuclear export of mRNAs within live cells. The absence of Tpr from the NPC predominantly reduces the probability of nuclear mRNAs entering the NPC for export. Complete depletion of Nup153 and Nup50 results in an mRNA nuclear export efficiency decrease of approximately four folds. mRNAs can gain their maximum successful export efficiency as the copy number of Nup153 increased from zero to only half the full complement natively within the NPC. Lastly, the absence of Tpr or Nup153 seems to alter the 3D export routes of mRNAs as they pass through the NPC. However, the removal of Nup50 alone has almost no impact upon mRNA export route and kinetics.
Collapse
|
12
|
Matsuda A, Mofrad MRK. Free energy calculations shed light on the nuclear pore complex's selective barrier nature. Biophys J 2021; 120:3628-3640. [PMID: 34339633 PMCID: PMC8456294 DOI: 10.1016/j.bpj.2021.07.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/27/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022] Open
Abstract
The nuclear pore complex (NPC) is the exclusive gateway for traffic control across the nuclear envelope. Although smaller cargoes (less than 5-9 nm in size) can freely diffuse through the NPC, the passage of larger cargoes is restricted to those accompanied by nuclear transport receptors (NTRs). This selective barrier nature of the NPC is putatively associated with the intrinsically disordered, phenylalanine-glycine repeat-domains containing nucleoporins, termed FG-Nups. The precise mechanism underlying how FG-Nups carry out such an exquisite task at high throughputs has, however, remained elusive and the subject of various hypotheses. From the thermodynamics perspective, free energy analysis can be a way to determine cargo's transportability because the traffic through the NPC must be in the direction of reducing the free energy. In this study, we developed a computational model to evaluate the free energy composed of the conformational entropy of FG-Nups and the energetic gain associated with binding interactions between FG-Nups and NTRs and investigated whether these physical features can be the basis of NPC's selectivity. Our results showed that the reduction in conformational entropy by inserting a cargo into the NPC increased the free energy by an amount substantially greater than the thermal energy (≫kBT), whereas the free energy change was negligible (
Collapse
Affiliation(s)
- Atsushi Matsuda
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California.
| |
Collapse
|
13
|
Sumner MC, Torrisi SB, Brickner DG, Brickner JH. Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates inter-chromosomal movement. eLife 2021; 10:66238. [PMID: 34002694 PMCID: PMC8195609 DOI: 10.7554/elife.66238] [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: 01/05/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Hundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed fractional Brownian motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random sub-diffusion and transient capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.
Collapse
Affiliation(s)
- Michael Chas Sumner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Steven B Torrisi
- Department of Physics, Harvard University, Cambridge, United States
| | - Donna G Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| |
Collapse
|
14
|
Modeling the nucleoporins that form the hairy pores. Biochem Soc Trans 2020; 48:1447-1461. [DOI: 10.1042/bst20190941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/03/2020] [Accepted: 07/16/2020] [Indexed: 11/17/2022]
Abstract
Sitting on the nuclear envelope, nuclear pore complexes (NPCs) control the molecular transport between the nucleus and the cytoplasm. Without definite open or close states, the NPC uses a family of intrinsically disordered nucleoporins called FG-Nups to construct a selective permeability barrier whose functional structure is unclear. Experimental advances have offered high-resolution molecular knowledge of the NPC scaffold and docking of the unfolded FG-Nups, however, the ‘hairy’ barrier structure still appears as blurred lobes even under the state-of-the-art microscopy. Without accurate experimental visualization, the molecular mechanism for the NPC-mediated transport remains a matter of debate. Modeling provides an alternative way to resolve this long-standing mystery. Here, we briefly review different methods employed in modeling the FG-Nups, arranging from all-atom molecular dynamics to mean-field theories. We discuss the advantage and limit of each modeling technique, and summarize the theoretical insights that, despite certain controversy, deepened our understanding of the hairy pore.
Collapse
|
15
|
Paci G, Zheng T, Caria J, Zilman A, Lemke EA. Molecular determinants of large cargo transport into the nucleus. eLife 2020; 9:e55963. [PMID: 32692309 PMCID: PMC7375812 DOI: 10.7554/elife.55963] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/18/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Among the thousands of molecules that cross the NPC, even very large (>15 nm) cargoes such as pathogens, mRNAs and pre-ribosomes can pass the NPC intact. For these cargoes, there is little quantitative understanding of the requirements for their nuclear import, especially the role of multivalent binding to transport receptors via nuclear localisation sequences (NLSs) and the effect of size on import efficiency. Here, we assayed nuclear import kinetics of 30 large cargo models based on four capsid-like particles in the size range of 17-36 nm, with tuneable numbers of up to 240 NLSs. We show that the requirements for nuclear transport can be recapitulated by a simple two-parameter biophysical model that correlates the import flux with the energetics of large cargo transport through the NPC. Together, our results reveal key molecular determinants of large cargo import in cells.
