1
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Leclerc S, Gupta A, Ruokolainen V, Chen JH, Kunnas K, Ekman AA, Niskanen H, Belevich I, Vihinen H, Turkki P, Perez-Berna AJ, Kapishnikov S, Mäntylä E, Harkiolaki M, Dufour E, Hytönen V, Pereiro E, McEnroe T, Fahy K, Kaikkonen MU, Jokitalo E, Larabell CA, Weinhardt V, Mattola S, Aho V, Vihinen-Ranta M. Progression of herpesvirus infection remodels mitochondrial organization and metabolism. PLoS Pathog 2024; 20:e1011829. [PMID: 38620036 PMCID: PMC11045090 DOI: 10.1371/journal.ppat.1011829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/15/2023] [Revised: 04/25/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized to the perinuclear area, a significant increase in the number and clustering of endoplasmic reticulum-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.
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Affiliation(s)
- Simon Leclerc
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Alka Gupta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Visa Ruokolainen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Kari Kunnas
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Axel A. Ekman
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Paula Turkki
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ana J. Perez-Berna
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, United Kingdom
| | - Eric Dufour
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa Hytönen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab laboratories, Tampere, Finland
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | | | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Venera Weinhardt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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2
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Czymmek KJ, Belevich I, Bischof J, Mathur A, Collinson L, Jokitalo E. Accelerating data sharing and reuse in volume electron microscopy. Nat Cell Biol 2024; 26:498-503. [PMID: 38609529 DOI: 10.1038/s41556-024-01381-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Affiliation(s)
- Kirk James Czymmek
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, USA
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Johanna Bischof
- Euro-BioImaging ERIC Bio-Hub, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Aastha Mathur
- Euro-BioImaging ERIC Bio-Hub, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, UK
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
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3
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Scharaw S, Sola-Carvajal A, Belevich I, Webb AT, Das S, Andersson S, Pentinmikko N, Villablanca EJ, Goldenring JR, Jokitalo E, Coffey RJ, Katajisto P. Golgi organization is a determinant of stem cell function in the small intestine. bioRxiv 2023:2023.03.23.533814. [PMID: 36993731 PMCID: PMC10055334 DOI: 10.1101/2023.03.23.533814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cell-to-cell signalling between niche and stem cells regulates tissue regeneration. While the identity of many mediating factors is known, it is largely unknown whether stem cells optimize their receptiveness to niche signals according to the niche organization. Here, we show that Lgr5+ small intestinal stem cells (ISCs) regulate the morphology and orientation of their secretory apparatus to match the niche architecture, and to increase transport efficiency of niche signal receptors. Unlike the progenitor cells lacking lateral niche contacts, ISCs orient Golgi apparatus laterally towards Paneth cells of the epithelial niche, and divide Golgi into multiple stacks reflecting the number of Paneth cell contacts. Stem cells with a higher number of lateral Golgi transported Epidermal growth factor receptor (Egfr) with a higher efficiency than cells with one Golgi. The lateral Golgi orientation and enhanced Egfr transport required A-kinase anchor protein 9 (Akap9), and was necessary for normal regenerative capacity in vitro . Moreover, reduced Akap9 in aged ISCs renders ISCs insensitive to niche-dependent modulation of Golgi stack number and transport efficiency. Our results reveal stem cell-specific Golgi complex configuration that facilitates efficient niche signal reception and tissue regeneration, which is compromised in the aged epithelium.
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4
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Kalmbach L, Bourdon M, Belevich I, Safran J, Lemaire A, Heo JO, Otero S, Blob B, Pelloux J, Jokitalo E, Helariutta Y. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis. Curr Biol 2023; 33:926-939.e9. [PMID: 36805125 DOI: 10.1016/j.cub.2023.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/12/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
In plants, the phloem distributes photosynthetic products for metabolism and storage over long distances. It relies on specialized cells, the sieve elements, which are enucleated and interconnected through large so-called sieve pores in their adjoining cell walls. Reverse genetics identified PECTATE LYASE-LIKE 12 (PLL12) as critical for plant growth and development. Using genetic complementations, we established that PLL12 is required exclusively late during sieve element differentiation. Structural homology modeling, enzyme inactivation, and overexpression suggest a vital role for PLL12 in sieve-element-specific pectin remodeling. While short distance symplastic diffusion is unaffected, the pll12 mutant is unable to accommodate sustained plant development due to an incapacity to accommodate increasing hydraulic demands on phloem long-distance transport as the plant grows-a defect that is aggravated when combined with another sieve-element-specific mutant callose synthase 7 (cals7). Establishing CALS7 as a specific sieve pore marker, we investigated the subcellular dynamics of callose deposition in the developing sieve plate. Using fluorescent CALS7 then allowed identifying structural defects in pll12 sieve pores that are moderate at the cellular level but become physiologically relevant due to the serial arrangement of sieve elements in the sieve tube. Overall, pectin degradation through PLL12 appears subtle in quantitative terms. We therefore speculate that PLL12 may act as a regulator to locally remove homogalacturonan, thus potentially enabling further extracellular enzymes to access and modify the cell wall during sieve pore maturation.
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Affiliation(s)
- Lothar Kalmbach
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ilya Belevich
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Josip Safran
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Adrien Lemaire
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Jung-Ok Heo
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Sofia Otero
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Bernhard Blob
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Jérôme Pelloux
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ykä Helariutta
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
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5
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Haase R, Fazeli E, Legland D, Doube M, Culley S, Belevich I, Jokitalo E, Schorb M, Klemm A, Tischer C. A Hitchhiker's Guide through the Bio-image Analysis Software Universe. FEBS Lett 2022; 596:2472-2485. [PMID: 35833863 DOI: 10.1002/1873-3468.14451] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 02/01/2022] [Revised: 05/01/2022] [Accepted: 05/12/2022] [Indexed: 11/06/2022]
Abstract
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from microscopy imaging data of biological samples. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software that we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the platform that best suits the user's needs, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.
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Affiliation(s)
- Robert Haase
- DFG Cluster of Excellence "Physics of Life", TU, Dresden, Germany.,Center for Systems Biology Dresden, Germany
| | - Elnaz Fazeli
- Biomedicum Imaging Unit, Faculty of Medicine and HiLIFE, University of Helsinki, Finland
| | - David Legland
- INRAE, UR BIA, F-44316, Nantes, France.,INRAE, PROBE research infrastructure, BIBS facility, F-44316, Nantes, France
| | - Michael Doube
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong
| | - Siân Culley
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, LondonSE1 1UL, UK
| | - Ilya Belevich
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.,Centre for Bioimage Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Klemm
- VI2 - Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, 752 37, Sweden
| | - Christian Tischer
- Centre for Bioimage Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Behanova A, Abdollahzadeh A, Belevich I, Jokitalo E, Sierra A, Tohka J. gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy. Comput Methods Programs Biomed 2022; 220:106802. [PMID: 35436661 DOI: 10.1016/j.cmpb.2022.106802] [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] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 03/31/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND OBJECTIVE Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultrastructure of the brain. In this work, we introduce a freely available Matlab-based gACSON software for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes of brain tissue samples. METHODS The software is equipped with a graphical user interface (GUI). It automatically segments the intra-axonal space of myelinated axons and their corresponding myelin sheaths and allows manual segmentation, proofreading, and interactive correction of the segmented components. gACSON analyzes the morphology of myelinated axons, such as axonal diameter, axonal eccentricity, myelin thickness, or g-ratio. RESULTS We illustrate the use of the software by segmenting and analyzing myelinated axons in six 3D-EM volumes of rat somatosensory cortex after sham surgery or traumatic brain injury (TBI). Our results suggest that the equivalent diameter of myelinated axons in somatosensory cortex was decreased in TBI animals five months after the injury. CONCLUSION Our results indicate that gACSON is a valuable tool for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes. It is freely available at https://github.com/AndreaBehan/g-ACSON under the MIT license.
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Affiliation(s)
- Andrea Behanova
- Department of Information Technology, Uppsala University, Uppsala, Sweden; Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ali Abdollahzadeh
- Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alejandra Sierra
- Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Jussi Tohka
- Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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7
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Pettersen HS, Belevich I, Røyset ES, Smistad E, Simpson MR, Jokitalo E, Reinertsen I, Bakke I, Pedersen A. Code-Free Development and Deployment of Deep Segmentation Models for Digital Pathology. Front Med (Lausanne) 2022; 8:816281. [PMID: 35155486 PMCID: PMC8829033 DOI: 10.3389/fmed.2021.816281] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Application of deep learning on histopathological whole slide images (WSIs) holds promise of improving diagnostic efficiency and reproducibility but is largely dependent on the ability to write computer code or purchase commercial solutions. We present a code-free pipeline utilizing free-to-use, open-source software (QuPath, DeepMIB, and FastPathology) for creating and deploying deep learning-based segmentation models for computational pathology. We demonstrate the pipeline on a use case of separating epithelium from stroma in colonic mucosa. A dataset of 251 annotated WSIs, comprising 140 hematoxylin-eosin (HE)-stained and 111 CD3 immunostained colon biopsy WSIs, were developed through active learning using the pipeline. On a hold-out test set of 36 HE and 21 CD3-stained WSIs a mean intersection over union score of 95.5 and 95.3% was achieved on epithelium segmentation. We demonstrate pathologist-level segmentation accuracy and clinical acceptable runtime performance and show that pathologists without programming experience can create near state-of-the-art segmentation solutions for histopathological WSIs using only free-to-use software. The study further demonstrates the strength of open-source solutions in its ability to create generalizable, open pipelines, of which trained models and predictions can seamlessly be exported in open formats and thereby used in external solutions. All scripts, trained models, a video tutorial, and the full dataset of 251 WSIs with ~31 k epithelium annotations are made openly available at https://github.com/andreped/NoCodeSeg to accelerate research in the field.
