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Kim HJ, Jin SP, Kang J, Bae SH, Son JB, Oh JH, Youn H, Kim SK, Kang KW, Chung JH. Uncovering the impact of UV radiation on mitochondria in dermal cells: a STED nanoscopy study. Sci Rep 2024; 14:8675. [PMID: 38622160 PMCID: PMC11018800 DOI: 10.1038/s41598-024-55778-z] [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: 06/23/2023] [Accepted: 02/26/2024] [Indexed: 04/17/2024] Open
Abstract
Mitochondria are essential organelles in cellular energy metabolism and other cellular functions. Mitochondrial dysfunction is closely linked to cellular damage and can potentially contribute to the aging process. The purpose of this study was to investigate the subcellular structure of mitochondria and their activities in various cellular environments using super-resolution stimulated emission depletion (STED) nanoscopy. We examined the morphological dispersion of mitochondria below the diffraction limit in sub-cultured human primary skin fibroblasts and mouse skin tissues. Confocal microscopy provides only the overall morphology of the mitochondrial membrane and an indiscerptible location of nucleoids within the diffraction limit. Conversely, super-resolution STED nanoscopy allowed us to resolve the nanoscale distribution of translocase clusters on the mitochondrial outer membrane and accurately quantify the number of nucleoids per cell in each sample. Comparable results were obtained by analyzing the translocase distribution in the mouse tissues. Furthermore, we precisely and quantitatively analyzed biomolecular distribution in nucleoids, such as the mitochondrial transcription factor A (TFAM), using STED nanoscopy. Our findings highlight the efficacy of super-resolution fluorescence imaging in quantifying aging-related changes on the mitochondrial sub-structure in cells and tissues.
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Affiliation(s)
- Hyung Jun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, Seoul, 03080, South Korea.
| | - Seon-Pil Jin
- Department of Dermatology, Seoul National University Hospital, Seoul, 03080, South Korea
- Department of Dermatology, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul, 03080, South Korea
| | - Jooyoun Kang
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - So Hyeon Bae
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jung Bae Son
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jang-Hee Oh
- Department of Dermatology, Seoul National University Hospital, Seoul, 03080, South Korea
- Department of Dermatology, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul, 03080, South Korea
| | - Hyewon Youn
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, 03080, South Korea
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, South Korea
| | - Keon Wook Kang
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, Seoul, 03080, South Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, 03080, South Korea.
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, South Korea.
| | - Jin Ho Chung
- Department of Dermatology, Seoul National University Hospital, Seoul, 03080, South Korea.
- Department of Dermatology, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul, 03080, South Korea.
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2
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Ding L, Liu Y, Wang L, Yang Y. Distinguishing the responsive mechanisms of fluorescent probes to hydrogen peroxide, proteins, and DNA/RNA. Phys Chem Chem Phys 2024; 26:7765-7771. [PMID: 38372974 DOI: 10.1039/d4cp00082j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The responsive mechanisms of cationic quinolinium-vinyl-N,N-dimethylaniline boronate (QVD-B) derivative probes to hydrogen peroxide (H2O2), proteins and DNA/RNA are theoretically investigated in this study. The potential energy curves of QVD-B scanned on a dihedral angle (N+-C-CC) in the first singlet (S1) state exhibit large torsional energy barriers. Additionally, the energy of the lowest unoccupied molecular orbital (LUMO) of an acceptor moiety (-3.14 eV) is lower than that of a donor moiety (-1.13 eV) in QVD-B. This demonstrates that photoinduced electron transfer (PET) quenches the fluorescence of QVD-B, as opposed to the previous report of intramolecular single-bond rotation. After reacting with H2O2, the reaction product of quinoline-vinyl-N,N-dimethylaniline (QVD) turns off the PET pathway and turns on the fluorescence at 550 nm, which is consistent with the experimental results (580 nm). Among the possible configurations of QVD-B that forms with proteins and DNA, the calculated fluorescence values of corresponding twisted QVD-B-P (638 nm) and QVD-B-D (686 nm) are consistent with the experimental results (632 and 688 nm). The frontier molecular orbital and electron-hole analysis show that the charge transfer distance follows the order of QVD (1.88 Å) < QVD-B-P (4.49 Å) < QVD-B-D (6.39 Å), which induces the fluorescence red-shifts of QVD-B-P and QVD-B-D compared to that of QVD. The multi-detection mechanism of the fluorescent probe QVD-B is attributed to PET progress and different degrees of local charge transfer after photoexcitation.