Collapse
Affiliation(s)
- Giulia Paci
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Tiantian Zheng
- Department of Physics, University of TorontoTorontoCanada
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Anton Zilman
- Department of Physics, University of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical Engineering (IBBME), University of TorontoTorontoCanada
| | - Edward A Lemke
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| |
Collapse
|
16
|
Mudumbi KC, Czapiewski R, Ruba A, Junod SL, Li Y, Luo W, Ngo C, Ospina V, Schirmer EC, Yang W. Nucleoplasmic signals promote directed transmembrane protein import simultaneously via multiple channels of nuclear pores. Nat Commun 2020; 11:2184. [PMID: 32366843 PMCID: PMC7198523 DOI: 10.1038/s41467-020-16033-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Roughly 10% of eukaryotic transmembrane proteins are found on the nuclear membrane, yet how such proteins target and translocate to the nucleus remains in dispute. Most models propose transport through the nuclear pore complexes, but a central outstanding question is whether transit occurs through their central or peripheral channels. Using live-cell high-speed super-resolution single-molecule microscopy we could distinguish protein translocation through the central and peripheral channels, finding that most inner nuclear membrane proteins use only the peripheral channels, but some apparently extend intrinsically disordered domains containing nuclear localization signals into the central channel for directed nuclear transport. These nucleoplasmic signals are critical for central channel transport as their mutation blocks use of the central channels; however, the mutated proteins can still complete their translocation using only the peripheral channels, albeit at a reduced rate. Such proteins can still translocate using only the peripheral channels when central channel is blocked, but blocking the peripheral channels blocks translocation through both channels. This suggests that peripheral channel transport is the default mechanism that was adapted in evolution to include aspects of receptor-mediated central channel transport for directed trafficking of certain membrane proteins.
Collapse
Affiliation(s)
- Krishna C Mudumbi
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.
| | - Rafal Czapiewski
- The Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Yichen Li
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Wangxi Luo
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Christina Ngo
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Valentina Ospina
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Eric C Schirmer
- The Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
| |
Collapse
|
17
|
Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell 2020; 177:1384-1403. [PMID: 31150619 DOI: 10.1016/j.cell.2019.05.016] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field.
Collapse
Affiliation(s)
- Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
18
|
Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
Collapse
Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| |
Collapse
|
19
|
Huang K, Tagliazucchi M, Park SH, Rabin Y, Szleifer I. Nanocompartmentalization of the Nuclear Pore Lumen. Biophys J 2019; 118:219-231. [PMID: 31839259 DOI: 10.1016/j.bpj.2019.11.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/23/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
The nuclear pore complex (NPC) employs the intrinsically disordered regions (IDRs) from a family of phenylalanine-glycine-rich nucleoporins (FG-Nups) to control nucleocytoplasmic transport. It has been a long-standing mystery how the IDR-mediated mass exchange can be rapid yet selective. Here, we use a computational microscope to show that nanocompartmentalization of IDR subdomains leads to a remarkably elaborate gating structure as programmed by the amino acid sequences. In particular, we reveal a heterogeneous permeability barrier that combines an inner ring barrier with two vestibular condensates. Throughout the NPC, we find a polarized electrostatic potential and a diffuse thermoreversible FG network featuring mosaic FG territories with low FG-FG pairing fraction. Our theoretical anatomy of the central transporter sheds light into the sequence-structure-function relationship of the FG-Nups and provides a picture of nucleocytoplasmic mass exchange that allows a reconciliation of transport efficiency and specificity.