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Affiliation(s)
- Henrik Sahlin Pettersen
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Elin Synnøve Røyset
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Erik Smistad
- Department of Health Research, SINTEF Digital, Trondheim, Norway
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Melanie Rae Simpson
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- The Clinical Research Unit for Central Norway, Trondheim, Norway
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ingerid Reinertsen
- Department of Health Research, SINTEF Digital, Trondheim, Norway
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Bakke
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - André Pedersen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Health Research, SINTEF Digital, Trondheim, Norway
- The Cancer Foundation, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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8
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Paterlini A, Belevich I. Serial Block Electron Microscopy to Study Plasmodesmata in the Vasculature of Arabidopsis thaliana Roots. Methods Mol Biol 2022; 2457:95-107. [PMID: 35349134 DOI: 10.1007/978-1-0716-2132-5_5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Serial block electron microscopy (SB-EM) is a technique that enables acquisition and reconstruction of 3D cellular volumes. The approach is valuable for the study of plasmodesmata (PD) as the relative positions of these structures are contained in the datasets. In this chapter, we describe how to prepare plant roots for SB-EM via fixation, embedding, and trimming steps. We also provide details and recommendations for later image acquisition and processing. The procedure is suitable to work on root vascular tissues.
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Affiliation(s)
| | - Ilya Belevich
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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9
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Kumar D, Lak B, Suntio T, Vihinen H, Belevich I, Viita T, Xiaonan L, Vartiainen A, Vartiainen M, Varjosalo M, Jokitalo E. RTN4B interacting protein FAM134C promotes ER membrane curvature and has a functional role in autophagy. Mol Biol Cell 2021; 32:1158-1170. [PMID: 33826365 PMCID: PMC8351555 DOI: 10.1091/mbc.e20-06-0409] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Indexed: 12/30/2022] Open
Abstract
The endoplasmic reticulum (ER) is composed of a controlled ratio of sheets and tubules, which are maintained by several proteins with multiple functions. Reticulons (RTNs), especially RTN4, and DP1/Yop1p family members are known to induce ER membrane curvature. RTN4B is the main RTN4 isoform expressed in nonneuronal cells. In this study, we identified FAM134C as a RTN4B interacting protein in mammalian, nonneuronal cells. FAM134C localized specifically to the ER tubules and sheet edges. Ultrastructural analysis revealed that overexpression of FAM134C induced the formation of unbranched, long tubules or dense globular structures composed of heavily branched narrow tubules. In both cases, tubules were nonmotile. ER tubulation was dependent on the reticulon homology domain (RHD) close to the N-terminus. FAM134C plays a role in the autophagy pathway as its level elevated significantly upon amino acid starvation but not during ER stress. Moreover, FAM134C depletion reduced the number and size of autophagic structures and the amount of ER as a cargo within autophagic structures under starvation conditions. Dominant-negative expression of FAM134C forms with mutated RHD or LC3 interacting region also led to a reduced number of autophagic structures. Our results suggest that FAM134C provides a link between regulation of ER architecture and ER turnover by promoting ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes.
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Affiliation(s)
| | - Behnam Lak
- Cell and Tissue Dynamics Research Program
| | | | - Helena Vihinen
- Cell and Tissue Dynamics Research Program.,Electron Microscopy Unit, and
| | - Ilya Belevich
- Cell and Tissue Dynamics Research Program.,Electron Microscopy Unit, and
| | | | - Liu Xiaonan
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Markku Varjosalo
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Cell and Tissue Dynamics Research Program.,Electron Microscopy Unit, and
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10
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Belevich I, Jokitalo E. DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation. PLoS Comput Biol 2021; 17:e1008374. [PMID: 33651804 PMCID: PMC7954287 DOI: 10.1371/journal.pcbi.1008374] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 11/05/2020] [Revised: 03/12/2021] [Accepted: 01/24/2021] [Indexed: 11/18/2022] Open
Abstract
We present DeepMIB, a new software package that is capable of training convolutional neural networks for segmentation of multidimensional microscopy datasets on any workstation. We demonstrate its successful application for segmentation of 2D and 3D electron and multicolor light microscopy datasets with isotropic and anisotropic voxels. We distribute DeepMIB as both an open-source multi-platform Matlab code and as compiled standalone application for Windows, MacOS and Linux. It comes in a single package that is simple to install and use as it does not require knowledge of programming. DeepMIB is suitable for everyone interested of bringing a power of deep learning into own image segmentation workflows.
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Affiliation(s)
- Ilya Belevich
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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11
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Abdollahzadeh A, Belevich I, Jokitalo E, Sierra A, Tohka J. DeepACSON automated segmentation of white matter in 3D electron microscopy. Commun Biol 2021; 4:179. [PMID: 33568775 PMCID: PMC7876004 DOI: 10.1038/s42003-021-01699-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue requires automated segmentation techniques. Current segmentation techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes and high-resolution EM volumes. On the other hand, segmenting low-resolution, large EM volumes requires methods to account for severe membrane discontinuities inescapable. Therefore, we developed DeepACSON, which performs DCNN-based semantic segmentation and shape-decomposition-based instance segmentation. DeepACSON instance segmentation uses the tubularity of myelinated axons and decomposes under-segmented myelinated axons into their constituent axons. We applied DeepACSON to ten EM volumes of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of mitochondria with excellent evaluation scores. DeepACSON quantified the morphology and spatial aspects of white matter ultrastructures, capturing nanoscopic morphological alterations five months after the injury.
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Affiliation(s)
- Ali Abdollahzadeh
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alejandra Sierra
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Jussi Tohka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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12
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Prabhakar N, Belevich I, Peurla M, Heiligenstein X, Chang HC, Sahlgren C, Jokitalo E, Rosenholm JM. Cell Volume (3D) Correlative Microscopy Facilitated by Intracellular Fluorescent Nanodiamonds as Multi-Modal Probes. Nanomaterials (Basel) 2020; 11:nano11010014. [PMID: 33374705 PMCID: PMC7822478 DOI: 10.3390/nano11010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/05/2023]
Abstract
Three-dimensional correlative light and electron microscopy (3D CLEM) is attaining popularity as a potential technique to explore the functional aspects of a cell together with high-resolution ultrastructural details across the cell volume. To perform such a 3D CLEM experiment, there is an imperative requirement for multi-modal probes that are both fluorescent and electron-dense. These multi-modal probes will serve as landmarks in matching up the large full cell volume datasets acquired by different imaging modalities. Fluorescent nanodiamonds (FNDs) are a unique nanosized, fluorescent, and electron-dense material from the nanocarbon family. We hereby propose a novel and straightforward method for executing 3D CLEM using FNDs as multi-modal landmarks. We demonstrate that FND is biocompatible and is easily identified both in living cell fluorescence imaging and in serial block-face scanning electron microscopy (SB-EM). We illustrate the method by registering multi-modal datasets.
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Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Correspondence:
| | - Ilya Belevich
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan;
| | - Cecilia Sahlgren
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Eija Jokitalo
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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13
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Salo RA, Belevich I, Jokitalo E, Gröhn O, Sierra A. Assessment of the structural complexity of diffusion MRI voxels using 3D electron microscopy in the rat brain. Neuroimage 2020; 225:117529. [PMID: 33147507 DOI: 10.1016/j.neuroimage.2020.117529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/20/2020] [Revised: 10/09/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
Validation and interpretation of diffusion magnetic resonance imaging (dMRI) requires detailed understanding of the actual microstructure restricting the diffusion of water molecules. In this study, we used serial block-face scanning electron microscopy (SBEM), a three-dimensional electron microscopy (3D-EM) technique, to image seven white and grey matter volumes in the rat brain. SBEM shows excellent contrast of cellular membranes, which are the major components restricting the diffusion of water in tissue. Additionally, we performed 3D structure tensor (3D-ST) analysis on the SBEM volumes and parameterised the resulting orientation distributions using Watson and angular central Gaussian (ACG) probability distributions as well as spherical harmonic (SH) decomposition. We analysed how these parameterisations described the underlying orientation distributions and compared their orientation and dispersion with corresponding parameters from two dMRI methods, neurite orientation dispersion and density imaging (NODDI) and constrained spherical deconvolution (CSD). Watson and ACG parameterisations and SH decomposition captured well the 3D-ST orientation distributions, but ACG and SH better represented the distributions due to its ability to model asymmetric dispersion. The dMRI parameters corresponded well with the 3D-ST parameters in the white matter volumes, but the correspondence was less evident in the more complex grey matter. SBEM imaging and 3D-ST analysis also revealed that the orientation distributions were often not axially symmetric, a property neatly captured by the ACG distribution. Overall, the ability of SBEM to image diffusion barriers in intricate detail, combined with 3D-ST analysis and parameterisation, provides a step forward toward interpreting and validating the dMRI signals in complex brain tissue microstructure.
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Affiliation(s)
- Raimo A Salo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Olli Gröhn
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Alejandra Sierra
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland.
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14
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Paterlini A, Belevich I, Jokitalo E, Helariutta Y. Computational Tools for Serial Block Electron Microscopy Reveal Plasmodesmata Distributions and Wall Environments. Plant Physiol 2020; 184:53-64. [PMID: 32719057 PMCID: PMC7479905 DOI: 10.1104/pp.20.00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/14/2020] [Indexed: 05/10/2023]
Abstract
Plasmodesmata are small channels that connect plant cells. While recent technological advances have facilitated analysis of the ultrastructure of these channels, there are limitations to efficiently addressing their presence over an entire cellular interface. Here, we highlight the value of serial block electron microscopy for this purpose. We developed a computational pipeline to study plasmodesmata distributions and detect the presence/absence of plasmodesmata clusters, or pit fields, at the phloem unloading interfaces of Arabidopsis (Arabidopsis thaliana) roots. Pit fields were visualized and quantified. As the wall environment of plasmodesmata is highly specialized, we also designed a tool to extract the thickness of the extracellular matrix at and outside of plasmodesmata positions. We detected and quantified clear wall thinning around plasmodesmata with differences between genotypes, including the recently published plm-2 sphingolipid mutant. Our tools open avenues for quantitative approaches in the analysis of symplastic trafficking.
