1
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Álvarez-Guerra I, Block E, Broeskamp F, Gabrijelčič S, Infant T, de Ory A, Habernig L, Andréasson C, Levine TP, Höög JL, Büttner S. LDO proteins and Vac8 form a vacuole-lipid droplet contact site to enable starvation-induced lipophagy in yeast. Dev Cell 2024; 59:759-775.e5. [PMID: 38354739 DOI: 10.1016/j.devcel.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/15/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Lipid droplets (LDs) are fat storage organelles critical for energy and lipid metabolism. Upon nutrient exhaustion, cells consume LDs via gradual lipolysis or via lipophagy, the en bloc uptake of LDs into the vacuole. Here, we show that LDs dock to the vacuolar membrane via a contact site that is required for lipophagy in yeast. The LD-localized LDO proteins carry an intrinsically disordered region that directly binds vacuolar Vac8 to form vCLIP, the vacuolar-LD contact site. Nutrient limitation drives vCLIP formation, and its inactivation blocks lipophagy, resulting in impaired caloric restriction-induced longevity. We establish a functional link between lipophagy and microautophagy of the nucleus, both requiring Vac8 to form respective contact sites upon metabolic stress. In sum, we identify the tethering machinery of vCLIP and find that Vac8 provides a platform for multiple and competing contact sites associated with autophagy.
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Affiliation(s)
- Irene Álvarez-Guerra
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Emma Block
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Filomena Broeskamp
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sonja Gabrijelčič
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Terence Infant
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Ana de Ory
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Tim P Levine
- UCL Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
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2
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Nešić N, Heiligenstein X, Zopf L, Blüml V, Keuenhof KS, Wagner M, Höög JL, Qi H, Li Z, Tsaramirsis G, Peddie CJ, Stojmenović M, Walter A. Automated segmentation of cell organelles in volume electron microscopy using deep learning. Microsc Res Tech 2024. [PMID: 38501891 DOI: 10.1002/jemt.24548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/05/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Recent advances in computing power triggered the use of artificial intelligence in image analysis in life sciences. To train these algorithms, a large enough set of certified labeled data is required. The trained neural network is then capable of producing accurate instance segmentation results that will then need to be re-assembled into the original dataset: the entire process requires substantial expertise and time to achieve quantifiable results. To speed-up the process, from cell organelle detection to quantification across electron microscopy modalities, we propose a deep-learning based approach for fast automatic outline segmentation (FAMOUS), that involves organelle detection combined with image morphology, and 3D meshing to automatically segment, visualize and quantify cell organelles within volume electron microscopy datasets. From start to finish, FAMOUS provides full segmentation results within a week on previously unseen datasets. FAMOUS was showcased on a HeLa cell dataset acquired using a focused ion beam scanning electron microscope, and on yeast cells acquired by transmission electron tomography. RESEARCH HIGHLIGHTS: Introducing a rapid, multimodal machine-learning workflow for the automatic segmentation of 3D cell organelles. Successfully applied to a variety of volume electron microscopy datasets and cell lines. Outperforming manual segmentation methods in time and accuracy. Enabling high-throughput quantitative cell biology.
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Affiliation(s)
- Nebojša Nešić
- Department of Computer Science and Electrical Engineering, Singidunum University, Belgrade, Serbia
| | | | - Lydia Zopf
- Austrian BioImaging, Vienna BioCenter Core Facilities, Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in the AUVA Trauma Research Center, Vienna, Austria
| | - Valentin Blüml
- Austrian BioImaging, Vienna BioCenter Core Facilities, Vienna, Austria
| | - Katharina S Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Michael Wagner
- Centre for Optical Technologies, Aalen University, Aalen, Germany
| | - Johanna L Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Heng Qi
- Department of Computer Science, Dalian University of Technology, Dalian, China
| | - Zhiyang Li
- Department of Computer Science, Dalian Maritime University, Dalian, China
| | - Georgios Tsaramirsis
- Faculty of Computer Information, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | | | - Miloš Stojmenović
- Department of Computer Science and Electrical Engineering, Singidunum University, Belgrade, Serbia
| | - Andreas Walter
- Centre for Optical Technologies, Aalen University, Aalen, Germany
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3
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Kohler V, Kohler A, Berglund LL, Hao X, Gersing S, Imhof A, Nyström T, Höög JL, Ott M, Andréasson C, Büttner S. Nuclear Hsp104 safeguards the dormant translation machinery during quiescence. Nat Commun 2024; 15:315. [PMID: 38182580 PMCID: PMC10770042 DOI: 10.1038/s41467-023-44538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