Collapse
Affiliation(s)
- Kai Huang
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois
| | - Mario Tagliazucchi
- DQIAQF and INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sung Hyun Park
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois
| | - Yitzhak Rabin
- Department of Physics and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Department of Chemistry, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.
| |
Collapse
|
20
|
Khalaf B, Roncador A, Pischedda F, Casini A, Thomas S, Piccoli G, Kiebler M, Macchi P. Ankyrin-G induces nucleoporin Nup358 to associate with the axon initial segment of neurons. J Cell Sci 2019; 132:jcs.222802. [PMID: 31427429 DOI: 10.1242/jcs.222802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Nup358 (also known as RanBP2) is a member of the large nucleoporin family that constitutes the nuclear pore complex. Depending on the cell type and the physiological state, Nup358 interacts with specific partner proteins and influences distinct mechanisms independent of its role in nucleocytoplasmic transport. Here, we provide evidence that Nup358 associates selectively with the axon initial segment (AIS) of mature neurons, mediated by the AIS scaffold protein ankyrin-G (AnkG, also known as Ank3). The N-terminus of Nup358 is demonstrated to be sufficient for its localization at the AIS. Further, we show that Nup358 is expressed as two isoforms, one full-length and another shorter form of Nup358. These isoforms differ in their subcellular distribution in neurons and expression level during neuronal development. Overall, the present study highlights an unprecedented localization of Nup358 within the AIS and suggests its involvement in neuronal function.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Bouchra Khalaf
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Alessandro Roncador
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Francesca Pischedda
- Dulbecco Telethon Laboratory of Biology of Synapses, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Antonio Casini
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Sabine Thomas
- Department for Cell Biology, Biomedical Center, Medical Faculty, Ludwig-Maximilian University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Giovanni Piccoli
- Dulbecco Telethon Laboratory of Biology of Synapses, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| | - Michael Kiebler
- Department for Cell Biology, Biomedical Center, Medical Faculty, Ludwig-Maximilian University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy
| |
Collapse
|
21
|
Abstract
The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo-electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
Collapse
Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| |
Collapse
|
22
|
The path of pre-ribosomes through the nuclear pore complex revealed by electron tomography. Nat Commun 2019; 10:497. [PMID: 30700705 PMCID: PMC6353910 DOI: 10.1038/s41467-019-08342-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 12/17/2018] [Indexed: 01/24/2023] Open
Abstract
Determining the path of single ribonucleoprotein (RNP) particles through the 100 nm-wide nuclear pore complex (NPC) by fluorescence microscopy remains challenging due to resolution limitation and RNP labeling constraints. By using high-pressure freezing and electron tomography, here we captured snapshots of the translocation of native RNP particles through NPCs in yeast and analyzed their trajectory at nanometer-scale resolution. Morphological and functional analyses indicate that these particles mostly correspond to pre-ribosomes. They are detected in 5–6% of the NPCs, with no apparent bias for NPCs adjacent to the nucleolus. Their path closely follows the central axis of the NPC through the nuclear and inner rings, but diverges at the cytoplasmic ring, suggesting interactions with the cytoplasmic nucleoporins. By applying a probabilistic queueing model to our data, we estimated that the dwell time of pre-ribosomes in the yeast NPC is ~90 ms. These data reveal distinct steps of pre-ribosome translocation through the NPC. Large protein complexes and ribonucleoprotein particles (RNPs) such as pre-ribosomes are transported from the nucleus to the cytoplasm through the nuclear pore complex (NPC). Here the authors use ultrafast freezing and electron tomography to catch snapshots of native RNPs crossing the NPC and estimate their transit time using a probabilistic model.
Collapse
|
23
|
The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study. Int J Mol Sci 2019; 20:ijms20030596. [PMID: 30704069 PMCID: PMC6387328 DOI: 10.3390/ijms20030596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/16/2023] Open
Abstract
Nuclear pore complexes (NPCs) are large protein complexes embedded in the nuclear envelope separating the cytoplasm from the nucleoplasm in eukaryotic cells. They function as selective gates for the transport of molecules in and out of the nucleus. The inner wall of the NPC is coated with intrinsically disordered proteins rich in phenylalanine-glycine repeats (FG-repeats), which are responsible for the intriguing selectivity of NPCs. The phosphorylation state of the FG-Nups is controlled by kinases and phosphatases. In the current study, we extended our one-bead-per-amino-acid (1BPA) model for intrinsically disordered proteins to account for phosphorylation. With this, we performed molecular dynamics simulations to probe the effect of phosphorylation on the Stokes radius of isolated FG-Nups, and on the structure and transport properties of the NPC. Our results indicate that phosphorylation causes a reduced attraction between the residues, leading to an extension of the FG-Nups and the formation of a significantly less dense FG-network inside the NPC. Furthermore, our simulations show that upon phosphorylation, the transport rate of inert molecules increases, while that of nuclear transport receptors decreases, which can be rationalized in terms of modified hydrophobic, electrostatic, and steric interactions. Altogether, our models provide a molecular framework to explain how extensive phosphorylation of FG-Nups decreases the selectivity of the NPC.