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Affiliation(s)
- Andrea Paterlini
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR United Kingdom
| | - Ilya Belevich
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Yrjö Helariutta
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR United Kingdom
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
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15
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Yan D, Yadav SR, Paterlini A, Nicolas WJ, Petit JD, Brocard L, Belevich I, Grison MS, Vaten A, Karami L, El-Showk S, Lee JY, Murawska GM, Mortimer J, Knoblauch M, Jokitalo E, Markham JE, Bayer EM, Helariutta Y. Publisher Correction: Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading. Nat Plants 2019; 5:1023. [PMID: 31420590 DOI: 10.1038/s41477-019-0513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Dawei Yan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Shri Ram Yadav
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Andrea Paterlini
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - William J Nicolas
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jules D Petit
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
| | - Lysiane Brocard
- Bordeaux Imaging Centre, Plant Imaging Platform, UMS 3420, INRA-CNRS-INSERM, University of Bordeaux, Villenave-d'Ornon, France
| | - Ilya Belevich
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Magali S Grison
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
| | - Anne Vaten
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leila Karami
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Horticulture, Faculty of Agriculture and Natural Resources, Persian Gulf University, Bushehr, Iran
| | - Sedeer El-Showk
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jung-Youn Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Gosia M Murawska
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Jenny Mortimer
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eija Jokitalo
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer E Markham
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France.
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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16
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Mulay SR, Honarpisheh MM, Foresto-Neto O, Shi C, Desai J, Zhao ZB, Marschner JA, Popper B, Buhl EM, Boor P, Linkermann A, Liapis H, Bilyy R, Herrmann M, Romagnani P, Belevich I, Jokitalo E, Becker JU, Anders HJ. Mitochondria Permeability Transition versus Necroptosis in Oxalate-Induced AKI. J Am Soc Nephrol 2019; 30:1857-1869. [PMID: 31296606 DOI: 10.1681/asn.2018121218] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [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: 12/12/2018] [Accepted: 05/16/2019] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Serum oxalate levels suddenly increase with certain dietary exposures or ethylene glycol poisoning and are a well known cause of AKI. Established contributors to oxalate crystal-induced renal necroinflammation include the NACHT, LRR and PYD domains-containing protein-3 (NLRP3) inflammasome and mixed lineage kinase domain-like (MLKL) protein-dependent tubule necroptosis. These studies examined the role of a novel form of necrosis triggered by altered mitochondrial function. METHODS To better understand the molecular pathophysiology of oxalate-induced AIK, we conducted in vitro studies in mouse and human kidney cells and in vivo studies in mice, including wild-type mice and knockout mice deficient in peptidylprolyl isomerase F (Ppif) or deficient in both Ppif and Mlkl. RESULTS Crystals of calcium oxalate, monosodium urate, or calcium pyrophosphate dihydrate, as well as silica microparticles, triggered cell necrosis involving PPIF-dependent mitochondrial permeability transition. This process involves crystal phagocytosis, lysosomal cathepsin leakage, and increased release of reactive oxygen species. Mice with acute oxalosis displayed calcium oxalate crystals inside distal tubular epithelial cells associated with mitochondrial changes characteristic of mitochondrial permeability transition. Mice lacking Ppif or Mlkl or given an inhibitor of mitochondrial permeability transition displayed attenuated oxalate-induced AKI. Dual genetic deletion of Ppif and Mlkl or pharmaceutical inhibition of necroptosis was partially redundant, implying interlinked roles of these two pathways of regulated necrosis in acute oxalosis. Similarly, inhibition of mitochondrial permeability transition suppressed crystal-induced cell death in primary human tubular epithelial cells. PPIF and phosphorylated MLKL localized to injured tubules in diagnostic human kidney biopsies of oxalosis-related AKI. CONCLUSIONS Mitochondrial permeability transition-related regulated necrosis and necroptosis both contribute to oxalate-induced AKI, identifying PPIF as a potential molecular target for renoprotective intervention.
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Affiliation(s)
- Shrikant Ramesh Mulay
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany; .,Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohsen M Honarpisheh
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Orestes Foresto-Neto
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Chongxu Shi
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Jyaysi Desai
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Zhi Bo Zhao
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Julian A Marschner
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Bastian Popper
- Biomedical Center, Core Facility Animal Models, Ludwig Maximilian University, Planegg-Martinsried, Germany
| | - Ewa Miriam Buhl
- Division of Nephrology, Institute of Pathology, Rheinisch-Westfälische Technische Hochschule University of Aachen, Aachen, Germany
| | - Peter Boor
- Division of Nephrology, Institute of Pathology, Rheinisch-Westfälische Technische Hochschule University of Aachen, Aachen, Germany
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Helen Liapis
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Arkana Laboratories, Little Rock, Arkansas
| | - Rostyslav Bilyy
- Department of Histology, Cytology, and Embryology, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Martin Herrmann
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Paola Romagnani
- Excellence Centre for Research, Transfer and High Education for the Development of De Novo Therapies, University of Florence, Florence, Italy
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland; and
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland; and
| | - Jan U Becker
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Hans-Joachim Anders
- Division of Nephrology, Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany;
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17
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Salo VT, Li S, Vihinen H, Hölttä-Vuori M, Szkalisity A, Horvath P, Belevich I, Peränen J, Thiele C, Somerharju P, Zhao H, Santinho A, Thiam AR, Jokitalo E, Ikonen E. Seipin Facilitates Triglyceride Flow to Lipid Droplet and Counteracts Droplet Ripening via Endoplasmic Reticulum Contact. Dev Cell 2019; 50:478-493.e9. [PMID: 31178403 DOI: 10.1016/j.devcel.2019.05.016] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [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: 11/02/2018] [Revised: 02/27/2019] [Accepted: 05/03/2019] [Indexed: 01/02/2023]
Abstract
Seipin is an oligomeric integral endoplasmic reticulum (ER) protein involved in lipid droplet (LD) biogenesis. To study the role of seipin in LD formation, we relocalized it to the nuclear envelope and found that LDs formed at these new seipin-defined sites. The sites were characterized by uniform seipin-mediated ER-LD necks. At low seipin content, LDs only grew at seipin sites, and tiny, growth-incompetent LDs appeared in a Rab18-dependent manner. When seipin was removed from ER-LD contacts within 1 h, no lipid metabolic defects were observed, but LDs became heterogeneous in size. Studies in seipin-ablated cells and model membranes revealed that this heterogeneity arises via a biophysical ripening process, with triglycerides partitioning from smaller to larger LDs through droplet-bilayer contacts. These results suggest that seipin supports the formation of structurally uniform ER-LD contacts and facilitates the delivery of triglycerides from ER to LDs. This counteracts ripening-induced shrinkage of small LDs.
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Affiliation(s)
- Veijo T Salo
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Shiqian Li
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maarit Hölttä-Vuori
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | | | | | - Ilya Belevich
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Johan Peränen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | | | - Pentti Somerharju
- Department of Biochemistry, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hongxia Zhao
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alexandre Santinho
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Universite de Paris, Paris, France
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Universite de Paris, Paris, France.
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Elina Ikonen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland.
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18
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Yan D, Yadav SR, Paterlini A, Nicolas WJ, Petit JD, Brocard L, Belevich I, Grison MS, Vaten A, Karami L, El-Showk S, Lee JY, Murawska GM, Mortimer J, Knoblauch M, Jokitalo E, Markham JE, Bayer EM, Helariutta Y. Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading. Nat Plants 2019; 5:604-615. [PMID: 31182845 PMCID: PMC6565433 DOI: 10.1038/s41477-019-0429-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/17/2019] [Indexed: 05/18/2023]
Abstract
During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene, PHLOEM UNLOADING MODULATOR (PLM), in the absence of which plasmodesmata-mediated symplastic transport through the phloem pole pericycle-endodermis interface is specifically enhanced. Increased unloading is attributable to a defect in the formation of the endoplasmic reticulum-plasma membrane tethers during plasmodesmal morphogenesis, resulting in the majority of pores lacking a visible cytoplasmic sleeve. PLM encodes a putative enzyme required for the biosynthesis of sphingolipids with very-long-chain fatty acid. Taken together, our results indicate that post-sieve element unloading involves sphingolipid metabolism, which affects plasmodesmal ultrastructure. They also raise the question of how and why plasmodesmata with no cytoplasmic sleeve facilitate molecular trafficking.
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Affiliation(s)
- Dawei Yan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Shri Ram Yadav
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Andrea Paterlini
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - William J Nicolas
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jules D Petit
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Research Centre, GX ABT, Université de Liège, Gembloux, Belgium
| | - Lysiane Brocard
- Bordeaux Imaging Centre, Plant Imaging Platform, UMS 3420, INRA-CNRS-INSERM, University of Bordeaux, Villenave-d'Ornon, France
| | - Ilya Belevich
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Magali S Grison
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
| | - Anne Vaten
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leila Karami
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Horticulture, Faculty of Agriculture and Natural Resources, Persian Gulf University, Bushehr, Iran
| | - Sedeer El-Showk
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jung-Youn Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Gosia M Murawska
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Jenny Mortimer
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eija Jokitalo
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer E Markham
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France.