The resilience of cellular proteostasis declines with age, which drives protein aggregation and compromises viability. The nucleus has emerged as a key quality control compartment that handles misfolded proteins produced by the cytosolic protein biosynthesis system. Here, we find that age-associated metabolic cues target the yeast protein disaggregase Hsp104 to the nucleus to maintain a functional nuclear proteome during quiescence. The switch to respiratory metabolism and the accompanying decrease in translation rates direct cytosolic Hsp104 to the nucleus to interact with latent translation initiation factor eIF2 and to suppress protein aggregation. Hindering Hsp104 from entering the nucleus in quiescent cells results in delayed re-entry into the cell cycle due to compromised resumption of protein synthesis. In sum, we report that cytosolic-nuclear partitioning of the Hsp104 disaggregase is a critical mechanism to protect the latent protein synthesis machinery during quiescence in yeast, ensuring the rapid restart of translation once nutrients are replenished.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Department of Molecular Biology, Umeå University, 90187, Umeå, Sweden
| | - Andreas Kohler
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Sarah Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 1165, Copenhagen, Denmark
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig Maximilian University of Munich, 82152, Planegg-Martinsried, Germany
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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5
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Vazquez‐Calvo C, Kohler V, Höög JL, Büttner S, Ott M. Newly imported proteins in mitochondria are particularly sensitive to aggregation. Acta Physiol (Oxf) 2023; 238:e13985. [PMID: 37171464 PMCID: PMC10909475 DOI: 10.1111/apha.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
AIM A functional proteome is essential for life and maintained by protein quality control (PQC) systems in the cytosol and organelles. Protein aggregation is an indicator of a decline of PQC linked to aging and disease. Mitochondrial PQC is critical to maintain mitochondrial function and thus cellular fitness. How mitochondria handle aggregated proteins is not well understood. Here we tested how the metabolic status impacts on formation and clearance of aggregates within yeast mitochondria and assessed which proteins are particularly sensitive to denaturation. METHODS Confocal microscopy, electron microscopy, immunoblotting and genetics were applied to assess mitochondrial aggregate handling in response to heat shock and ethanol using the mitochondrial disaggregase Hsp78 as a marker for protein aggregates. RESULTS We show that aggregates formed upon heat or ethanol stress with different dynamics depending on the metabolic state. While fermenting cells displayed numerous small aggregates that coalesced into one large foci that was resistant to clearance, respiring cells showed less aggregates and cleared these aggregates more efficiently. Acute inhibition of mitochondrial translation had no effect, while preventing protein import into mitochondria by inhibition of cytosolic translation prevented aggregate formation. CONCLUSION Collectively, our data show that the metabolic state of the cells impacts the dynamics of aggregate formation and clearance, and that mainly newly imported and not yet assembled proteins are prone to form aggregates. Because mitochondrial functionality is crucial for cellular metabolism, these results highlight the importance of efficient protein biogenesis to maintain the mitochondrial proteome operational during metabolic adaptations and cellular stress.
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Affiliation(s)
- Carmela Vazquez‐Calvo
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Johanna L. Höög
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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6
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Schneider KL, Ahmadpour D, Keuenhof KS, Eisele-Bürger AM, Berglund LL, Eisele F, Babazadeh R, Höög JL, Nyström T, Widlund PO. Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates. J Biol Chem 2022; 298:102476. [PMID: 36096201 PMCID: PMC9636550 DOI: 10.1016/j.jbc.2022.102476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
The accumulation of misfolded proteins is a hallmark of aging and many neurodegenerative diseases, making it important to understand how the cellular machinery recognizes and processes such proteins. A key question in this respect is whether misfolded proteins are handled in a similar way regardless of their genetic origin. To approach this question, we compared how three different misfolded proteins, guk1-7, gus1-3, and pro3-1, are handled by the cell. We show that all three are nontoxic, even though highly overexpressed, highlighting their usefulness in analyzing the cellular response to misfolding in the absence of severe stress. We found significant differences between the aggregation and disaggregation behavior of the misfolded proteins. Specifically, gus1-3 formed some aggregates that did not efficiently recruit the protein disaggregase Hsp104 and did not colocalize with the other misfolded reporter proteins. Strikingly, while all three misfolded proteins generally coaggregated and colocalized to specific sites in the cell, disaggregation was notably different; the rate of aggregate clearance of pro3-1 was faster than that of the other misfolded proteins, and its clearance rate was not hindered when pro3-1 colocalized with a slowly resolved misfolded protein. Finally, we observed using super-resolution light microscopy as well as immunogold labeling EM in which both showed an even distribution of the different misfolded proteins within an inclusion, suggesting that misfolding characteristics and remodeling, rather than spatial compartmentalization, allows for differential clearance of these misfolding reporters residing in the same inclusion. Taken together, our results highlight how properties of misfolded proteins can significantly affect processing.
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Affiliation(s)
- Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Katharina S Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Maria Eisele-Bürger
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden; Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lisa Larsson Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Per O Widlund
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden.