Collapse
|
24
|
Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M. In situ architecture of the algal nuclear pore complex. Nat Commun 2018; 9:2361. [PMID: 29915221 PMCID: PMC6006428 DOI: 10.1038/s41467-018-04739-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.
Collapse
Affiliation(s)
- Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Center for Structural Systems Biology (CSSB), Notkestrasse 85, 22607, Hamburg, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Daniela Strenkert
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Patrice A Salomé
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| |
Collapse
|
25
|
Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy. Proc Natl Acad Sci U S A 2018; 115:E3969-E3977. [PMID: 29632211 DOI: 10.1073/pnas.1719398115] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.
Collapse
|
26
|
Abstract
Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.
Collapse
|
27
|
Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS NANO 2018; 12:1508-1518. [PMID: 29350911 PMCID: PMC5834394 DOI: 10.1021/acsnano.7b08044] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.
Collapse
Affiliation(s)
- Patrick D. Ellis Fisher
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - Luke K. Davis
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| |
Collapse
|
28
|
Reid KM, Sunanda P, Raghothama S, Krishnan V. Ensemble characterization of an intrinsically disordered FG-Nup peptide and its F>A mutant in DMSO-d6. Biopolymers 2017; 108. [DOI: 10.1002/bip.23036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/13/2017] [Accepted: 06/26/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry; California State University; Fresno California 93740
| | - Punnepalli Sunanda
- NMR Research Centre, Indian Institute of Science; Bangalore 560012 India
| | - S. Raghothama
- NMR Research Centre, Indian Institute of Science; Bangalore 560012 India
| | - V.V. Krishnan
- Department of Chemistry; California State University; Fresno California 93740
- Department of Pathology and Laboratory Medicine, University of California School of Medicine; Davis California 95616
| |
Collapse
|
29
|
Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
Collapse
Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
| |
Collapse
|
30
|
Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z. Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. J Phys Chem B 2017; 121:3871-3881. [PMID: 28291359 DOI: 10.1021/acs.jpcb.7b00672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle time scales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network. Here we present two examples to illustrate the challenges and techniques involved in integrating structural data into stochastic simulations. First, a tomographic reconstruction of Saccharomyces cerevisiae is used to construct the geometry of an entire cell through which a simple stochastic model of an inducible genetic switch is studied. Second, a tomogram of the nuclear periphery in a HeLa cell is converted directly to the simulation geometry through which we study the effects of cellular substructure on the stochastic dynamics of gene repression. These simple chemical models allow us to illustrate how to build whole-cell simulations using cryo-ET derived geometry and the challenges involved in such a process.
Collapse
Affiliation(s)
- Tyler M Earnest
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| | - Reika Watanabe
- Department of Chemistry and Biochemistry, University of California , San Diego, California, United States
| | - John E Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| | - Julia Mahamid
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry , Munich, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry , Munich, Germany
| | - Elizabeth Villa
- Department of Chemistry and Biochemistry, University of California , San Diego, California, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| |
Collapse
|
31
|
Sagulenko E, Nouwens A, Webb RI, Green K, Yee B, Morgan G, Leis A, Lee KC, Butler MK, Chia N, Pham UTP, Lindgreen S, Catchpole R, Poole AM, Fuerst JA. Nuclear Pore-Like Structures in a Compartmentalized Bacterium. PLoS One 2017; 12:e0169432. [PMID: 28146565 PMCID: PMC5287468 DOI: 10.1371/journal.pone.0169432] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/02/2016] [Indexed: 01/02/2023] Open
Abstract
Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.