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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19
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Kumar D, Golchoubian B, Belevich I, Jokitalo E, Schlaitz AL. REEP3 and REEP4 determine the tubular morphology of the endoplasmic reticulum during mitosis. Mol Biol Cell 2019; 30:1377-1389. [PMID: 30995177 PMCID: PMC6724692 DOI: 10.1091/mbc.e18-11-0698] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is extensively remodeled during metazoan open mitosis. However, whether the ER becomes more tubular or more cisternal during mitosis is controversial, and dedicated factors governing the morphology of the mitotic ER have remained elusive. Here, we describe the ER membrane proteins REEP3 and REEP4 as major determinants of ER morphology in metaphase cells. REEP3/4 are specifically required for generating the high-curvature morphology of mitotic ER and promote ER tubulation through their reticulon homology domains (RHDs). This ER-shaping activity of REEP3/4 is distinct from their previously described function to clear ER from metaphase chromatin. We further show that related REEP proteins do not contribute to mitotic ER shaping and provide evidence that the REEP3/4 carboxyterminus mediates regulation of the proteins. These findings confirm that ER converts to higher curvature during mitosis, identify REEP3/4 as specific and crucial morphogenic factors mediating ER tubulation during mitosis, and define the first cell cycle-specific role for RHD proteins.
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Affiliation(s)
- Darshan Kumar
- Cell and Molecular Biology Program, University of Helsinki, FI-00014 Helsinki, Finland
| | - Banafsheh Golchoubian
- Center for Molecular Biology of Heidelberg University (ZMBH), D-69120 Heidelberg, Germany
| | - Ilya Belevich
- Cell and Molecular Biology Program, University of Helsinki, FI-00014 Helsinki, Finland.,Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Eija Jokitalo
- Cell and Molecular Biology Program, University of Helsinki, FI-00014 Helsinki, Finland.,Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Anne-Lore Schlaitz
- Center for Molecular Biology of Heidelberg University (ZMBH), D-69120 Heidelberg, Germany
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20
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Abstract
Axonal structure underlies white matter functionality and plays a major role in brain connectivity. The current literature on the axonal structure is based on the analysis of two-dimensional (2D) cross-sections, which, as we demonstrate, is precarious. To be able to quantify three-dimensional (3D) axonal morphology, we developed a novel pipeline, called ACSON (AutomatiC 3D Segmentation and morphometry Of axoNs), for automated 3D segmentation and morphometric analysis of the white matter ultrastructure. The automated pipeline eliminates the need for time-consuming manual segmentation of 3D datasets. ACSON segments myelin, myelinated and unmyelinated axons, mitochondria, cells and vacuoles, and analyzes the morphology of myelinated axons. We applied the pipeline to serial block-face scanning electron microscopy images of the corpus callosum of sham-operated (n = 2) and brain injured (n = 3) rats 5 months after the injury. The 3D morphometry showed that cross-sections of myelinated axons were elliptic rather than circular, and their diameter varied substantially along their longitudinal axis. It also showed a significant reduction in the myelinated axon diameter of the ipsilateral corpus callosum of rats 5 months after brain injury, indicating ongoing axonal alterations even at this chronic time-point.
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Affiliation(s)
- Ali Abdollahzadeh
- Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Tohka
- Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Alejandra Sierra
- Biomedical Imaging Unit, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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21
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Danilova T, Belevich I, Li H, Palm E, Jokitalo E, Otonkoski T, Lindahl M. MANF Is Required for the Postnatal Expansion and Maintenance of Pancreatic β-Cell Mass in Mice. Diabetes 2019; 68:66-80. [PMID: 30305368 DOI: 10.2337/db17-1149] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 09/30/2018] [Indexed: 11/13/2022]
Abstract
Global lack of mesencephalic astrocyte-derived neurotropic factor (MANF) leads to progressive postnatal loss of β-cell mass and insulin-dependent diabetes in mice. Similar to Manf-/- mice, embryonic ablation of MANF specifically from the pancreas results in diabetes. In this study, we assessed the importance of MANF for the postnatal expansion of pancreatic β-cell mass and for adult β-cell maintenance in mice. Detailed analysis of Pdx-1Cre+/- ::Manffl/fl mice revealed mosaic MANF expression in postnatal pancreata and a significant correlation between the number of MANF-positive β-cells and β-cell mass in individual mice. In vitro, recombinant MANF induced β-cell proliferation in islets from aged mice and protected from hyperglycemia-induced endoplasmic reticulum (ER) stress. Consequently, excision of MANF from β-cells of adult MIP-1CreERT::Manffl/fl mice resulted in reduced β-cell mass and diabetes caused largely by β-cell ER stress and apoptosis, possibly accompanied by β-cell dedifferentiation and reduced rates of β-cell proliferation. Thus, MANF expression in adult mouse β-cells is needed for their maintenance in vivo. We also revealed a mechanistic link between ER stress and inflammatory signaling pathways leading to β-cell death in the absence of MANF. Hence, MANF might be a potential target for regenerative therapy in diabetes.
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Affiliation(s)
- Tatiana Danilova
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ilya Belevich
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Huini Li
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Erik Palm
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
- Children's Hospital, Helsinki University Central Hospital, Helsinki, Finland
| | - Maria Lindahl
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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22
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Salo RA, Belevich I, Manninen E, Jokitalo E, Gröhn O, Sierra A. Quantification of anisotropy and orientation in 3D electron microscopy and diffusion tensor imaging in injured rat brain. Neuroimage 2018; 172:404-414. [PMID: 29412154 DOI: 10.1016/j.neuroimage.2018.01.087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/16/2018] [Accepted: 01/30/2018] [Indexed: 11/26/2022] Open
Abstract
Diffusion tensor imaging (DTI) reveals microstructural features of grey and white matter non-invasively. The contrast produced by DTI, however, is not fully understood and requires further validation. We used serial block-face scanning electron microscopy (SBEM) to acquire tissue metrics, i.e., anisotropy and orientation, using three-dimensional Fourier transform-based (3D-FT) analysis, to correlate with fractional anisotropy and orientation in DTI. SBEM produces high-resolution 3D data at the mesoscopic scale with good contrast of cellular membranes. We analysed selected samples from cingulum, corpus callosum, and perilesional cortex of sham-operated and traumatic brain injury (TBI) rats. Principal orientations produced by DTI and 3D-FT in all samples were in good agreement. Anisotropy values showed similar patterns of change in corresponding DTI and 3D-FT parameters in sham-operated and TBI rats. While DTI and 3D-FT anisotropy values were similar in grey matter, 3D-FT anisotropy values were consistently lower than fractional anisotropy values from DTI in white matter. We also evaluated the effect of resolution in 3D-FT analysis. Despite small angular differences in grey matter samples, lower resolution datasets provided reliable results, allowing for analysis of larger fields of view. Overall, 3D SBEM allows for more sophisticated validation studies of diffusion imaging contrast from a tissue microstructural perspective.
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Affiliation(s)
- Raimo A Salo
- Biomedical Imaging Unit, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Eppu Manninen
- Biomedical Imaging Unit, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Olli Gröhn
- Biomedical Imaging Unit, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Alejandra Sierra
- Biomedical Imaging Unit, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland.
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23
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Lehti S, Nguyen SD, Belevich I, Vihinen H, Heikkilä HM, Soliymani R, Käkelä R, Saksi J, Jauhiainen M, Grabowski GA, Kummu O, Hörkkö S, Baumann M, Lindsberg PJ, Jokitalo E, Kovanen PT, Öörni K. Extracellular Lipids Accumulate in Human Carotid Arteries as Distinct Three-Dimensional Structures and Have Proinflammatory Properties. Am J Pathol 2017; 188:525-538. [PMID: 29154769 DOI: 10.1016/j.ajpath.2017.09.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/11/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022]
Abstract
Lipid accumulation is a key characteristic of advancing atherosclerotic lesions. Herein, we analyzed the ultrastructure of the accumulated lipids in endarterectomized human carotid atherosclerotic plaques using three-dimensional (3D) electron microscopy, a method never used in this context before. 3D electron microscopy revealed intracellular lipid droplets and extracellular lipoprotein particles. Most of the particles were aggregated, and some connected to needle-shaped or sheet-like cholesterol crystals. Proteomic analysis of isolated extracellular lipoprotein particles revealed that apolipoprotein B is their main protein component, indicating their origin from low-density lipoprotein, intermediate-density lipoprotein, very-low-density lipoprotein, lipoprotein (a), or chylomicron remnants. The particles also contained small exchangeable apolipoproteins, complement components, and immunoglobulins. Lipidomic analysis revealed differences between plasma lipoproteins and the particles, thereby indicating involvement of lipolytic enzymes in their generation. Incubation of human monocyte-derived macrophages with the isolated extracellular lipoprotein particles or with plasma lipoproteins that had been lipolytically modified in vitro induced intracellular lipid accumulation and triggered inflammasome activation in them. Taken together, extracellular lipids accumulate in human carotid plaques as distinct 3D structures that include aggregated and fused lipoprotein particles and cholesterol crystals. The particles originate from plasma lipoproteins, show signs of lipolytic modifications, and associate with cholesterol crystals. By inducing intracellular cholesterol accumulation (ie, foam cell formation) and inflammasome activation, the extracellular lipoprotein particles may actively enhance atherogenesis.
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Affiliation(s)
- Satu Lehti
- Atherosclerosis Research Laboratory, Wihuri Research Institute, Helsinki, Finland
| | - Su D Nguyen
- Atherosclerosis Research Laboratory, Wihuri Research Institute, Helsinki, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hanna M Heikkilä
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Rabah Soliymani
- Clinical Proteomics Core Facility, Medicum-Biochemistry and Developmental Biology, School of Medicine, University of Helsinki, Helsinki, Finland
| | - Reijo Käkelä
- Helsinki University Lipidomics Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jani Saksi
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Matti Jauhiainen
- National Institute for Health and Welfare, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Gregory A Grabowski
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Kiniksa Pharmaceuticals, Ltd., Wellesley, Massachusetts
| | - Outi Kummu
- Medical Microbiology and Immunology, Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Sohvi Hörkkö
- Medical Microbiology and Immunology, Research Unit of Biomedicine, University of Oulu, Oulu, Finland; Medical Research Center and Nordlab Oulu, University Hospital and University of Oulu, Oulu, Finland
| | - Marc Baumann
- Clinical Proteomics Core Facility, Medicum-Biochemistry and Developmental Biology, School of Medicine, University of Helsinki, Helsinki, Finland
| | - Perttu J Lindsberg
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri T Kovanen
- Atherosclerosis Research Laboratory, Wihuri Research Institute, Helsinki, Finland
| | - Katariina Öörni
- Atherosclerosis Research Laboratory, Wihuri Research Institute, Helsinki, Finland; Helsinki University Lipidomics Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland.