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Affiliation(s)
- Lina Ding
- School of Chemistry and Chemical Engineering, School of Physics, Henan Normal University, Xinxiang 453007, P. R. China.
| | - Yang Liu
- School of Chemistry and Chemical Engineering, School of Physics, Henan Normal University, Xinxiang 453007, P. R. China.
| | - Liang Wang
- School of Chemistry and Chemical Engineering, School of Physics, Henan Normal University, Xinxiang 453007, P. R. China.
| | - Yonggang Yang
- School of Chemistry and Chemical Engineering, School of Physics, Henan Normal University, Xinxiang 453007, P. R. China.
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3
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Wang R, Lei H, Wang H, Qi L, Liu Y, Liu Y, Shi Y, Chen J, Shen QT. Dysregulated inter-mitochondrial crosstalk in glioblastoma cells revealed by in situ cryo-electron tomography. Proc Natl Acad Sci U S A 2024; 121:e2311160121. [PMID: 38377189 PMCID: PMC10907319 DOI: 10.1073/pnas.2311160121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
Glioblastomas (GBMs) are the most lethal primary brain tumors with limited survival, even under aggressive treatments. The current therapeutics for GBMs are flawed due to the failure to accurately discriminate between normal proliferating cells and distinctive tumor cells. Mitochondria are essential to GBMs and serve as potential therapeutical targets. Here, we utilize cryo-electron tomography to quantitatively investigate nanoscale details of randomly sampled mitochondria in their native cellular context of GBM cells. Our results show that compared with cancer-free brain cells, GBM cells own more inter-mitochondrial junctions of several types for communications. Furthermore, our tomograms unveil microtubule-dependent mitochondrial nanotunnel-like bridges in the GBM cells as another inter-mitochondrial structure. These quantified inter-mitochondrial features, together with other mitochondria-organelle and intra-mitochondrial ones, are sufficient to distinguish GBM cells from cancer-free brain cells under scrutiny with predictive modeling. Our findings decipher high-resolution inter-mitochondrial structural signatures and provide clues for diagnosis and therapeutic interventions for GBM and other mitochondria-related diseases.
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Affiliation(s)
- Rui Wang
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
| | - Huan Lei
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
| | - Hongxiang Wang
- Department of Neurosurgery, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Lei Qi
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- Biomedical Research Center for Structural Analysis, Shandong University, Jinan250012, China
| | - Yu’e Liu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai200092, China
| | - Yunhui Liu
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai200092, China
- Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai200092, China
| | - Juxiang Chen
- Department of Neurosurgery, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Qing-Tao Shen
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
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4
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Pieczara A, Arellano Reyes RA, Keyes TE, Dawiec P, Baranska M. New Highly Sensitive and Specific Raman Probe for Live Cell Imaging of Mitochondrial Function. ACS Sens 2024; 9:995-1003. [PMID: 38334979 PMCID: PMC10897933 DOI: 10.1021/acssensors.3c02576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
For Raman hyperspectral detection and imaging in live cells, it is very desirable to create novel probes with strong and unique Raman vibrations in the biological silent region (1800-2800 cm-1). The use of molecular probes in Raman imaging is a relatively new technique in subcellular research; however, it is developing very rapidly. Compared with the label-free method, it allows for a more sensitive and selective visualization of organelles within a single cell. Biological systems are incredibly complex and heterogeneous. Directly visualizing biological structures and activities at the cellular and subcellular levels remains by far one of the most intuitive and powerful ways to study biological problems. Each organelle plays a specific and essential role in cellular processes, but importantly for cells to survive, mitochondrial function must be reliable. Motivated by earlier attempts and successes of biorthogonal chemical imaging, we develop a tool supporting Raman imaging of cells to track biochemical changes associated with mitochondrial function at the cellular level in an in vitro model. In this work, we present a newly synthesized highly sensitive RAR-BR Raman probe for the selective imaging of mitochondria in live endothelial cells.