Collapse
Affiliation(s)
- Evgeny Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard I. Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin Yee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Garry Morgan
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Leis
- CSIRO - Livestock Industries, Australian Animal Health Laboratory, Biosecurity Microscopy Facility (ABMF), Geelong, Victoria, Australia
| | - Kuo-Chang Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Margaret K. Butler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Chia
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Uyen Thi Phuong Pham
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Stinus Lindgreen
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ryan Catchpole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Anthony M. Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Allan Wilson Centre, University of Canterbury, Christchurch, New Zealand
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John A. Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| |
Collapse
|
32
|
Ando D, Gopinathan A. Cooperative Interactions between Different Classes of Disordered Proteins Play a Functional Role in the Nuclear Pore Complex of Baker's Yeast. PLoS One 2017; 12:e0169455. [PMID: 28068389 PMCID: PMC5222603 DOI: 10.1371/journal.pone.0169455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 12/16/2016] [Indexed: 12/02/2022] Open
Abstract
Nucleocytoplasmic transport is highly selective, efficient, and is regulated by a poorly understood mechanism involving hundreds of disordered FG nucleoporin proteins (FG nups) lining the inside wall of the nuclear pore complex (NPC). Previous research has concluded that FG nups in Baker's yeast (S. cerevisiae) are present in a bimodal distribution, with the "Forest Model" classifying FG nups as either di-block polymer like "trees" or single-block polymer like "shrubs". Using a combination of coarse-grained modeling and polymer brush modeling, the function of the di-block FG nups has previously been hypothesized in the Di-block Copolymer Brush Gate (DCBG) model to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC. In this manuscript we work to extend the original DCBG model by first performing coarse grained simulations of the single-block FG nups which confirm that they have a single block polymer structure rather than the di-block structure of tree nups. Our molecular simulations also demonstrate that these single-block FG nups are likely cohesive, compact, collapsed coil polymers, implying that these FG nups are generally localized to their grafting location within the NPC. We find that adding a layer of single-block FG nups to the DCBG model increases the range of cargo sizes which are able to translocate the pore through a cooperative effect involving single-block and di-block FG nups. This effect can explain the puzzling connection between single-block FG nup deletion mutants in S. cerevisiae and the resulting failure of certain large cargo transport through the NPC. Facilitation of large cargo transport via single-block and di-block FG nup cooperativity in the nuclear pore could provide a model mechanism for designing future biomimetic pores of greater applicability.
Collapse
Affiliation(s)
- David Ando
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Joint BioEnergy Institute, Emeryville, CA, United States of America
| | - Ajay Gopinathan
- Department of Physics, University of California, Merced, CA, United States of America
| |
Collapse
|
33
|
Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 2016; 167:1215-1228.e25. [PMID: 27839866 DOI: 10.1016/j.cell.2016.10.028] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/20/2016] [Accepted: 10/14/2016] [Indexed: 12/28/2022]
Abstract
The last steps in mRNA export and remodeling are performed by the Nup82 complex, a large conserved assembly at the cytoplasmic face of the nuclear pore complex (NPC). By integrating diverse structural data, we have determined the molecular architecture of the native Nup82 complex at subnanometer precision. The complex consists of two compositionally identical multiprotein subunits that adopt different configurations. The Nup82 complex fits into the NPC through the outer ring Nup84 complex. Our map shows that this entire 14-MDa Nup82-Nup84 complex assembly positions the cytoplasmic mRNA export factor docking sites and messenger ribonucleoprotein (mRNP) remodeling machinery right over the NPC's central channel rather than on distal cytoplasmic filaments, as previously supposed. We suggest that this configuration efficiently captures and remodels exporting mRNP particles immediately upon reaching the cytoplasmic side of the NPC.
Collapse
Affiliation(s)
| | - Seung Joong Kim
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Paula Upla
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Riccardo Pellarin
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, 75015 Paris, France
| | - Michael Gagnon
- Département de Biochimie et Médecine Moléculaire, University of Montréal, Montréal, QC H3C3J7, Canada
| | - Ilan E Chemmama
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Rosemary Williams
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - William J Rice
- Simons Electron Microscopy Center at New York Structural Biology Center, New York, NY 10027, USA
| | - David L Stokes
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, University of Montréal, Montréal, QC H3C3J7, Canada
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
34
|
Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. Simple rules for passive diffusion through the nuclear pore complex. J Cell Biol 2016; 215:57-76. [PMID: 27697925 PMCID: PMC5057280 DOI: 10.1083/jcb.201601004] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 09/06/2016] [Indexed: 02/07/2023] Open
Abstract
Passive macromolecular diffusion through nuclear pore complexes is thought to decrease dramatically beyond ∼40 kD. Using time-resolved fluorescence microscopy and Brownian dynamics simulations, Timney et al. show that this barrier is in fact much softer, decreasing along a continuum. Passive macromolecular diffusion through nuclear pore complexes (NPCs) is thought to decrease dramatically beyond a 30–60-kD size threshold. Using thousands of independent time-resolved fluorescence microscopy measurements in vivo, we show that the NPC lacks such a firm size threshold; instead, it forms a soft barrier to passive diffusion that intensifies gradually with increasing molecular mass in both the wild-type and mutant strains with various subsets of phenylalanine-glycine (FG) domains and different levels of baseline passive permeability. Brownian dynamics simulations replicate these findings and indicate that the soft barrier results from the highly dynamic FG repeat domains and the diffusing macromolecules mutually constraining and competing for available volume in the interior of the NPC, setting up entropic repulsion forces. We found that FG domains with exceptionally high net charge and low hydropathy near the cytoplasmic end of the central channel contribute more strongly to obstruction of passive diffusion than to facilitated transport, revealing a compartmentalized functional arrangement within the NPC.
