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Chen J, Stephan T, Gaedke F, Liu T, Li Y, Schauss A, Chen P, Wulff V, Jakobs S, Jüngst C, Chen Z. An aldehyde-crosslinking mitochondrial probe for STED imaging in fixed cells. Proc Natl Acad Sci U S A 2024; 121:e2317703121. [PMID: 38687792 PMCID: PMC11087744 DOI: 10.1073/pnas.2317703121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fluorescence labeling of chemically fixed specimens, especially immunolabeling, plays a vital role in super-resolution imaging as it offers a convenient way to visualize cellular structures like mitochondria or the distribution of biomolecules with high detail. Despite the development of various distinct probes that enable super-resolved stimulated emission depletion (STED) imaging of mitochondria in live cells, most of these membrane-potential-dependent fluorophores cannot be retained well in mitochondria after chemical fixation. This lack of suitable mitochondrial probes has limited STED imaging of mitochondria to live cell samples. In this study, we introduce a mitochondria-specific probe, PK Mito Orange FX (PKMO FX), which features a fixation-driven cross-linking motif and accumulates in the mitochondrial inner membrane. It exhibits high fluorescence retention after chemical fixation and efficient depletion at 775 nm, enabling nanoscopic imaging both before and after aldehyde fixation. We demonstrate the compatibility of this probe with conventional immunolabeling and other strategies commonly used for fluorescence labeling of fixed samples. Moreover, we show that PKMO FX facilitates correlative super-resolution light and electron microscopy, enabling the correlation of multicolor fluorescence images and transmission EM images via the characteristic mitochondrial pattern. Our probe further expands the mitochondrial toolkit for multimodal microscopy at nanometer resolutions.
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Affiliation(s)
- Jingting Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
| | - Felix Gaedke
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Yiyan Li
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Astrid Schauss
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Peng Chen
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
| | - Veronika Wulff
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology Translational, Neuroinflammation and Automated Microscopy, Göttingen37075, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Göttingen, Göttingen37099, Germany
| | - Christian Jüngst
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
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2
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Li F, Xiang R, Liu Y, Hu G, Jiang Q, Jia T. Approaches and challenges in identifying, quantifying, and manipulating dynamic mitochondrial genome variations. Cell Signal 2024; 117:111123. [PMID: 38417637 DOI: 10.1016/j.cellsig.2024.111123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/14/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Mitochondria, the cellular powerhouses, possess their own unique genetic system, including replication, transcription, and translation. Studying these processes is crucial for comprehending mitochondrial disorders, energy production, and their related diseases. Over the past decades, various approaches have been applied in detecting and quantifying mitochondrial genome variations with also the purpose of manipulation of mitochondria or mitochondrial genome for therapeutics. Understanding the scope and limitations of above strategies is not only fundamental to the understanding of basic biology but also critical for exploring disease-related novel target(s), as well to develop innovative therapies. Here, this review provides an overview of different tools and techniques for accurate mitochondrial genome variations identification, quantification, and discuss novel strategies for the manipulation of mitochondria to develop innovative therapeutic interventions, through combining the insights gained from the study of mitochondrial genetics with ongoing single cell omics combined with advanced single molecular tools.
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Affiliation(s)
- Fei Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Run Xiang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yue Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guoliang Hu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Quanbo Jiang
- Light, Nanomaterials, Nanotechnologies (L2n) Laboratory, CNRS EMR 7004, University of Technology of Troyes, 12 rue Marie Curie, 10004 Troyes, France
| | - Tao Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; CNRS-UMR9187, INSERM U1196, PSL-Research University, 91405 Orsay, France; CNRS-UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France.
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3
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Sun CL, Van Gilst M, Crowder CM. Hypoxia-induced mitochondrial stress granules. Cell Death Dis 2023; 14:448. [PMID: 37468471 PMCID: PMC10356818 DOI: 10.1038/s41419-023-05988-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Perturbations of mitochondrial proteostasis have been associated with aging, neurodegenerative diseases, and recently with hypoxic injury. While examining hypoxia-induced mitochondrial protein aggregation in C. elegans, we found that sublethal hypoxia, sodium azide, or heat shock-induced abundant ethidium bromide staining mitochondrial granules that preceded evidence of protein aggregation. Genetic manipulations that reduce cellular and organismal hypoxic death block the formation of these mitochondrial stress granules (mitoSG). Knockdown of mitochondrial nucleoid proteins also blocked the formation of mitoSG by a mechanism distinct from the mitochondrial unfolded protein response. Lack of the major mitochondrial matrix protease LONP-1 resulted in the constitutive formation of mitoSG without external stress. Ethidium bromide-staining RNA-containing mitochondrial granules were also observed in rat cardiomyocytes treated with sodium azide, a hypoxia mimetic. Mitochondrial stress granules are an early mitochondrial pathology controlled by LONP and the nucleoid, preceding hypoxia-induced protein aggregation.