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7
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Stenberg S, Li J, Gjuvsland AB, Persson K, Demitz-Helin E, González Peña C, Yue JX, Gilchrist C, Ärengård T, Ghiaci P, Larsson-Berghund L, Zackrisson M, Smits S, Hallin J, Höög JL, Molin M, Liti G, Omholt SW, Warringer J. Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation. eLife 2022; 11:76095. [PMID: 35801695 PMCID: PMC9427111 DOI: 10.7554/elife.76095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/07/2022] [Indexed: 11/15/2022] Open
Abstract
Deletion of mitochondrial DNA in eukaryotes is currently attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show that this process critically involves the antioxidant enzyme superoxide dismutase 2 and two-way mitochondrial-nuclear communication through Rtg2 and Rtg3. While mitochondrial DNA homeostasis is rapidly restored after cessation of a short-term superoxide stress, long-term stress causes maladaptive persistence of the deletion process, leading to complete annihilation of the cellular pool of intact mitochondrial genomes and irrevocable loss of respiratory ability. This shows that oxidative stress-induced mitochondrial impairment may be under strict regulatory control. If the results extend to human cells, the results may prove to be of etiological as well as therapeutic importance with regard to age-related mitochondrial impairment and disease.
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Affiliation(s)
- Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jing Li
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Arne B Gjuvsland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Erik Demitz-Helin
- Department of Chemistry and Molecular Biology, University of Gothenburg, erikdemitzhelin, Sweden
| | - Carles González Peña
- Department of Chemistry and Molecular Biology, University of Gothenburg, Argentona, Spain
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ciaran Gilchrist
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Timmy Ärengård
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Payam Ghiaci
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Larsson-Berghund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Zackrisson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Silvana Smits
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Hallin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Molin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Gianni Liti
- Institute for Research on Cancer and Aging, Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Stig W Omholt
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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8
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Keuenhof KS, Larsson Berglund L, Malmgren Hill S, Schneider KL, Widlund PO, Nyström T, Höög JL. Large organellar changes occur during mild heat shock in yeast. J Cell Sci 2021; 135:271806. [PMID: 34378783 PMCID: PMC8403982 DOI: 10.1242/jcs.258325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
When the temperature is increased, the heat-shock response is activated to protect the cellular environment. The transcriptomics and proteomics of this process are intensively studied, while information about how the cell responds structurally to heat stress is mostly lacking. Here, Saccharomyces cerevisiae were subjected to a mild continuous heat shock (38°C) and intermittently cryo-immobilised for electron microscopy. Through measuring changes in all distinguishable organelle numbers, sizes and morphologies in over 2100 electron micrographs, a major restructuring of the internal architecture of the cell during the progressive heat shock was revealed. The cell grew larger but most organelles within it expanded even more, shrinking the volume of the cytoplasm. Organelles responded to heat shock at different times, both in terms of size and number, and adaptations of the morphology of some organelles (such as the vacuole) were observed. Multivesicular bodies grew by almost 70%, indicating a previously unknown involvement in the heat-shock response. A previously undescribed electron-translucent structure accumulated close to the plasma membrane. This all-encompassing approach provides a detailed chronological progression of organelle adaptation throughout the cellular heat-stress response.
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Affiliation(s)
- Katharina S Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 41390, Sweden
| | - Lisa Larsson Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 41390, Sweden.,Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Sandra Malmgren Hill
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden.,Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK
| | - Kara L Schneider
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Per O Widlund
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Johanna L Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 41390, Sweden
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9
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Panagaki D, Croft JT, Keuenhof K, Larsson Berglund L, Andersson S, Kohler V, Büttner S, Tamás MJ, Nyström T, Neutze R, Höög JL. Nuclear envelope budding is a response to cellular stress. Proc Natl Acad Sci U S A 2021; 118:e2020997118. [PMID: 34290138 PMCID: PMC8325156 DOI: 10.1073/pnas.2020997118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nuclear envelope budding (NEB) is a recently discovered alternative pathway for nucleocytoplasmic communication distinct from the movement of material through the nuclear pore complex. Through quantitative electron microscopy and tomography, we demonstrate how NEB is evolutionarily conserved from early protists to human cells. In the yeast Saccharomyces cerevisiae, NEB events occur with higher frequency during heat shock, upon exposure to arsenite or hydrogen peroxide, and when the proteasome is inhibited. Yeast cells treated with azetidine-2-carboxylic acid, a proline analog that induces protein misfolding, display the most dramatic increase in NEB, suggesting a causal link to protein quality control. This link was further supported by both localization of ubiquitin and Hsp104 to protein aggregates and NEB events, and the evolution of these structures during heat shock. We hypothesize that NEB is part of normal cellular physiology in a vast range of species and that in S. cerevisiae NEB comprises a stress response aiding the transport of protein aggregates across the nuclear envelope.