Collapse
Affiliation(s)
- Benjamin L Timney
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065
| | - Barak Raveh
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158
| | - Roxana Mironska
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065
| | - Jill M Trivedi
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158
| | - Daniel Russel
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065
| |
Collapse
|
35
|
Abstract
The nuclear envelope is a unique topological structure formed by lipid membranes in eukaryotic cells. Unlike other membrane structures, the nuclear envelope comprises two concentric membrane shells fused at numerous sites with toroid-shaped pores that impart a "geometric" genus on the order of thousands. Despite the intriguing architecture and vital biological functions of the nuclear membranes, how they achieve and maintain such a unique arrangement remains unknown. Here, we used the theory of elasticity and differential geometry to analyze the equilibrium shape and stability of this structure. Our results show that modest in- and out-of-plane stresses present in the membranes not only can define the pore geometry, but also provide a mechanism for destabilizing membranes beyond a critical size and set the stage for the formation of new pores. Our results suggest a mechanism wherein nanoscale buckling instabilities can define the global topology of a nuclear envelope-like structure.
Collapse
|
36
|
Abstract
Nuclear pore complexes (NPCs) perforate the nuclear envelope and serve as the primary transport gates for molecular exchange between nucleus and cytoplasm. Stripping the megadalton complex down to its most essential organizational elements, one can divide the NPC into scaffold components and the disordered elements attached to them that generate a selective barrier between compartments. These structural elements exhibit flexibility, which may hold a clue in understanding NPC assembly and function. Here we review the current status of NPC research with a focus on the functional implications of its structural and compositional heterogeneity.
Collapse
|
37
|
Moussavi-Baygi R, Mofrad MRK. Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex. Sci Rep 2016; 6:29991. [PMID: 27470900 PMCID: PMC4965864 DOI: 10.1038/srep29991] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/24/2016] [Indexed: 11/23/2022] Open
Abstract
Conformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in, and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center, and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC, and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in, and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores.
Collapse
Affiliation(s)
- R. Moussavi-Baygi
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - M. R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
38
|
Palazzo AF, Truong M. Single particle imaging of mRNAs crossing the nuclear pore: Surfing on the edge. Bioessays 2016; 38:744-50. [DOI: 10.1002/bies.201600038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Mathew Truong
- Department of Biochemistry; University of Toronto; Toronto ON Canada
| |
Collapse
|
39
|
Hoelz A, Glavy JS, Beck M. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up. Nat Struct Mol Biol 2016; 23:624-30. [PMID: 27273515 DOI: 10.1038/nsmb.3244] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/13/2016] [Indexed: 01/16/2023]
Abstract
Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.
Collapse
Affiliation(s)
- André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Joseph S Glavy
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| |
Collapse
|
40
|
Zahn R, Osmanović D, Ehret S, Araya Callis C, Frey S, Stewart M, You C, Görlich D, Hoogenboom BW, Richter RP. A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies. eLife 2016; 5. [PMID: 27058170 PMCID: PMC4874776 DOI: 10.7554/elife.14119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.
Collapse
Affiliation(s)
- Raphael Zahn
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | - Dino Osmanović
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom.,Department of Physics, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Severin Ehret
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | | | - Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Changjiang You
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Ralf P Richter
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain.,Laboratory of Interdisciplinary Physics, University Grenoble Alpes - CNRS, Grenoble, France.,Max-Planck-Institute for Intelligent Systems, Stuttgart, Germany
| |
Collapse
|
41
|
Musser SM, Grünwald D. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches. J Mol Biol 2016; 428:2091-119. [PMID: 26944195 DOI: 10.1016/j.jmb.2016.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/05/2016] [Accepted: 02/17/2016] [Indexed: 01/06/2023]
Abstract
Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.