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24
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Siletsky SA, Belevich I, Belevich NP, Soulimane T, Wikström M. Time-resolved generation of membrane potential by ba 3 cytochrome c oxidase from Thermus thermophilus coupled to single electron injection into the O and O H states. Biochim Biophys Acta Bioenerg 2017; 1858:915-926. [PMID: 28807731 DOI: 10.1016/j.bbabio.2017.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 10/19/2022]
Abstract
Two electrogenic phases with characteristic times of ~14μs and ~290μs are resolved in the kinetics of membrane potential generation coupled to single-electron reduction of the oxidized "relaxed" O state of ba3 oxidase from T. thermophilus (O→E transition). The rapid phase reflects electron redistribution between CuA and heme b. The slow phase includes electron redistribution from both CuA and heme b to heme a3, and electrogenic proton transfer coupled to reduction of heme a3. The distance of proton translocation corresponds to uptake of a proton from the inner water phase into the binuclear center where heme a3 is reduced, but there is no proton pumping and no reduction of CuB. Single-electron reduction of the oxidized "unrelaxed" state (OH→EH transition) is accompanied by electrogenic reduction of the heme b/heme a3 pair by CuA in a "fast" phase (~22μs) and transfer of protons in "middle" and "slow" electrogenic phases (~0.185ms and ~0.78ms) coupled to electron redistribution from the heme b/heme a3 pair to the CuB site. The "middle" and "slow" electrogenic phases seem to be associated with transfer of protons to the proton-loading site (PLS) of the proton pump, but when all injected electrons reach CuB the electronic charge appears to be compensated by back-leakage of the protons from the PLS into the binuclear site. Thus proton pumping occurs only to the extent of ~0.1 H+/e-, probably due to the formed membrane potential in the experiment.
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Affiliation(s)
- Sergey A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
| | - Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
| | - Nikolai P Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
| | - Tewfik Soulimane
- Department of Chemical Sciences and Bernal Research Institute, University of Limerick, Ireland
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
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25
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Salo VT, Belevich I, Li S, Karhinen L, Vihinen H, Vigouroux C, Magré J, Thiele C, Hölttä-Vuori M, Jokitalo E, Ikonen E. Seipin regulates ER-lipid droplet contacts and cargo delivery. EMBO J 2016; 35:2699-2716. [PMID: 27879284 PMCID: PMC5167346 DOI: 10.15252/embj.201695170] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [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: 07/20/2016] [Revised: 10/22/2016] [Accepted: 10/24/2016] [Indexed: 11/10/2022] Open
Abstract
Seipin is an endoplasmic reticulum (ER) membrane protein implicated in lipid droplet (LD) biogenesis and mutated in severe congenital lipodystrophy (BSCL2). Here, we show that seipin is stably associated with nascent ER–LD contacts in human cells, typically via one mobile focal point per LD. Seipin appears critical for such contacts since ER–LD contacts were completely missing or morphologically aberrant in seipin knockout and BSCL2 patient cells. In parallel, LD mobility was increased and protein delivery from the ER to LDs to promote LD growth was decreased. Moreover, while growing LDs normally acquire lipid and protein constituents from the ER, this process was compromised in seipin‐deficient cells. In the absence of seipin, the initial synthesis of neutral lipids from exogenous fatty acid was normal, but fatty acid incorporation into neutral lipids in cells with pre‐existing LDs was impaired. Together, our data suggest that seipin helps to connect newly formed LDs to the ER and that by stabilizing ER–LD contacts seipin facilitates the incorporation of protein and lipid cargo into growing LDs in human cells.
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Affiliation(s)
- Veijo T Salo
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ilya Belevich
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shiqian Li
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Leena Karhinen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Corinne Vigouroux
- Sorbonne Universités, UPMC Univ Paris 6, Inserm UMR_S938, Saint-Antoine Research Center, Institute of Cardiometabolism And Nutrition, AP-HP, Saint-Antoine Hospital Department of Molecular Biology and Genetics, Paris, France
| | - Jocelyne Magré
- l'Institut du Thorax, INSERM CNRS UNIV Nantes, Nantes, France
| | | | - Maarit Hölttä-Vuori
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland .,Minerva Foundation Institute for Medical Research, Helsinki, Finland
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26
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Rämö O, Kumar D, Gucciardo E, Joensuu M, Saarekas M, Vihinen H, Belevich I, Smolander OP, Qian K, Auvinen P, Jokitalo E. NOGO-A/RTN4A and NOGO-B/RTN4B are simultaneously expressed in epithelial, fibroblast and neuronal cells and maintain ER morphology. Sci Rep 2016; 6:35969. [PMID: 27786289 PMCID: PMC5081510 DOI: 10.1038/srep35969] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 04/12/2016] [Accepted: 10/07/2016] [Indexed: 02/08/2023] Open
Abstract
Reticulons (RTNs) are a large family of membrane associated proteins with various functions. NOGO-A/RTN4A has a well-known function in limiting neurite outgrowth and restricting the plasticity of the mammalian central nervous system. On the other hand, Reticulon 4 proteins were shown to be involved in forming and maintaining endoplasmic reticulum (ER) tubules. Using comparative transcriptome analysis and qPCR, we show here that NOGO-B/RTN4B and NOGO-A/RTN4A are simultaneously expressed in cultured epithelial, fibroblast and neuronal cells. Electron tomography combined with immunolabelling reveal that both isoforms localize preferably to curved membranes on ER tubules and sheet edges. Morphological analysis of cells with manipulated levels of NOGO-B/RTN4B revealed that it is required for maintenance of normal ER shape; over-expression changes the sheet/tubule balance strongly towards tubules and causes the deformation of the cell shape while depletion of the protein induces formation of large peripheral ER sheets.
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Affiliation(s)
- Olli Rämö
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Darshan Kumar
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Erika Gucciardo
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Merja Joensuu
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maiju Saarekas
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ilya Belevich
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kui Qian
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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27
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Abstract
Understanding the structure-function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.
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Affiliation(s)
- Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Merja Joensuu
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Darshan Kumar
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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28
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Furuta KM, Yadav SR, Lehesranta S, Belevich I, Miyashima S, Heo JO, Vatén A, Lindgren O, De Rybel B, Van Isterdael G, Somervuo P, Lichtenberger R, Rocha R, Thitamadee S, Tähtiharju S, Auvinen P, Beeckman T, Jokitalo E, Helariutta Y. Plant development. Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation. Science 2014; 345:933-7. [PMID: 25081480 DOI: 10.1126/science.1253736] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Photoassimilates such as sugars are transported through phloem sieve element cells in plants. Adapted for effective transport, sieve elements develop as enucleated living cells. We used electron microscope imaging and three-dimensional reconstruction to follow sieve element morphogenesis in Arabidopsis. We show that sieve element differentiation involves enucleation, in which the nuclear contents are released and degraded in the cytoplasm at the same time as other organelles are rearranged and the cytosol is degraded. These cellular reorganizations are orchestrated by the genetically redundant NAC domain-containing transcription factors, NAC45 and NAC86 (NAC45/86). Among the NAC45/86 targets, we identified a family of genes required for enucleation that encode proteins with nuclease domains. Thus, sieve elements differentiate through a specialized autolysis mechanism.
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Affiliation(s)
- Kaori Miyashima Furuta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Shri Ram Yadav
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Satu Lehesranta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Ilya Belevich
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Shunsuke Miyashima
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Jung-ok Heo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Anne Vatén
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Ove Lindgren
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium. Department of Plant System Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
| | - Gert Van Isterdael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium. Department of Plant System Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
| | - Panu Somervuo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Raffael Lichtenberger
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Raquel Rocha
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Siripong Thitamadee
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Sari Tähtiharju
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium. Department of Plant System Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
| | - Eija Jokitalo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland.
| | - Ykä Helariutta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland. Cardiff University Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK. The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.
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29
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Anttonen T, Belevich I, Kirjavainen A, Laos M, Brakebusch C, Jokitalo E, Pirvola U. How to bury the dead: elimination of apoptotic hair cells from the hearing organ of the mouse. J Assoc Res Otolaryngol 2014; 15:975-92. [PMID: 25074370 DOI: 10.1007/s10162-014-0480-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/01/2014] [Indexed: 12/20/2022] Open
Abstract
Hair cell death is a major cause of hearing impairment. Preservation of surface barrier upon hair cell loss is critical to prevent leakage of potassium-rich endolymph into the organ of Corti and to prevent expansion of cellular damage. Understanding of wound healing in this cytoarchitecturally complex organ requires ultrastructural 3D visualization. Powered by the serial block-face scanning electron microscopy, we penetrate into the cell biological mechanisms in the acute response of outer hair cells and glial-like Deiters' cells to ototoxic trauma in vivo. We show that Deiters' cells function as phagocytes. Upon trauma, their phalangeal processes swell and the resulting close cellular contacts allow engulfment of apoptotic cell debris. Apical domains of dying hair cells are eliminated from the inner ear sensory epithelia, an event thought to depend on supporting cells' actomyosin contractile activity. We show that in the case of apoptotic outer hair cells of the organ of Corti, elimination of their apices is preceded by strong cell body shrinkage, emphasizing the role of the dying cell itself in the cleavage. Our data reveal that the resealing of epithelial surface by junctional extensions of Deiters' cells is dynamically reinforced by newly polymerized F-actin belts. By analyzing Cdc42-inactivated Deiters' cells with defects in actin dynamics and surface closure, we show that compromised barrier integrity shifts hair cell death from apoptosis to necrosis and leads to expanded hair cell and nerve fiber damage. Our results have implications concerning therapeutic protective and regenerative interventions, because both interventions should maintain barrier integrity.