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Affiliation(s)
- Dimitra Panagaki
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jacob T Croft
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Katharina Keuenhof
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Stefanie Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Verena Kohler
- Department of Molecular Bioscienses, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Bioscienses, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden;
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10
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Eisele F, Eisele-Bürger AM, Hao X, Berglund LL, Höög JL, Liu B, Nyström T. An Hsp90 co-chaperone links protein folding and degradation and is part of a conserved protein quality control. Cell Rep 2021; 35:109328. [PMID: 34192536 DOI: 10.1016/j.celrep.2021.109328] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/30/2020] [Accepted: 06/09/2021] [Indexed: 10/21/2022] Open
Abstract
In this paper, we show that the essential Hsp90 co-chaperone Sgt1 is a member of a general protein quality control network that links folding and degradation through its participation in the degradation of misfolded proteins both in the cytosol and the endoplasmic reticulum (ER). Sgt1-dependent protein degradation acts in a parallel pathway to the ubiquitin ligase (E3) and ubiquitin chain elongase (E4), Hul5, and overproduction of Hul5 partly suppresses defects in cells with reduced Sgt1 activity. Upon proteostatic stress, Sgt1 accumulates transiently, in an Hsp90- and proteasome-dependent manner, with quality control sites (Q-bodies) of both yeast and human cells that co-localize with Vps13, a protein that creates organelle contact sites. Misfolding disease proteins, such as synphilin-1 involved in Parkinson's disease, are also sequestered to these compartments and require Sgt1 for their clearance.
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Affiliation(s)
- Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden.
| | - Anna Maria Eisele-Bürger
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden; Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, 75007 Uppsala, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden
| | - Lisa Larsson Berglund
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden; Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90 Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90 Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90 Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden.
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11
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Crescitelli R, Lässer C, Jang SC, Cvjetkovic A, Malmhäll C, Karimi N, Höög JL, Johansson I, Fuchs J, Thorsell A, Gho YS, Olofsson Bagge R, Lötvall J. Subpopulations of extracellular vesicles from human metastatic melanoma tissue identified by quantitative proteomics after optimized isolation. J Extracell Vesicles 2020; 9:1722433. [PMID: 32128073 PMCID: PMC7034452 DOI: 10.1080/20013078.2020.1722433] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 01/08/2023] Open
Abstract
The majority of extracellular vesicle (EV) studies conducted to date have been performed on cell lines with little knowledge on how well these represent the characteristics of EVs in vivo. The aim of this study was to establish a method to isolate and categorize subpopulations of EVs isolated directly from tumour tissue. First we established an isolation protocol for subpopulations of EVs from metastatic melanoma tissue, which included enzymatic treatment (collagenase D and DNase). Small and large EVs were isolated with differential ultracentrifugation, and these were further separated into high and low-density (HD and LD) fractions. All EV subpopulations were then analysed in depth using electron microscopy, Bioanalyzer®, nanoparticle tracking analysis, and quantitative mass spectrometry analysis. Subpopulations of EVs with distinct size, morphology, and RNA and protein cargo could be isolated from the metastatic melanoma tissue. LD EVs showed an RNA profile with the presence of 18S and 28S ribosomal subunits. In contrast, HD EVs had RNA profiles with small or no peaks for ribosomal RNA subunits. Quantitative proteomics showed that several proteins such as flotillin-1 were enriched in both large and small LD EVs, while ADAM10 were exclusively enriched in small LD EVs. In contrast, mitofilin was enriched only in the large EVs. We conclude that enzymatic treatments improve EV isolation from dense fibrotic tissue without any apparent effect on molecular or morphological characteristics. By providing a detailed categorization of several subpopulations of EVs isolated directly from tumour tissues, we might better understand the function of EVs in tumour biology and their possible use in biomarker discovery.
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Affiliation(s)
- Rossella Crescitelli
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Lässer
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Su Chul Jang
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Aleksander Cvjetkovic
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Carina Malmhäll
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Nasibeh Karimi
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, Faculty of Natural Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Iva Johansson
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomic Core Facility, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Annika Thorsell
- Proteomic Core Facility, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - R Olofsson Bagge
- Sahlgrenska Cancer Center, Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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12
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Zabeo D, Croft JT, Höög JL. Axonemal doublet microtubules can split into two complete singlets in human sperm flagellum tips. FEBS Lett 2019; 593:892-902. [PMID: 30959570 PMCID: PMC6594080 DOI: 10.1002/1873-3468.13379] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/14/2022]
Abstract
Motile flagella are crucial for human fertility and embryonic development. The distal tip of the flagellum is where growth and intra-flagellar transport are coordinated. In most model organisms, but not all, the distal tip includes a 'singlet region', where axonemal doublet microtubules (dMT) terminate and only complete A-tubules extend as singlet microtubules (sMT) to the tip. How a human flagellar tip is structured is unknown. Here, the flagellar tip structure of human spermatozoa was investigated by cryo-electron tomography, revealing the formation of a complete sMT from both the A-tubule and B-tubule of dMTs. This different tip arrangement in human spermatozoa shows the need to investigate human flagella directly in order to understand their role in health and disease.