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Affiliation(s)
- Chun-Ling Sun
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - Marc Van Gilst
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - C Michael Crowder
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Department of Genome Science, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
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4
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Pavluch V, Špaček T, Engstová H, Dlasková A, Ježek P. Possible frequent multiple mitochondrial DNA copies in a single nucleoid in HeLa cells. Sci Rep 2023; 13:5788. [PMID: 37031254 PMCID: PMC10082775 DOI: 10.1038/s41598-023-33012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/05/2023] [Indexed: 04/10/2023] Open
Abstract
Previously, a number of ~ 1.4 of mitochondrial DNA (mtDNA) molecules in a single nucleoid was reported, which would reflect a minimum nucleoid division. We applied 3D-double-color direct stochastic optical reconstruction microscopy (dSTORM), i.e. nanoscopy with ~ 25-40 nm x,y-resolution, together with our novel method of Delaunay segmentation of 3D data to identify unbiased 3D-overlaps. Noncoding D-loops were recognized in HeLa cells by mtDNA fluorescence in situ hybridization (mtFISH) 7S-DNA 250-bp probe, containing biotin, visualized by anti-biotin/Cy3B-conjugated antibodies. Other mtFISH probes with biotin or Alexa Fluor 647 (A647) against ATP6-COX3 gene overlaps (1,100 bp) were also used. Nucleoids were imaged by anti-DNA/(A647-)-Cy3B-conjugated antibodies. Resulting histograms counting mtFISH-loci/nucleoid overlaps demonstrated that 45% to 70% of visualized nucleoids contained two or more D-loops or ATP6-COX3-loci, indicating two or more mtDNA molecules per nucleoid. With increasing number of mtDNA per nucleoid, diameters were larger and their distribution histograms peaked at ~ 300 nm. A wide nucleoid diameter distribution was obtained also using 2D-STED for their imaging by anti-DNA/A647. At unchanged mtDNA copy number in osteosarcoma 143B cells, TFAM expression increased nucleoid spatial density 1.67-fold, indicating expansion of existing mtDNA and its redistribution into more nucleoids upon the higher TFAM/mtDNA stoichiometry. Validation of nucleoid imaging was also done with two TFAM mutants unable to bend or dimerize, respectively, which reduced both copy number and nucleoid spatial density by 80%. We conclude that frequently more than one mtDNA molecule exists within a single nucleoid in HeLa cells and that mitochondrial nucleoids do exist in a non-uniform size range.
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Affiliation(s)
- Vojtěch Pavluch
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Tomáš Špaček
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Engstová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrea Dlasková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Ježek
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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5
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Singh D, Regar R, Soppina P, Soppina V, Kanvah S. Imaging of mitochondria/lysosomes in live cells and C. elegans. Org Biomol Chem 2023; 21:2220-2231. [PMID: 36805145 DOI: 10.1039/d3ob00086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Two rhodamine-phenothiazine conjugates, RP1 and RP2, were synthesized, and their photophysical properties, subcellular localization, and photocytotoxicity were investigated. We observed robust localization of RP1 in mitochondria and dual localization in mitochondria and lysosomes with RP2 in live cells. Live cell imaging with these probes allowed us to track the dynamics of mitochondria and lysosomes during ROS-induced mitochondrial damage and the subsequent lysosomal digestion of the damaged mitochondria. The fluorophores also demonstrated preferential accumulation in cancer cells compared to normal cells and had strong photo-cytotoxicity. However, no cytotoxicity was observed in the dark. The mitochondrial staining and light-induced ROS production were not limited to mammalian cell lines, but were also observed in the animal model C. elegans. The study demonstrated the potential applications of these probes in visualizing the mitochondria-lysosome cross-talk after ROS production and for photodynamic therapy.
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Affiliation(s)
- Deepmala Singh
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gujarat-382055, India.
| | - Ramprasad Regar
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gujarat-382055, India.
| | - Pushpanjali Soppina
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gujarat-382055, India. .,Department of Biotechnology and Bioinformatics, Sambalpur University, Sambalpur, Orissa 768019, India
| | - Virupakshi Soppina
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gujarat-382055, India.
| | - Sriram Kanvah
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gujarat-382055, India.