Collapse
Affiliation(s)
- Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, 1114 TAMU, College Station, TX 77843, USA.
| | - David Grünwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
42
|
Energetics of Transport through the Nuclear Pore Complex. PLoS One 2016; 11:e0148876. [PMID: 26894898 PMCID: PMC4764519 DOI: 10.1371/journal.pone.0148876] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/25/2016] [Indexed: 01/30/2023] Open
Abstract
Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered proteins that line the central channel of the NPC and the transporting cargoes is the determining factor, but the exact mechanism of transport is yet unknown. Here, we use coarse-grained molecular dynamics simulations to quantify the energy barrier that has to be overcome for molecules to pass through the NPC. We focus on two aspects of transport. First, the passive transport of model cargo molecules with different sizes is studied and the size selectivity feature of the NPC is investigated. Our results show that the transport probability of cargoes is significantly reduced when they are larger than ∼5 nm in diameter. Secondly, we show that incorporating hydrophobic binding spots on the surface of the cargo effectively decreases the energy barrier of the pore. Finally, a simple transport model is proposed which characterizes the energy barrier of the NPC as a function of diameter and hydrophobicity of the transporting particles.
Collapse
|
43
|
Asakawa H, Yang HJ, Hiraoka Y, Haraguchi T. Virtual Nuclear Envelope Breakdown and Its Regulators in Fission Yeast Meiosis. Front Cell Dev Biol 2016; 4:5. [PMID: 26870731 PMCID: PMC4735346 DOI: 10.3389/fcell.2016.00005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/15/2016] [Indexed: 11/24/2022] Open
Abstract
Ran, a small GTPase, is required for the spindle formation and nuclear envelope (NE) formation. After NE breakdown (NEBD) during mitosis in metazoan cells, the Ran-GTP gradient across the NE is lost and Ran-GTP becomes concentrated around chromatin, thus affecting the stability of microtubules and promoting the assembly of spindle microtubules and segregation of chromosomes. Mitosis in which chromosomes are segregated subsequent to NEBD is called “open mitosis.” In contrast, many fungi undergo a process termed “closed mitosis” in which chromosome segregation and spindle formation occur without NEBD. Although the fission yeast Schizosaccharomyces pombe undergoes a closed mitosis, it exhibits a short period during meiosis (anaphase of the second meiosis; called “anaphase II”) when nuclear and cytoplasmic proteins are mixed in the presence of intact NE and nuclear pore complexes (NPC). This “virtual” nuclear envelope breakdown (vNEBD) involves changes in the localization of RanGAP1, an activator of Ran-GTP hydrolysis. Recently, Nup132, a component of the structural core Nup107-160 subcomplex of the NPC, has been shown to be involved in the maintenance of the nuclear cytoplasmic barrier in yeast meiosis. In this review, we highlight the possible roles of RanGAP1 and Nup132 in vNEBD and discuss the biological significance of vNEBD in S. pombe meiosis.
Collapse
Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University Suita, Japan
| | - Hui-Ju Yang
- Graduate School of Frontier Biosciences, Osaka University Suita, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; Cell Biology Group, Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobe, Japan; Graduate School of Science, Department of Biology, Osaka UniversityToyonaka, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; Cell Biology Group, Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobe, Japan; Graduate School of Science, Department of Biology, Osaka UniversityToyonaka, Japan
| |
Collapse
|
44
|
Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy. J Mol Biol 2016; 428:2001-10. [PMID: 26791760 PMCID: PMC4898182 DOI: 10.1016/j.jmb.2016.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/02/2015] [Accepted: 01/06/2016] [Indexed: 11/21/2022]
Abstract
Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC. Overview over three-dimensional electron microscopic analysis of the nuclear pore complex. Review of recent integrative structural biology studies of the nuclear pore complex scaffold architecture.