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Affiliation(s)
- Tommi Anttonen
- Department of Biosciences, University of Helsinki, P.O. Box 56 (Viikinkaari 1), 00014, Helsinki, Finland
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30
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Dettmer J, Ursache R, Campilho A, Miyashima S, Belevich I, O'Regan S, Mullendore DL, Yadav SR, Lanz C, Beverina L, Papagni A, Schneeberger K, Weigel D, Stierhof YD, Moritz T, Knoblauch M, Jokitalo E, Helariutta Y. CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication. Nat Commun 2014; 5:4276. [PMID: 25008948 DOI: 10.1038/ncomms5276] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 06/02/2014] [Indexed: 11/09/2022] Open
Abstract
Phloem, a plant tissue responsible for long-distance molecular transport, harbours specific junctions, sieve areas, between the conducting cells. To date, little is known about the molecular framework related to the biogenesis of these sieve areas. Here we identify mutations at the CHER1/AtCTL1 locus of Arabidopsis thaliana. The mutations cause several phenotypic abnormalities, including reduced pore density and altered pore structure in the sieve areas associated with impaired phloem function. CHER1 encodes a member of a poorly characterized choline transporter-like protein family in plants and animals. We show that CHER1 facilitates choline transport, localizes to the trans-Golgi network, and during cytokinesis is associated with the phragmoplast. Consistent with its function in the elaboration of the sieve areas, CHER1 has a sustained, polar localization in the forming sieve plates. Our results indicate that the regulation of choline levels is crucial for phloem development and conductivity in plants.
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Affiliation(s)
- Jan Dettmer
- 1] Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058 Erlangen, Germany [2]
| | - Robertas Ursache
- 1] Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FIN-00014, Finland [2]
| | - Ana Campilho
- 1] Institute for Molecular and Cell Biology (IBMC), University of Porto, Porto 4150-180, Portugal [2]
| | - Shunsuke Miyashima
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FIN-00014, Finland
| | - Ilya Belevich
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FIN-00014, Finland
| | - Seana O'Regan
- Neurophotonics Laboratory, CNRS/Université Paris Descartes, 45, rue des Saints-Pères, 75270 Paris, France
| | - Daniel Leroy Mullendore
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236, USA
| | - Shri Ram Yadav
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FIN-00014, Finland
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Luca Beverina
- Department of Materials Science, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Antonio Papagni
- Department of Materials Science, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Department for Plant Developmental Biology, 50829 Cologne, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - York-Dieter Stierhof
- ZMBP, Mikroskopie, Universität Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236, USA
| | - Eija Jokitalo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FIN-00014, Finland
| | - Ykä Helariutta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FIN-00014, Finland
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Majaneva M, Remonen I, Rintala JM, Belevich I, Kremp A, Setälä O, Jokitalo E, Blomster J. Rhinomonas nottbecki n. sp. (cryptomonadales) and molecular phylogeny of the family Pyrenomonadaceae. J Eukaryot Microbiol 2014; 61:480-92. [PMID: 24913840 DOI: 10.1111/jeu.12128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 05/13/2013] [Revised: 03/09/2014] [Accepted: 03/14/2014] [Indexed: 11/30/2022]
Abstract
The cryptomonad Rhinomonas nottbecki n. sp., isolated from the Baltic Sea, is described from live and fixed cells studied by light, scanning, and transmission electron microscopy together with sequences of the partial nucleus- and nucleomorph-encoded 18S rRNA genes as well as the nucleus-encoded ITS1, 5.8S, ITS2, and the 5'-end of the 28S rRNA gene regions. The sequence analyses include comparison with 43 strains from the family Pyrenomonadaceae. Rhinomonas nottbecki cells are dorsoventrally flattened, obloid in shape; 10.0-17.2 μm long, 5.5-8.1 μm thick, and 4.4-8.8 μm wide. The inner periplast has roughly hexagonal plates. Rhinomonas nottbecki cells resemble those of Rhinomonas reticulata, but the nucleomorph 18S rRNA gene of R. nottbecki differs by 2% from that of R. reticulata, while the ITS region by 11%. The intraspecific variability in the ITS region of R. nottbecki is 5%. In addition, the predicted ITS2 secondary structures are different in R. nottbecki and R. reticulata. The family Pyrenomonadaceae includes three clades: Clade A, Clade B, and Clade C. All Rhinomonas sequences branched within the Clade C, while the genus Rhodomonas is paraphyletic. The analyses suggest that the genus Storeatula is an alternating morphotype of the genera Rhinomonas and Rhodomonas and that the family Pyrenomonadaceae includes some species that were described multiple times, as well as novel species.
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Affiliation(s)
- Markus Majaneva
- Tvärminne Zoological Station, University of Helsinki, Hanko, 10900, Finland; Marine Centre, Finnish Environment Institute, Helsinki, 00560, Finland; Department of Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
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Joensuu M, Belevich I, Rämö O, Nevzorov I, Vihinen H, Puhka M, Witkos TM, Lowe M, Vartiainen MK, Jokitalo E. ER sheet persistence is coupled to myosin 1c-regulated dynamic actin filament arrays. Mol Biol Cell 2014; 25:1111-26. [PMID: 24523293 PMCID: PMC3967974 DOI: 10.1091/mbc.e13-12-0712] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 11/11/2022] Open
Abstract
The endoplasmic reticulum (ER) comprises a dynamic three-dimensional (3D) network with diverse structural and functional domains. Proper ER operation requires an intricate balance within and between dynamics, morphology, and functions, but how these processes are coupled in cells has been unclear. Using live-cell imaging and 3D electron microscopy, we identify a specific subset of actin filaments localizing to polygons defined by ER sheets and tubules and describe a role for these actin arrays in ER sheet persistence and, thereby, in maintenance of the characteristic network architecture by showing that actin depolymerization leads to increased sheet fluctuation and transformations and results in small and less abundant sheet remnants and a defective ER network distribution. Furthermore, we identify myosin 1c localizing to the ER-associated actin filament arrays and reveal a novel role for myosin 1c in regulating these actin structures, as myosin 1c manipulations lead to loss of the actin filaments and to similar ER phenotype as observed after actin depolymerization. We propose that ER-associated actin filaments have a role in ER sheet persistence regulation and thus support the maintenance of sheets as a stationary subdomain of the dynamic ER network.
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Affiliation(s)
- Merja Joensuu
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Ilya Belevich
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
- Electron Microscopy Unit, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Olli Rämö
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Ilya Nevzorov
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
- Electron Microscopy Unit, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Maija Puhka
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Tomasz M. Witkos
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Martin Lowe
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Maria K. Vartiainen
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Cell and Molecular Biology Program, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
- Electron Microscopy Unit, Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
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Siletsky SA, Belevich I, Soulimane T, Verkhovsky MI, Wikström M. The fifth electron in the fully reduced caa3 from Thermus thermophilus is competent in proton pumping. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2013; 1827:1-9. [DOI: 10.1016/j.bbabio.2012.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 11/26/2022]
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Anttonen T, Kirjavainen A, Belevich I, Laos M, Richardson WD, Jokitalo E, Brakebusch C, Pirvola U. Cdc42-dependent structural development of auditory supporting cells is required for wound healing at adulthood. Sci Rep 2012; 2:978. [PMID: 23248743 PMCID: PMC3523287 DOI: 10.1038/srep00978] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 09/19/2012] [Accepted: 11/14/2012] [Indexed: 11/20/2022] Open
Abstract
Cdc42 regulates the initial establishment of cytoskeletal and junctional structures, but only little is known about its role at later stages of cellular differentiation. We studied Cdc42′s role in vivo in auditory supporting cells, epithelial cells with high structural complexity. Cdc42 inactivation was induced early postnatally using the Cdc42loxP/loxP;Fgfr3-iCre-ERT2 mice. Cdc42 depletion impaired elongation of adherens junctions and F-actin belts, leading to constriction of the sensory epithelial surface. Fragmented F-actin belts, junctions containing ectopic lumens and misexpression of a basolateral membrane protein in the apical domain were observed. These defects and changes in aPKCλ/ι expression suggested that apical polarization is impaired. Following a lesion at adulthood, supporting cells with Cdc42 loss-induced maturational defects collapsed and failed to remodel F-actin belts, a process that is critical to scar formation. Thus, Cdc42 is required for structural differentiation of auditory supporting cells and this proper maturation is necessary for wound healing in adults.
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Affiliation(s)
- Tommi Anttonen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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35
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Puhka M, Joensuu M, Vihinen H, Belevich I, Jokitalo E. Progressive sheet-to-tubule transformation is a general mechanism for endoplasmic reticulum partitioning in dividing mammalian cells. Mol Biol Cell 2012; 23:2424-32. [PMID: 22573885 PMCID: PMC3386207 DOI: 10.1091/mbc.e10-12-0950] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [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] [Indexed: 11/18/2022] Open
Abstract
During mitosis, ER network reorganization can lead to packing of the ER into tight concentric layers at the cell cortex and occurs in tandem with rounding of the cell. Morphometric and 3D EM analysis shows that in addition to reorganization, ER sheets undergo transformation toward more fenestrated and tubular forms before anaphase in mammalian cells. The endoplasmic reticulum (ER) is both structurally and functionally complex, consisting of a dynamic network of interconnected sheets and tubules. To achieve a more comprehensive view of ER organization in interphase and mitotic cells and to address a discrepancy in the field (i.e., whether ER sheets persist, or are transformed to tubules, during mitosis), we analyzed the ER in four different mammalian cell lines using live-cell imaging, high-resolution electron microscopy, and three dimensional electron microscopy. In interphase cells, we found great variation in network organization and sheet structures among different cell lines. In mitotic cells, we show that the ER undergoes both spatial reorganization and structural transformation of sheets toward more fenestrated and tubular forms. However, the extent of spatial reorganization and sheet-to-tubule transformation varies among cell lines. Fenestration and tubulation of the ER correlates with a reduced number of membrane-bound ribosomes.