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6
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D’Amato M, Morra F, Di Meo I, Tiranti V. Mitochondrial Transplantation in Mitochondrial Medicine: Current Challenges and Future Perspectives. Int J Mol Sci 2023; 24:ijms24031969. [PMID: 36768312 PMCID: PMC9916997 DOI: 10.3390/ijms24031969] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Mitochondrial diseases (MDs) are inherited genetic conditions characterized by pathogenic mutations in nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Current therapies are still far from being fully effective and from covering the broad spectrum of mutations in mtDNA. For example, unlike heteroplasmic conditions, MDs caused by homoplasmic mtDNA mutations do not yet benefit from advances in molecular approaches. An attractive method of providing dysfunctional cells and/or tissues with healthy mitochondria is mitochondrial transplantation. In this review, we discuss what is known about intercellular transfer of mitochondria and the methods used to transfer mitochondria both in vitro and in vivo, and we provide an outlook on future therapeutic applications. Overall, the transfer of healthy mitochondria containing wild-type mtDNA copies could induce a heteroplasmic shift even when homoplasmic mtDNA variants are present, with the aim of attenuating or preventing the progression of pathological clinical phenotypes. In summary, mitochondrial transplantation is a challenging but potentially ground-breaking option for the treatment of various mitochondrial pathologies, although several questions remain to be addressed before its application in mitochondrial medicine.
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7
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Annuario E, Ng K, Vagnoni A. High-Resolution Imaging of Mitochondria and Mitochondrial Nucleoids in Differentiated SH-SY5Y Cells. Methods Mol Biol 2022; 2431:291-310. [PMID: 35412283 DOI: 10.1007/978-1-0716-1990-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mitochondria are highly dynamic organelles which form intricate networks with complex dynamics. Mitochondrial transport and distribution are essential to ensure proper cell function, especially in cells with an extremely polarised morphology such as neurons. A layer of complexity is added when considering mitochondria have their own genome, packaged into nucleoids. Major mitochondrial morphological transitions, for example mitochondrial division, often occur in conjunction with mitochondrial DNA (mtDNA) replication and changes in the dynamic behaviour of the nucleoids. However, the relationship between mtDNA dynamics and mitochondrial motility in the processes of neurons has been largely overlooked. In this chapter, we describe a method for live imaging of mitochondria and nucleoids in differentiated SH-SY5Y cells by instant structured illumination microscopy (iSIM). We also include a detailed protocol for the differentiation of SH-SY5Y cells into cells with a pronounced neuronal-like morphology and show examples of coordinated mitochondrial and nucleoid motility in the long processes of these cells.
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Affiliation(s)
- Emily Annuario
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Kristal Ng
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alessio Vagnoni
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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8
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Zhang C, Xue Y, Wang L, Wu Q, Fang B, Sheng Y, Bai H, Peng B, Yang N, Li L. Progress on the Physiological Function of Mitochondrial DNA and Its Specific Detection and Therapy. Chembiochem 2021; 23:e202100474. [PMID: 34661371 DOI: 10.1002/cbic.202100474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/16/2021] [Indexed: 11/10/2022]
Abstract
Mitochondrial DNA (mtDNA) is the genetic information of mitochondrion, and its structure is circular double-stranded. Despite the diminutive size of the mitochondrial genome, mtDNA mutations are an important cause of mitochondrial diseases which are characterized by defects in oxidative phosphorylation (OXPHOS). Mitochondrial diseases are involved in multiple systems, particularly in the organs that are highly dependent on aerobic metabolism. The diagnosis of mitochondrial disease is more complicated since mtDNA mutations can cause various clinical symptoms. To realize more accurate diagnosis and treatment of mitochondrial diseases, the detection of mtDNA and the design of drugs acting on it are extremely important. Over the past few years, many probes and therapeutic drugs targeting mtDNA have been developed, making significant contributions to fundamental research including elucidation of the mechanisms of mitochondrial diseases at the genetic level. In this review, we summarize the structure, function, and detection approaches for mtDNA. The most current topics in this field, such as mechanistic exploration and treatment of mtDNA mutation-related disorders, are also reviewed. Specific attention is given to discussing the design and development of these probes and drugs for mtDNA. We hope that this review will provide readers with a comprehensive understanding of the importance of mtDNA, and promote the development of effective molecules for theragnosis of mtDNA mutation-related diseases.