Collapse
|
45
|
Complex Commingling: Nucleoporins and the Spindle Assembly Checkpoint. Cells 2015; 4:706-25. [PMID: 26540075 PMCID: PMC4695854 DOI: 10.3390/cells4040706] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/12/2015] [Accepted: 10/28/2015] [Indexed: 12/14/2022] Open
Abstract
The segregation of the chromosomes during mitosis is an important process, in which the replicated DNA content is properly allocated into two daughter cells. To ensure their genomic integrity, cells present an essential surveillance mechanism known as the spindle assembly checkpoint (SAC), which monitors the bipolar attachment of the mitotic spindle to chromosomes to prevent errors that would result in chromosome mis-segregation and aneuploidy. Multiple components of the nuclear pore complex (NPC), a gigantic protein complex that forms a channel through the nuclear envelope to allow nucleocytoplasmic exchange of macromolecules, were shown to be critical for faithful cell division and implicated in the regulation of different steps of the mitotic process, including kinetochore and spindle assembly as well as the SAC. In this review, we will describe current knowledge about the interconnection between the NPC and the SAC in an evolutional perspective, which primarily relies on the two mitotic checkpoint regulators, Mad1 and Mad2. We will further discuss the role of NPC constituents, the nucleoporins, in kinetochore and spindle assembly and the formation of the mitotic checkpoint complex during mitosis and interphase.
Collapse
|
46
|
Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A. Architecture of the fungal nuclear pore inner ring complex. Science 2015; 350:56-64. [PMID: 26316600 DOI: 10.1126/science.aac9176] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022]
Abstract
The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.
Collapse
Affiliation(s)
- Tobias Stuwe
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Christopher J Bley
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Karsten Thierbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Stefan Petrovic
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Sandra Schilbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel J Mayo
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Thibaud Perriches
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Emily J Rundlet
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Young E Jeon
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Leslie N Collins
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ferdinand M Huber
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel H Lin
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica Fischer
- Biochemistry Center of Heidelberg University, 69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, 69120 Heidelberg, Germany
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA.
| |
Collapse
|
47
|
Dickmanns A, Kehlenbach RH, Fahrenkrog B. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 320:171-233. [PMID: 26614874 DOI: 10.1016/bs.ircmb.2015.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.
Collapse
Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
| |
Collapse
|
48
|
Kelley K, Knockenhauer KE, Kabachinski G, Schwartz TU. Atomic structure of the Y complex of the nuclear pore. Nat Struct Mol Biol 2015; 22:425-431. [PMID: 25822992 PMCID: PMC4424061 DOI: 10.1038/nsmb.2998] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/05/2015] [Indexed: 01/08/2023]
Abstract
The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.
Collapse
Affiliation(s)
- Kotaro Kelley
- Department of Biology, Massachusetts Institute of Technology Cambridge, MA USA
| | | | - Greg Kabachinski
- Department of Biology, Massachusetts Institute of Technology Cambridge, MA USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology Cambridge, MA USA
| |
Collapse
|
49
|
Gay S, Foiani M. Nuclear envelope and chromatin, lock and key of genome integrity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 317:267-330. [PMID: 26008788 DOI: 10.1016/bs.ircmb.2015.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
More than as an inert separation between the inside and outside of the nucleus, the nuclear envelope (NE) constitutes an active toll, which controls the import and export of molecules, and also a hub for a diversity of genomic processes, such as transcription, DNA repair, and chromatin dynamics. Proteins localized at the inner surface of the NE (such as lamins, nuclear pore proteins, lamin-associated proteins) interact with chromatin in a dynamic manner, contributing to the establishment of topological domains. In this review, we address the complex interplay between chromatin and NE. We discuss the divergence of this cross talk during evolution and comment both on the current established models and the most recent findings. In particular, we focus our attention on how the NE cooperates with chromatin in protecting the genome integrity.
Collapse
Affiliation(s)
- Sophie Gay
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy; Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
50
|
Quantifying nucleoporin stoichiometry inside single nuclear pore complexes in vivo. Sci Rep 2015; 5:9372. [PMID: 25797490 PMCID: PMC4894440 DOI: 10.1038/srep09372] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/02/2015] [Indexed: 11/25/2022] Open
Abstract
The nuclear pore complex (NPC) is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring-scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. NPCs are composed of ~30 different nucleoporins (Nups), averaged at 8, 16 or 32 copies per NPC. This estimate has not been confirmed for individual NPCs in living cells due to the inherent difficulty of counting proteins inside single supramolecular complexes. Here we used single-molecule SPEED microscopy to directly count the copy-number of twenty-four different Nups within individual NPCs of live yeast, and found agreement as well as significant deviation from previous estimates. As expected, we counted 8 copies of four peripheral Nups and 16 copies of fourteen scaffold Nups. Unexpectedly, we counted a maximum of 16 copies of Nsp1 and Nic96, rather than 32 as previously estimated; and found only 10–15 copies of six other Nups, rather than 8 or 16 copies as expected. This in situ molecular-counting technology can test structure-function models of NPCs and other supramolecular structures in cells.
Collapse
|