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Affiliation(s)
- Davide Zabeo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jacob T Croft
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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13
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Zabeo D, Heumann JM, Schwartz CL, Suzuki-Shinjo A, Morgan G, Widlund PO, Höög JL. A lumenal interrupted helix in human sperm tail microtubules. Sci Rep 2018; 8:2727. [PMID: 29426884 PMCID: PMC5807425 DOI: 10.1038/s41598-018-21165-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/26/2018] [Indexed: 01/16/2023] Open
Abstract
Eukaryotic flagella are complex cellular extensions involved in many human diseases gathered under the term ciliopathies. Currently, detailed insights on flagellar structure come mostly from studies on protists. Here, cryo-electron tomography (cryo-ET) was performed on intact human spermatozoon tails and showed a variable number of microtubules in the singlet region (inside the end-piece). Inside the microtubule plus end, a novel left-handed interrupted helix which extends several micrometers was discovered. This structure was named Tail Axoneme Intra-Lumenal Spiral (TAILS) and binds directly to 11 protofilaments on the internal microtubule wall, in a coaxial fashion with the surrounding microtubule lattice. It leaves a gap over the microtubule seam, which was directly visualized in both singlet and doublet microtubules. We speculate that TAILS may stabilize microtubules, enable rapid swimming or play a role in controlling the swimming direction of spermatozoa.
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Affiliation(s)
- Davide Zabeo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, 41390, Sweden
| | - John M Heumann
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Cindi L Schwartz
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Azusa Suzuki-Shinjo
- Krefting Research Centre, University of Gothenburg, Gothenburg, 41390, Sweden
| | - Garry Morgan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Per O Widlund
- Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, 41390, Sweden.
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14
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Abstract
Extracellular vesicles (EVs) are produced by all known organisms and are important for cell communication and physiology. Great morphological diversity has been described regarding EVs found in body fluids such as blood plasma, breast milk, and ejaculate. However, a detailed morphological analysis has never been performed on exosomes when purified from a single cell type. In this study we analysed and quantified, via multiple electron microscopy techniques, the morphology of exosomes purified from the human mast cell line HMC-1. The results revealed a wide diversity in exosome morphology, suggesting that subpopulations of exosomes with different and specific functions may exist. Our findings imply that a new, more efficient way of defining exosome subpopulations is necessary. A system was proposed where exosomes were classified into nine different categories according to their size and shape. Three additional morphological features were also found in exosomes regardless of their morphological classification. These findings show that exosomes purified from a single cell line are also morphologically diverse, similar to previous observations for EVs in body fluids. This knowledge can help to improve the interpretation of experimental results and widen our general understanding of the biological functions of exosomes.
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Affiliation(s)
- Davide Zabeo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Cecilia Lässer
- Krefting Research Center, University of Gothenburg, Gothenburg, Sweden
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratories, Heidelberg, Germany
| | - Jan Lötvall
- Krefting Research Center, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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15
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Cvjetkovic A, Jang SC, Konečná B, Höög JL, Sihlbom C, Lässer C, Lötvall J. Detailed Analysis of Protein Topology of Extracellular Vesicles-Evidence of Unconventional Membrane Protein Orientation. Sci Rep 2016; 6:36338. [PMID: 27821849 PMCID: PMC5099568 DOI: 10.1038/srep36338] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are important mediators of intercellular communication that change the recipient cell by shuttling lipids, RNA, or protein cargo between cells. Here, we investigate the topology of the protein cargo found in EVs, as this topology can fundamentally influence the biological effects of EVs. A multiple proteomics approach, combining proteinase treatment and biotin tagging, shows that many proteins of cytosolic origin are localized on the surface of EVs. A detailed analysis of the EV proteome at the peptide level revealed that a number of EV membrane proteins are present in a topologically reversed orientation compared to what is annotated. Two examples of such proteins, SCAMP3 and STX4, were confirmed to have a reversed topology. This reversed typology was determined using flow cytometry and fluorescent microscopy with antibodies directed toward their cytoplasmic epitopes. These results describe a novel workflow to define the EV proteome and the orientation of each protein, including membrane protein topology. These data are fundamentally important to understanding the EV proteome and required to fully explain EV biogenesis as well as biological function in recipient cells.
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Affiliation(s)
- Aleksander Cvjetkovic
- Krefting Research Center, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Su Chul Jang
- Krefting Research Center, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Barbora Konečná
- Krefting Research Center, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Johanna L Höög
- Krefting Research Center, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, Faculty of Natural Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Lässer
- Krefting Research Center, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lötvall
- Krefting Research Center, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
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16
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Höög JL, Lacomble S, Bouchet-Marquis C, Briggs L, Park K, Hoenger A, Gull K. 3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction. PLoS Negl Trop Dis 2016; 10:e0004312. [PMID: 26820516 PMCID: PMC4731218 DOI: 10.1371/journal.pntd.0004312] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/29/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cellular junctions are crucial for the formation of multicellular organisms, where they anchor cells to each other and/or supportive tissue and enable cell-to-cell communication. Some unicellular organisms, such as the parasitic protist Trypanosoma brucei, also have complex cellular junctions. The flagella connector (FC) is a three-layered transmembrane junction that moves with the growing tip of a new flagellum and attaches it to the side of the old flagellum. The FC moves via an unknown molecular mechanism, independent of new flagellum growth. Here we describe the detailed 3D architecture of the FC suggesting explanations for how it functions and its mechanism of motility. METHODOLOGY/PRINCIPAL FINDINGS We have used a combination of electron tomography and cryo-electron tomography to reveal the 3D architecture of the FC. Cryo-electron tomography revealed layers of repetitive filamentous electron densities between the two flagella in the interstitial zone. Though the FC does not change in length and width during the growth of the new flagellum, the interstitial zone thickness decreases as the FC matures. This investigation also shows interactions between the FC layers and the axonemes of the new and old flagellum, sufficiently strong to displace the axoneme in the old flagellum. We describe a novel filament, the flagella connector fibre, found between the FC and the axoneme in the old flagellum. CONCLUSIONS/SIGNIFICANCE The FC is similar to other cellular junctions in that filamentous proteins bridge the extracellular space and are anchored to underlying cytoskeletal structures; however, it is built between different portions of the same cell and is unique because of its intrinsic motility. The detailed description of its structure will be an important tool to use in attributing structure / function relationships as its molecular components are discovered in the future. The FC is involved in the inheritance of cell shape, which is important for the life cycle of this human parasite.