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Affiliation(s)
- Anna Pieczara
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
- Jagiellonian
University in Kraków, Doctoral School
of Exact and Natural Sciences, 11 Lojasiewicza Street, 30-348 Krakow, Poland
| | - Ruben Arturo Arellano Reyes
- School
of Chemical Sciences, Dublin City University, 592, 628 Collins Ave Ext, Whitehall
Dublin 9, D09 E432 Dublin, Ireland
| | - Tia E. Keyes
- School
of Chemical Sciences, Dublin City University, 592, 628 Collins Ave Ext, Whitehall
Dublin 9, D09 E432 Dublin, Ireland
| | - Patrycja Dawiec
- Jagiellonian
University in Kraków, Doctoral School
of Exact and Natural Sciences, 11 Lojasiewicza Street, 30-348 Krakow, Poland
- Faculty
of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland
| | - Malgorzata Baranska
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
- Faculty
of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland
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5
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Nandi S, Sarkar N. Interactions between Lipid Vesicle Membranes and Single Amino Acid Fibrils: Probable Origin of Specific Neurological Disorders. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1971-1987. [PMID: 38240221 DOI: 10.1021/acs.langmuir.3c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Amyloid fibrils are known to be responsible for several neurological disorders, like Alzheimer's disease (AD), Parkinson's disease (PD), etc. For decades, mostly proteins and peptide-based amyloid fibrils have been focused on, and the topic has acknowledged the rise, development, understanding of, and controversy, as well. However, the single amino acid based amyloid fibrils, responsible for several disorders, such as phenylketonuria, tyrosenimia type II, hypermethioninemia, etc., have gotten scientific attention lately. To understand the molecular level pathogenesis of such disorders originated due to the accumulation of single amino acid-based amyloid fibrils, interaction of these fibrils with phospholipid vesicle membranes is found to be an excellent cell-free in vitro setup. Based on such an in vitro setup, these fibrils show a generic mechanism of membrane insertion driven by electrostatic and hydrophobic effects inside the membrane that reduces the integral rigidity of the membrane. Alteration of such fundamental properties of the membrane, therefore, might be referred to as one of the prime pathological factors for the development of these neurological disorders. Hence, such interactions must be investigated in cellular and intracellular compartments to design suitable therapeutic modulators against fibrils.
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Affiliation(s)
- Sourav Nandi
- Yale School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India
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6
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Neikirk K, Lopez EG, Marshall AG, Alghanem A, Krystofiak E, Kula B, Smith N, Shao J, Katti P, Hinton A. Call to action to properly utilize electron microscopy to measure organelles to monitor disease. Eur J Cell Biol 2023; 102:151365. [PMID: 37864884 DOI: 10.1016/j.ejcb.2023.151365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023] Open
Abstract
This review provides an overview of the current methods for quantifying mitochondrial ultrastructure, including cristae morphology, mitochondrial contact sites, and recycling machinery and a guide to utilizing electron microscopy to effectively measure these organelles. Quantitative analysis of mitochondrial ultrastructure is essential for understanding mitochondrial biology and developing therapeutic strategies for mitochondrial-related diseases. Techniques such as transmission electron microscopy (TEM) and serial block face-scanning electron microscopy, as well as how they can be combined with other techniques including confocal microscopy, super-resolution microscopy, and correlative light and electron microscopy are discussed. Beyond their limitations and challenges, we also offer specific magnifications that may be best suited for TEM analysis of mitochondrial, endoplasmic reticulum, and recycling machinery. Finally, perspectives on future quantification methods are offered.
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Affiliation(s)
- Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Edgar-Garza Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Ahmad Alghanem
- King Abdullah International Medical Research Center (KAIMRC), Ali Al Arini, Ar Rimayah, Riyadh 11481, Saudi Arabia
| | - Evan Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Bartosz Kula
- Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester, School of Medicine and Dentistry, Rochester 14642, USA
| | - Nathan Smith
- Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester, School of Medicine and Dentistry, Rochester 14642, USA
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA, USA
| | - Prasanna Katti
- National Heart, Lung and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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7
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Rickard BP, Overchuk M, Chappell VA, Kemal Ruhi M, Sinawang PD, Nguyen Hoang TT, Akin D, Demirci U, Franco W, Fenton SE, Santos JH, Rizvi I. Methods to Evaluate Changes in Mitochondrial Structure and Function in Cancer. Cancers (Basel) 2023; 15:2564. [PMID: 37174030 PMCID: PMC10177605 DOI: 10.3390/cancers15092564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Mitochondria are regulators of key cellular processes, including energy production and redox homeostasis. Mitochondrial dysfunction is associated with various human diseases, including cancer. Importantly, both structural and functional changes can alter mitochondrial function. Morphologic and quantifiable changes in mitochondria can affect their function and contribute to disease. Structural mitochondrial changes include alterations in cristae morphology, mitochondrial DNA integrity and quantity, and dynamics, such as fission and fusion. Functional parameters related to mitochondrial biology include the production of reactive oxygen species, bioenergetic capacity, calcium retention, and membrane potential. Although these parameters can occur independently of one another, changes in mitochondrial structure and function are often interrelated. Thus, evaluating changes in both mitochondrial structure and function is crucial to understanding the molecular events involved in disease onset and progression. This review focuses on the relationship between alterations in mitochondrial structure and function and cancer, with a particular emphasis on gynecologic malignancies. Selecting methods with tractable parameters may be critical to identifying and targeting mitochondria-related therapeutic options. Methods to measure changes in mitochondrial structure and function, with the associated benefits and limitations, are summarized.