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Affiliation(s)
- Congcong Zhang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Yufei Xue
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Lan Wang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Bin Fang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Yu Sheng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Naidi Yang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China.,The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, Fujian, P. R. China
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9
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Palomba E, Tirelli V, de Alteriis E, Parascandola P, Landi C, Mazzoleni S, Sanchez M. A cytofluorimetric analysis of a Saccharomyces cerevisiae population cultured in a fed-batch bioreactor. PLoS One 2021; 16:e0248382. [PMID: 34111115 PMCID: PMC8191950 DOI: 10.1371/journal.pone.0248382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a reference model system and one of the widely used microorganisms in many biotechnological processes. In industrial yeast applications, combined strategies aim to maximize biomass/product yield, with the fed-batch culture being one of the most frequently used. Flow cytometry (FCM) is widely applied in biotechnological processes and represents a key methodology to monitor cell population dynamics. We propose here an application of FCM in the analysis of yeast cell cycle along the time course of a typical S. cerevisiae fed-batch culture. We used two different dyes, SYTOX Green and SYBR Green, with the aim to better define each stage of cell cycle during S. cerevisiae fed-batch culture. The results provide novel insights in the use of FCM cell cycle analysis for the real-time monitoring of S. cerevisiae bioprocesses.
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Affiliation(s)
- Emanuela Palomba
- Department of Research Infrastructures for marine biological resources (RIMAR), Stazione Zoologica “Anton Dohrn”, Villa Comunale, Napoli, Italy
| | | | | | - Palma Parascandola
- Department of Industrial Engineering, University of Salerno, Salerno, Italy
| | - Carmine Landi
- Department of Industrial Engineering, University of Salerno, Salerno, Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, Naples, Italy
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Rome, Italy
- * E-mail:
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10
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Chin MY, Espinosa JA, Pohan G, Markossian S, Arkin MR. Reimagining dots and dashes: Visualizing structure and function of organelles for high-content imaging analysis. Cell Chem Biol 2021; 28:320-337. [PMID: 33600764 PMCID: PMC7995685 DOI: 10.1016/j.chembiol.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022]
Abstract
Organelles are responsible for biochemical and cellular processes that sustain life and their dysfunction causes diseases from cancer to neurodegeneration. While researchers are continuing to appreciate new roles of organelles in disease, the rapid development of specifically targeted fluorescent probes that report on the structure and function of organelles will be critical to accelerate drug discovery. Here, we highlight four organelles that collectively exemplify the progression of phenotypic discovery, starting with mitochondria, where many functional probes have been described, then continuing with lysosomes and Golgi and concluding with nascently described membraneless organelles. We introduce emerging probe designs to explore organelle-specific morphology and dynamics and highlight recent case studies using high-content analysis to stimulate further development of probes and approaches for organellar high-throughput screening.
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Affiliation(s)
- Marcus Y Chin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Jether Amos Espinosa
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Grace Pohan
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.
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11
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Prole DL, Chinnery PF, Jones NS. Visualizing, quantifying, and manipulating mitochondrial DNA in vivo. J Biol Chem 2020; 295:17588-17601. [PMID: 33454000 PMCID: PMC7762947 DOI: 10.1074/jbc.rev120.015101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Indexed: 01/06/2023] Open
Abstract
Mitochondrial DNA (mtDNA) encodes proteins and RNAs that support the functions of mitochondria and thereby numerous physiological processes. Mutations of mtDNA can cause mitochondrial diseases and are implicated in aging. The mtDNA within cells is organized into nucleoids within the mitochondrial matrix, but how mtDNA nucleoids are formed and regulated within cells remains incompletely resolved. Visualization of mtDNA within cells is a powerful means by which mechanistic insight can be gained. Manipulation of the amount and sequence of mtDNA within cells is important experimentally and for developing therapeutic interventions to treat mitochondrial disease. This review details recent developments and opportunities for improvements in the experimental tools and techniques that can be used to visualize, quantify, and manipulate the properties of mtDNA within cells.
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Affiliation(s)
- David L Prole
- Department of Mathematics, Imperial College London, London, United Kingdom; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom; Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London, United Kingdom.
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12
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Abstract
The mitochondrial genome encodes 13 proteins that are components of the oxidative phosphorylation system (OXPHOS), suggesting that precise regulation of these genes is crucial for maintaining OXPHOS functions, including ATP production, calcium buffering, cell signaling, ROS production, and apoptosis. Furthermore, heteroplasmy or mis-regulation of gene expression in mitochondria frequently is associated with human mitochondrial diseases. Thus, various approaches have been developed to investigate the roles of genes encoded by the mitochondrial genome. In this review, we will discuss a wide range of techniques available for investigating the mitochondrial genome, mitochondrial transcription, and mitochondrial translation, which provide a useful guide to understanding mitochondrial gene expression.
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Affiliation(s)
- Dongkeun Park
- Department of Biological Sciences, School of Life Sciences, Ulsan 44919, Korea
- National Creative Research Initiative Center for Proteostasis, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Soyeon Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan 44919, Korea
- National Creative Research Initiative Center for Proteostasis, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Kyung-Tai Min
- Department of Biological Sciences, School of Life Sciences, Ulsan 44919, Korea
- National Creative Research Initiative Center for Proteostasis, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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