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Affiliation(s)
- Johanna L. Höög
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- The Boulder Laboratory for 3D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail: ,
| | - Sylvain Lacomble
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Laura Briggs
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Kristin Park
- The Boulder Laboratory for 3D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Andreas Hoenger
- The Boulder Laboratory for 3D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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17
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Höög JL, Lötvall J. Diversity of extracellular vesicles in human ejaculates revealed by cryo-electron microscopy. J Extracell Vesicles 2015; 4:28680. [PMID: 26563734 PMCID: PMC4643196 DOI: 10.3402/jev.v4.28680] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/04/2015] [Accepted: 10/11/2015] [Indexed: 12/19/2022] Open
Abstract
Human ejaculates contain extracellular vesicles (EVs), that to a large extent are considered to originate from the prostate gland, and are often denominated “prostasomes.” These EVs are important for human fertility, for example by promoting sperm motility and by inducing immune tolerance of the female immune system to the spermatozoa. So far, the EVs present in human ejaculate have not been studied in their native state, inside the seminal fluid without prior purification and isolation procedures. Using cryo-electron microscopy and tomography, we performed a comprehensive inventory of human ejaculate EVs. The sample was neither centrifuged, fixed, filtered or sectioned, nor were heavy metals added. Approximately 1,500 extracellular structures were imaged and categorized. The extracellular environment of human ejaculate was found to be diverse, with 5 major subcategories of EVs and 6 subcategories of extracellular membrane compartments, including lamellar bodies. Furthermore, 3 morphological features, including electron density, double membrane bilayers and coated surface, are described in all subcategories. This study reveals that the extracellular environment in human ejaculate is multifaceted. Several novel morphological EV subcategories are identified and clues to their cellular origin may be found in their morphology. This inventory is therefore important for developing future experimental approaches, and to interpret previously published data to understand the role of EVs for human male fertility.
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Affiliation(s)
- Johanna L Höög
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden;
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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18
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Weber B, Tranfield EM, Höög JL, Baum D, Antony C, Hyman T, Verbavatz JM, Prohaska S. Automated stitching of microtubule centerlines across serial electron tomograms. PLoS One 2014; 9:e113222. [PMID: 25438148 PMCID: PMC4249889 DOI: 10.1371/journal.pone.0113222] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/30/2014] [Indexed: 01/17/2023] Open
Abstract
Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.
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Affiliation(s)
- Britta Weber
- Zuse Institute Berlin, Berlin, Germany
- Max Planck Institute for Molecular Biology and Genetics, Dresden, Germany
| | | | - Johanna L. Höög
- Max Planck Institute for Molecular Biology and Genetics, Dresden, Germany
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Claude Antony
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tony Hyman
- Max Planck Institute for Molecular Biology and Genetics, Dresden, Germany
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19
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Kováčik L, Kereïche S, Höög JL, Jůda P, Matula P, Raška I. Corrigendum to "A simple Fourier filter for suppression of the missing wedge ray artefacts in single-axis electron tomographic reconstructions" [J. Struct. Biol. 186(1) (2014) 141-152]. J Struct Biol 2014; 187:93. [PMID: 28843317 PMCID: PMC5614799 DOI: 10.1016/j.jsb.2014.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lubomír Kováčik
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic.
| | - Sami Kereïche
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic
| | - Johanna L Höög
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; MPI-CBG, Photenhauerstr. 108, 01307 Dresden, Germany
| | - Pavel Jůda
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic
| | - Pavel Matula
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Ivan Raška
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic
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20
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Kováčik L, Kereïche S, Kerïeche S, Höög JL, Jůda P, Matula P, Raška I. A simple Fourier filter for suppression of the missing wedge ray artefacts in single-axis electron tomographic reconstructions. J Struct Biol 2014; 186:141-52. [PMID: 24556578 PMCID: PMC3991334 DOI: 10.1016/j.jsb.2014.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 10/31/2022]
Abstract
The limited specimen tilting range that is typically available in electron tomography gives rise to a region in the Fourier space of the reconstructed object where experimental data are unavailable - the missing wedge. Since this region is sharply delimited from the area of available data, the reconstructed signal is typically hampered by convolution with its impulse response, which gives rise to the well-known missing wedge artefacts in 3D reconstructions. Despite the recent progress in the field of reconstruction and regularization techniques, the missing wedge artefacts remain untreated in most current reconstruction workflows in structural biology. Therefore we have designed a simple Fourier angular filter that effectively suppresses the ray artefacts in the single-axis tilting projection acquisition scheme, making single-axis tomographic reconstructions easier to interpret in particular at low signal-to-noise ratio in acquired projections. The proposed filter can be easily incorporated into current electron tomographic reconstruction schemes.