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Affiliation(s)
- Maija Puhka
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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36
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Rintanen M, Belevich I, Verkhovsky MI. Electrogenic events upon photolysis of CO from fully reduced cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2012; 1817:269-75. [DOI: 10.1016/j.bbabio.2011.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/07/2011] [Accepted: 11/09/2011] [Indexed: 10/15/2022]
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Siletsky SA, Belevich I, Belevich NP, Soulimane T, Verkhovsky MI. Time-resolved single-turnover of caa3 oxidase from Thermus thermophilus. Fifth electron of the fully reduced enzyme converts OH into EH state. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2011; 1807:1162-9. [DOI: 10.1016/j.bbabio.2011.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/05/2011] [Accepted: 05/08/2011] [Indexed: 11/30/2022]
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Siletsky SA, Belevich I, Wikström M, Soulimane T, Verkhovsky MI. Time-resolved OH→EH transition of the aberrant ba3 oxidase from Thermus thermophilus. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2009; 1787:201-5. [DOI: 10.1016/j.bbabio.2008.12.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Borisov VB, Belevich I, Bloch DA, Mogi T, Verkhovsky MI. Glutamate 107 in Subunit I of Cytochrome bd from Escherichia coli Is Part of a Transmembrane Intraprotein Pathway Conducting Protons from the Cytoplasm to the Heme b595/Heme d Active Site. Biochemistry 2008; 47:7907-14. [DOI: 10.1021/bi800435a] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vitaliy B. Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation, Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), 00014, Helsinki, Finland, and Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ilya Belevich
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation, Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), 00014, Helsinki, Finland, and Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dmitry A. Bloch
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation, Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), 00014, Helsinki, Finland, and Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsushi Mogi
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation, Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), 00014, Helsinki, Finland, and Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Michael I. Verkhovsky
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation, Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), 00014, Helsinki, Finland, and Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Abstract
Cytochrome c oxidase (CcO) is a terminal protein of the respiratory chain in eukaryotes and some bacteria. It catalyzes most of the biologic oxygen consumption on earth done by aerobic organisms. During the catalytic reaction, CcO reduces dioxygen to water and uses the energy released in this process to maintain the electrochemical proton gradient by functioning as a redox-linked proton pump. Even though the structures of several terminal oxidases are known, they are not sufficient in themselves to explain the molecular mechanism of proton pumping. Thus, additional extensive studies of CcO by varieties of biophysical and biochemical approaches are involved to shed light on the mechanism of proton translocation. In this review, we summarize the current level of knowledge about CcO, including the latest model developed to explain the CcO proton-pumping mechanism.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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41
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Belevich I, Borisov VB, Bloch DA, Konstantinov AA, Verkhovsky MI. Cytochrome bd from Azotobacter vinelandii: Evidence for High-Affinity Oxygen Binding. Biochemistry 2007; 46:11177-84. [PMID: 17784736 DOI: 10.1021/bi700862u] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome bd from Azotobacter vinelandii is a respiratory quinol oxidase that is highly efficient in reducing intracellular oxygen concentration, thus enabling nitrogen fixation under ambient aerobic conditions. Equilibrium measurements of O2 binding to ferrous heme d in the one-electron-reduced form of the A. vinelandii enzyme give Kd(O2) = 0.5 microM, close to the value for the Escherichia coli cytochrome bd (ca. 0.3 microM); thus, both enzymes have similar, high affinity for oxygen. The reaction of the A. vinelandii cytochrome bd in the one-electron-reduced and fully reduced states with O2 is extremely fast approaching the diffusion-controlled limit in water. In the fully reduced state, the rate of O2 binding depends linearly on the oxygen concentration consistently with a simple, single-step process. In contrast, in the one-electron-reduced state the rate of oxygen binding is hyperbolic, implying a more complex binding pattern. Two possible explanations for the saturation kinetics are considered: (A) There is a spectroscopically silent prebinding of oxygen to an unidentified low-affinity saturatable site followed by the oxygen transfer to heme d. (B) Oxygen binding to heme d requires an "activated" state of the enzyme in which an oxygen channel connecting heme d to the bulk is open. This channel is permanently open in the fully reduced enzyme (hence no saturation behavior) but flickers between the open and closed states in the one-electron-reduced enzyme.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), 00014, Helsinki, Finland
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Belevich I, Borisov VB, Verkhovsky MI. Discovery of the True Peroxy Intermediate in the Catalytic Cycle of Terminal Oxidases by Real-time Measurement. J Biol Chem 2007; 282:28514-28519. [PMID: 17690093 DOI: 10.1074/jbc.m705562200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sequence of the catalytic intermediates in the reaction of cytochrome bd terminal oxidases from Escherichia coli and Azotobacter vinelandii with oxygen was monitored in real time by absorption spectroscopy and electrometry. The initial binding of O(2) to the fully reduced enzyme is followed by the fast (5 micros) conversion of the oxy complex to a novel, previously unresolved intermediate. In this transition, low spin heme b(558) remains reduced while high spin heme b(595) is oxidized with formation of a new heme d-oxygen species with an absorption maximum at 635 nm. Reduction of O(2) by two electrons is sufficient to produce (hydro)peroxide bound to ferric heme d. In this case, the O-O bond is left intact and the newly detected intermediate must be a peroxy complex of heme d (Fe (3+)(d)-O-O-(H)) corresponding to compound 0 in peroxidases. The alternative scenario where the O-O bond is broken as in the P(M) intermediate of heme-copper oxidases and compound I of peroxidases is not very likely, because it would require oxidation of a nearby amino acid residue or the porphyrin ring that is energetically unfavorable in the presence of the reduced heme b(558) in the proximity of the catalytic center. The formation of the peroxy intermediate is not coupled to membrane potential generation, indicating that hemes d and b(595) are located at the same depth of the membrane dielectric. The lifetime of the new intermediate is 47 micros; it decays into oxoferryl species due to oxidation of low spin heme b(558) that is linked to significant charge translocation across the membrane.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, Post Office Box 65 (Viikinkaari 1), FI-00014 Helsinki, Finland
| | - Vitaliy B Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Michael I Verkhovsky
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, Post Office Box 65 (Viikinkaari 1), FI-00014 Helsinki, Finland.
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Belevich I, Bloch DA, Belevich N, Wikström M, Verkhovsky MI. Exploring the proton pump mechanism of cytochrome c oxidase in real time. Proc Natl Acad Sci U S A 2007; 104:2685-90. [PMID: 17293458 PMCID: PMC1796784 DOI: 10.1073/pnas.0608794104] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts free energy from O(2) reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump. Although the structures of several oxidases are known, the molecular mechanism of redox-linked proton translocation has remained elusive. Here, correlated internal electron and proton transfer reactions were tracked in real time by spectroscopic and electrometric techniques after laser-activated electron injection into the oxidized enzyme. The observed kinetics establish the long-sought reaction sequence of the proton pump mechanism and describe some of its thermodynamic properties. The 10-micros electron transfer to heme a raises the pK(a) of a "pump site," which is loaded by a proton from the inside of the membrane in 150 micros. This loading increases the redox potentials of both hemes a and a(3), which allows electron equilibration between them at the same rate. Then, in 0.8 ms, another proton is transferred from the inside to the heme a(3)/Cu(B) center, and the electron is transferred to Cu(B). Finally, in 2.6 ms, the preloaded proton is released from the pump site to the opposite side of the membrane.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Dmitry A. Bloch
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Nikolai Belevich
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Michael I. Verkhovsky
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
- *To whom correspondence should be addressed at:
Institute of Biotechnology, University of Helsinki, Biocenter 3, P.O. Box 65, Viikinkaari 1, FI–00014, Helsinki, Finland. E-mail:
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Verkhovsky MI, Belevich I, Bloch DA, Wikström M. Elementary steps of proton translocation in the catalytic cycle of cytochrome oxidase. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2006; 1757:401-7. [PMID: 16829227 DOI: 10.1016/j.bbabio.2006.05.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 05/18/2006] [Accepted: 05/18/2006] [Indexed: 11/30/2022]
Abstract
Proton translocation in the catalytic cycle of cytochrome c oxidase (CcO) proceeds sequentially in a four-stroke manner. Every electron donated by cytochrome c drives the enzyme from one of four relatively stable intermediates to another, and each of these transitions is coupled to proton translocation across the membrane, and to uptake of another proton for production of water in the catalytic site. Using cytochrome c oxidase from Paracoccus denitrificans we have studied the kinetics of electron transfer and electric potential generation during several such transitions, two of which are reported here. The extent of electric potential generation during initial electron equilibration between CuA and heme a confirms that this reaction is not kinetically linked to vectorial proton transfer, whereas oxidation of heme a is kinetically coupled to the main proton translocation events during functioning of the proton pump. We find that the rates and amplitudes in multiphase heme a oxidation are different in the OH-->EH and PM-->F steps of the catalytic cycle, and that this is reflected in the kinetics of electric potential generation. We discuss this difference in terms of different driving forces and relate our results, and data from the literature, to proposed mechanisms of proton pumping in cytochrome c oxidase.