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Affiliation(s)
- Lubomír Kováčik
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic.
| | | | - Sami Kerïeche
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic
| | - Johanna L Höög
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; MPI-CBG, Photenhauerstr. 108, 01307 Dresden, Germany
| | - Pavel Jůda
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic
| | - Pavel Matula
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Ivan Raška
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Albertov 4, 128 01 Prague 2, Czech Republic
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21
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Abstract
Defects in flagella growth are related to a number of human diseases. Central to flagellar growth is the organization of microtubules that polymerize from basal bodies to form the axoneme, which consists of hundreds of proteins. Flagella exist in all eukaryotic phyla, but neither the mechanism by which flagella grow nor the conservation of this process in evolution are known. Here, we study how protein complexes assemble onto the growing axoneme tip using (cryo) electron tomography. In Chlamydomonas reinhardtii microtubules and associated proteins are added simultaneously. However, in Trypanosoma brucei, disorganized arrays of microtubules are arranged into the axoneme structure by the later addition of preformed protein complexes. Post assembly, the T. brucei transition zone alters structure and its association with the central pair loosens. We conclude that there are multiple ways to form a flagellum and that species-specific structural knowledge is critical before evaluating flagellar defects. DOI:http://dx.doi.org/10.7554/eLife.01479.001 Some cells have a whip-like appendage called a flagellum. This is most often used to propel the cell, notably in sperm cells, but it can also be involved in sensing cues in the surrounding environment. Flagella are found in all three domains of life—the eukaryotes (which include the animals), bacteria and ancient, single-celled organisms called Archaea—and they perform similar functions in each domain. However, they also differ significantly in their protein composition, overall structure, and mechanism of propulsion. The core of the flagellum in eukaryotes is made up of 20 hollow filaments called ‘microtubules’ arranged so that nine pairs of microtubules form a ring around two central microtubules. The core also contains many other proteins, but it is not clear how all these components come together to make a working flagellum. Moreover, it is not known if the flagella of different groups of eukaryotes are all assembled in the same way. Now, Höög et al. have discovered that although the core structure of the eukaryote flagellum is highly conserved, it can be assembled in markedly different ways. Some species of eukaryote—such as Chlamydomonas reinhardtii, a single-celled green alga, and Trypanosoma brucei, the protist parasite that causes African sleeping sickness—must grow new flagella when their cells divide, so that each new cell can swim. Using a form of electron microscopy called electron tomography, Höög et al. could see the detailed structure of the growing flagella in three dimensions. At first the cores of the flagella in these two distantly related species grow in the same way. However as the flagella get longer their cores grow in completely different ways. The microtubule filaments in longer flagella grow in a synchronized manner in the alga, but in a disorganized way in the protist. The results of Höög et al. illustrate that it is not advisable to draw generalised conclusions based on studies of a few model species. However, since defects in flagella are known to cause several diseases in humans, this knowledge might inform future studies aimed at developing treatments for infertility, respiratory problems, and certain kinds of cancer. DOI:http://dx.doi.org/10.7554/eLife.01479.002
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Affiliation(s)
- Johanna L Höög
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Höög JL, Bouchet-Marquis C, McIntosh JR, Hoenger A, Gull K. Cryo-electron tomography and 3-D analysis of the intact flagellum in Trypanosoma brucei. J Struct Biol 2012; 178:189-98. [PMID: 22285651 PMCID: PMC3355306 DOI: 10.1016/j.jsb.2012.01.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 01/04/2012] [Accepted: 01/12/2012] [Indexed: 12/19/2022]
Abstract
Trypanosoma brucei is a uni-cellular protist that causes African sleeping sickness. These parasites have a flagellum that is attached to the cell body and is indispensible for its motility. The flagellum consists of a canonical 9+2 axoneme and a paraflagellar rod (PFR), an intricate tripartite, fibrous structure that is connected to the axoneme. In this paper we describe results from cryo-electron tomography of unperturbed flagella. This method revealed novel structures that are likely involved in attaching the flagellum to the cell. We also show the first cryo-electron tomographic images of a basal body in situ, revealing electron dense structures inside its triplet microtubules. Sub-tomogram averaging of the PFR revealed that its distal region is organized as an orthorhombic crystal.