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Affiliation(s)
- Michael I Verkhovsky
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, FIN-00014 University of Helsinki, Helsinki, Finland.
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45
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Belevich I, Verkhovsky MI, Wikström M. Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase. Nature 2006; 440:829-32. [PMID: 16598262 DOI: 10.1038/nature04619] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Accepted: 02/01/2006] [Indexed: 11/09/2022]
Abstract
Electron transfer in cell respiration is coupled to proton translocation across mitochondrial and bacterial membranes, which is a primary event of biological energy transduction. The resulting electrochemical proton gradient is used to power energy-requiring reactions, such as ATP synthesis. Cytochrome c oxidase is a key component of the respiratory chain, which harnesses dioxygen as a sink for electrons and links O2 reduction to proton pumping. Electrons from cytochrome c are transferred sequentially to the O2 reduction site of cytochrome c oxidase via two other metal centres, Cu(A) and haem a, and this is coupled to vectorial proton transfer across the membrane by a hitherto unknown mechanism. On the basis of the kinetics of proton uptake and release on the two aqueous sides of the membrane, it was recently suggested that proton pumping by cytochrome c oxidase is not mechanistically coupled to internal electron transfer. Here we have monitored translocation of electrical charge equivalents as well as electron transfer within cytochrome c oxidase in real time. The results show that electron transfer from haem a to the O2 reduction site initiates the proton pump mechanism by being kinetically linked to an internal vectorial proton transfer. This reaction drives the proton pump and occurs before relaxation steps in which protons are taken up from the aqueous space on one side of the membrane and released on the other.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, FIN-00014 University of Helsinki, Helsinki, Finland
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Ribacka C, Verkhovsky MI, Belevich I, Bloch DA, Puustinen A, Wikström M. An elementary reaction step of the proton pump is revealed by mutation of tryptophan-164 to phenylalanine in cytochrome c oxidase from Paracoccus denitrificans. Biochemistry 2006; 44:16502-12. [PMID: 16342941 DOI: 10.1021/bi0511336] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase couples reduction of dioxygen to water to translocation of protons over the inner mitochondrial or bacterial membrane. A likely proton acceptor for pumped protons is the Delta-propionate of heme a(3), which may receive the proton via water molecules from a conserved glutamic acid (E278 in subunit I of the Paracoccus denitrificans enzyme) and which receives a hydrogen bond from a conserved tryptophan, W164. Here, W164 was mutated to phenylalanine (W164F) to further explore the role of the heme a(3) Delta-propionate in proton translocation. FTIR spectroscopy showed changes in vibrations possibly attributable to heme propionates, and the midpoint redox potential of heme a(3) decreased by approximately 50 mV. The reaction of the oxidized W164F enzyme with hydrogen peroxide yielded substantial amounts of the intermediate F' even at high pH, which suggests that the mutation rearranges the local electric field in the binuclear center that controls the peroxide reaction. The steady-state proton translocation stoichiometry of the W164F enzyme dropped to approximately 0.5 H(+)/e(-) in cells and reconstituted proteoliposomes. Time-resolved electrometric measurements showed that when the fully reduced W164F enzyme reacted with O(2), the membrane potential generated in the fast phase of this reaction was far too small to account either for full proton pumping or uptake of a substrate proton from the inside of the proteoliposomes. Time-resolved optical spectroscopy showed that this fast electrometric phase occurred with kinetics corresponding to the transition from state A to P(R), whereas the subsequent transition to the F state was strongly delayed. This is due to a delay of reprotonation of E278 via the D-pathway, which was confirmed by observation of a slowed rate of Cu(A) oxidation and which explains the small amplitude of the fast charge transfer phase. Surprisingly, the W164F mutation thus mimics a weak block of the D-pathway, which is interpreted as an effect on the side chain isomerization of E278. The fast charge translocation may be due to transfer of a proton from E278 to a "pump site" above the heme groups and is likely to occur also in wild-type enzyme, though not distinguished earlier due to the high-amplitude membrane potential formation during the P(R)--> F transition.
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Affiliation(s)
- Camilla Ribacka
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), FIN-00014, Helsinki, Finland.
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Belevich I, Tuukkanen A, Wikström M, Verkhovsky MI. Proton-Coupled Electron Equilibrium in Soluble and Membrane-Bound Cytochrome c Oxidase from Paracoccus denitrificans. Biochemistry 2006; 45:4000-6. [PMID: 16548527 DOI: 10.1021/bi052458p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pH dependence of electron and proton re-equilibration upon CO photolysis from two-electron-reduced aa3 oxidase was followed by time-resolved electrometry and optical spectroscopy. Optical spectroscopy on soluble Paracoccus denitrificans enzyme at alkaline pH revealed a slow (1 ms) component of electron re-equilibration coupled to the release of protons from the catalytic site. In the work [Brändén, M., et al. (2003) Biochemistry 42, 13178-13184], it was proposed that this proton is released from a water molecule in the catalytic site, located deep in the membrane dielectric. Movement of charged particles such as protons across the dielectric should create an electric potential. However, recording of the time course of the potential generation did not show any potential development in the millisecond time domain, but instead, potential generation was found with an apparent time constant of 50-100 micros. This potential was generated upon proton release from the level of the binuclear catalytic site through the K-channel, because mutation in this channel abolishes the potential generation altogether. The apparent inconsistency between results from optical spectroscopy and electrometry was solved by optical experiments on the membrane-incorporated enzyme. Reconstituting the enzyme into proteoliposomes speeds up the slow electron redistribution process by a factor of 10 and shows the same time constant as potential generation. The possible mechanism of such dramatic change in the rate of proton transfer is discussed.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
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Belevich I, Borisov VB, Konstantinov AA, Verkhovsky MI. Oxygenated complex of cytochrome bd from Escherichia coli: stability and photolability. FEBS Lett 2005; 579:4567-70. [PMID: 16087180 DOI: 10.1016/j.febslet.2005.07.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 07/08/2005] [Accepted: 07/08/2005] [Indexed: 11/26/2022]
Abstract
Cytochrome bd is one of the two terminal ubiquinol oxidases in the respiratory chain of Escherichia coli catalyzing reduction of O2 to H2O. The enzyme is expressed under low oxygen tension; due to high affinity for O2 it is isolated mainly as a stable oxygenated complex. Direct measurement of O2 binding to heme d in the one-electron reduced isolated enzyme gives K(d(O2)) of approximately 280 nM. It is possible to photolyse the heme d oxy-complex by illumination of the enzyme for several minutes under microaerobic conditions; the light-induced difference absorption spectrum is virtually identical to the inverted spectrum of O2 binding to heme d.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FIN-00014 Helsinki, Finland
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Belevich I, Borisov VB, Zhang J, Yang K, Konstantinov AA, Gennis RB, Verkhovsky MI. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc Natl Acad Sci U S A 2005; 102:3657-62. [PMID: 15728392 PMCID: PMC553295 DOI: 10.1073/pnas.0405683102] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [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: 08/04/2004] [Accepted: 01/28/2005] [Indexed: 11/18/2022] Open
Abstract
Time-resolved electron transfer and electrogenic H(+) translocation have been compared in a bd-type quinol oxidase from Escherichia coli and its E445A mutant. The high-spin heme b(595) is found to be retained by the enzyme in contrast to the original proposal, but it is not reducible even by excess of dithionite. When preincubated with the reductants, both the WT (b(558)(2+), b(595)(2+), d(2+)) and E445A mutant oxidase (b(558)(2+), b(595)(3+), d(2+)) bind O(2) rapidly, but formation of the oxoferryl state in the mutant is approximately 100-fold slower than in the WT enzyme. At the same time, the E445A substitution does not affect intraprotein electron re-equilibration after the photolysis of CO bound to ferrous heme d in the one-electron-reduced enzyme (the so-called "electron backflow"). The backflow is coupled to membrane potential generation. Electron transfer between hemes d and b(558) is electrogenic. In contrast, electron transfer between hemes d and b(595) is not electrogenic, although heme b(595) is the major electron acceptor for heme d during the backflow, and therefore is not likely to be accompanied by net H(+) uptake or release. The E445A replacement does not alter electron distribution between hemes b(595) and d in the one-electron reduced cytochrome bd [E(m)(d) > E(m)(b(595)), where E(m) is the midpoint redox potential]; however, it precludes reduction of heme b(595), given heme d has been reduced already by the first electron. Presumably, E445 is one of the two redox-linked ionizable groups required for charge compensation of the di-heme oxygen-reducing site (b(595), d) upon its full reduction by two electrons.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), FIN-00014 Helsinki, Finland
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Bloch D, Belevich I, Jasaitis A, Ribacka C, Puustinen A, Verkhovsky MI, Wikström M. The catalytic cycle of cytochrome c oxidase is not the sum of its two halves. Proc Natl Acad Sci U S A 2003; 101:529-33. [PMID: 14699047 PMCID: PMC327181 DOI: 10.1073/pnas.0306036101] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Membrane-bound cytochrome c oxidase catalyzes cell respiration in aerobic organisms and is a primary energy transducer in biology. The two halves of the catalytic cycle may be studied separately: in an oxidative phase, the enzyme is oxidized by O(2), and in a reductive phase, the oxidized enzyme is reduced before binding the next O(2) molecule. Here we show by time-resolved membrane potential and pH measurements with cytochrome oxidase liposomes that, with both phases in succession, two protons are translocated during each phase, one during each individual electron transfer step. However, when the reductive phase is not immediately preceded by oxidation, it follows a different reaction pathway no longer coupled to proton pumping. Metastable states with altered redox properties of the metal centers are accessed during turnover and relax when external electron donors are exhausted but recover after enzyme reduction and reoxidation by O(2). The efficiency of ATP synthesis might be regulated by switching between the two catalytic pathways.
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Affiliation(s)
- Dmitry Bloch
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), FIN-00014, Helsinki, Finland
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