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Affiliation(s)
- Johanna L Höög
- The Boulder Laboratory for 3-D Electron Microscopy of Cells, MCD-Biology, University of Colorado at Boulder, Boulder, CO 80309-0347, USA.
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Höög JL, Huisman SM, Sebö-Lemke Z, Sandblad L, McIntosh JR, Antony C, Brunner D. Electron tomography reveals a flared morphology on growing microtubule ends. J Cell Sci 2011; 124:693-8. [PMID: 21303925 DOI: 10.1242/jcs.072967] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microtubules (MTs) exhibit dynamic instability, alternating between phases of growth and shortening, mostly at their uncapped plus ends. Based on results from cryo-electron microscopy it was proposed that growing MTs display mainly curved sheets and blunt ends; during depolymerisation curled 'ramshorns' predominate. Observations of MTs in mitotic cells have suggested that the situation in vivo differs from that in vitro, but so far, a clear comparison between in vivo and in vitro results has not been possible because MT end structures could not be correlated directly with the dynamic state of that particular MT. Here we combine light microscopy and electron tomography (ET) to show that growing MT plus ends in the fission yeast Schizosaccharomyces pombe display predominantly a flared morphology. This indicates that MT polymerisation in vivo and in vitro can follow different paths.
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Affiliation(s)
- Johanna L Höög
- European Molecular Biology Laboratories, Cell Biology and Biophysics Program, D-69117 Heidelberg, Germany.
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Gluenz E, Höög JL, Smith AE, Dawe HR, Shaw MK, Gull K. Beyond 9+0: noncanonical axoneme structures characterize sensory cilia from protists to humans. FASEB J 2010; 24:3117-21. [PMID: 20371625 DOI: 10.1096/fj.09-151381] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intracellular amastigote stages of parasites such as Leishmania are often referred to as aflagellate. They do, however, possess a short axoneme of cryptic function. Here, our examination of the structure of this axoneme leads to a testable hypothesis of its role in the cell biology of pathogenicity. We show a striking similarity between the microtubule axoneme structure of the Leishmania mexicana parasite infecting a macrophage and vertebrate primary cilia. In both, the 9-fold microtubule doublet symmetry is broken by the incursion of one or more microtubule doublets into the axoneme core, giving rise to an architecture that we term here the 9v (variable) axoneme. Three-dimensional reconstructions revealed that no particular doublet initiated the symmetry break, and moreover it often involved 2 doublets. The tip of the L. mexicana flagellum was frequently intimately associated with the macrophage vacuole membrane. We propose that the main function of the amastigote flagellum is to act as a sensory organelle with important functions in host-parasite interactions and signaling in the intracellular stage of the L. mexicana life cycle.
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Affiliation(s)
- Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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25
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Abstract
Trypanosoma brucei is a unicellular parasite causing African sleeping sickness in cattle and humans. Due to the ease with which these cells can be cultured and genetically manipulated, it has emerged as a model organism for the kinetoplastids.In this chapter we describe the preparation of T. brucei for transmission electron microscopy. A thorough explanation of conventional sample preparation through chemical fixation of whole cells and detergent extracted cytoskeletons followed by dehydration and Epon embedding is given. We also introduce a novel high-pressure freezing protocol, which followed by rapid freeze substitution and HM20 embedding generates T. brucei samples displaying good cell morphology, which are suitable for immunocytochemistry.
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Affiliation(s)
- Johanna L Höög
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX13RE, United Kingdom
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Höög JL, Schwartz C, Noon AT, O'Toole ET, Mastronarde DN, McIntosh JR, Antony C. Organization of interphase microtubules in fission yeast analyzed by electron tomography. Dev Cell 2007; 12:349-61. [PMID: 17336902 DOI: 10.1016/j.devcel.2007.01.020] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2006] [Revised: 12/08/2006] [Accepted: 01/24/2007] [Indexed: 11/26/2022]
Abstract
Polarized cells, such as neuronal, epithelial, and fungal cells, all display a specialized organization of their microtubules (MTs). The interphase MT cytoskeleton of the rod-shaped fission yeast, Schizosaccharomyces pombe, has been extensively described by fluorescence microscopy. Here, we describe a large-scale, electron tomography investigation of S. pombe, including a 3D reconstruction of a complete eukaryotic cell volume at sufficient resolution to show both how many MTs there are in a bundle and their detailed architecture. Most cytoplasmic MTs are open at one end and capped at the other, providing evidence about their polarity. Electron-dense bridges between the MTs themselves and between MTs and the nuclear envelope were frequently observed. Finally, we have investigated structure/function relationships between MTs and both mitochondria and vesicles. Our analysis shows that electron tomography of well-preserved cells is ideally suited for describing fine ultrastructural details that were not visible with previous techniques.
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Affiliation(s)
- Johanna L Höög
- European Molecular Biology Laboratory, Cell Biology and Biophysics Program, D-69117 Heidelberg, Germany
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27
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Affiliation(s)
- J L Höög
- Electron Microscopy Facility, Cell Biology and Biophysics Program, European Molecular Biology Laboratories, 69117 Heidelberg, Germany
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