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Affiliation(s)
- Brittany P. Rickard
- Curriculum in Toxicology & Environmental Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marta Overchuk
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, and North Carolina State University, Raleigh, NC 27695, USA
| | - Vesna A. Chappell
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Mustafa Kemal Ruhi
- Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey
| | - Prima Dewi Sinawang
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Tina Thuy Nguyen Hoang
- Department of Biomedical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Demir Akin
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Palo Alto, CA 94304, USA
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Palo Alto, CA 94304, USA
| | - Walfre Franco
- Department of Biomedical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Suzanne E. Fenton
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Janine H. Santos
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Imran Rizvi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, and North Carolina State University, Raleigh, NC 27695, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Center for Environmental Health and Susceptibility, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Durel B, Kervrann C, Bertolin G. Quantitative dSTORM super-resolution microscopy localizes Aurora kinase A/AURKA in the mitochondrial matrix. Biol Cell 2021; 113:458-473. [PMID: 34463964 DOI: 10.1111/boc.202100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND INFORMATION Mitochondria are dynamic organelles playing essential metabolic and signaling functions in cells. Their ultrastructure has largely been investigated with electron microscopy (EM) techniques. However, quantifying protein-protein proximities using EM is extremely challenging. Super-resolution microscopy techniques as direct stochastic optical reconstruction microscopy (dSTORM) now provide a fluorescent-based, quantitative alternative to EM. Recently, super-resolution microscopy approaches including dSTORM led to valuable advances in our knowledge of mitochondrial ultrastructure, and in linking it with new insights in organelle functions. Nevertheless, dSTORM is mostly used to image integral mitochondrial proteins, and there is little or no information on proteins transiently present at this compartment. The cancer-related Aurora kinase A/AURKA is a protein localized at various subcellular locations, including mitochondria. RESULTS We first demonstrate that dSTORM coupled to GcoPS can resolve protein proximities within individual submitochondrial compartments. Then, we show that dSTORM provides sufficient spatial resolution to visualize and quantify the most abundant pool of endogenous AURKA in the mitochondrial matrix, as previously shown for overexpressed AURKA. In addition, we uncover a smaller pool of AURKA localized at the OMM, which could have a potential functional readout. We conclude by demonstrating that aldehyde-based fixatives are more specific for the OMM pool of the kinase instead. CONCLUSIONS Our results indicate that dSTORM coupled to GcoPS colocalization analysis is a suitable approach to explore the compartmentalization of non-integral mitochondrial proteins as AURKA, in a qualitative and quantitative manner. This method also opens up the possibility of analyzing the proximity between AURKA and its multiple mitochondrial partners with exquisite spatial resolution, thereby allowing novel insights into the mitochondrial functions controlled by AURKA. SIGNIFICANCE Probing and quantifying the presence of endogenous AURKA - a cell cycle-related protein localized at mitochondria - in the different organelle subcompartments, using quantitative dSTORM super-resolution microscopy.
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Affiliation(s)
- Béatrice Durel
- Cell Imaging Platform, Structure Fédérative de Recherche Necker, INSERM US24, CNRS UMS3633, Paris, F-75015, France
| | - Charles Kervrann
- Serpico Project-Team, Inria - Centre Inria Rennes-Bretagne Atlantique, CNRS UMR144, Campus Universitaire de Beaulieu, Rennes, F-35042, France.,Institut Curie, PSL Research University, Paris, F-75005, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Institute of Genetics and Development of Rennes), UMR 6290, Rennes, F-35000, France
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9
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Zhao T, Hao H, Wang Z, Liang Y, Feng K, He M, Yun X, Bianco PR, Sun Y, Yao B, Lei M. Multi-color structured illumination microscopy for live cell imaging based on the enhanced image recombination transform algorithm. BIOMEDICAL OPTICS EXPRESS 2021; 12:3474-3484. [PMID: 34221673 PMCID: PMC8221967 DOI: 10.1364/boe.423171] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 05/02/2023]
Abstract
Structured illumination microscopy (SIM) has attracted considerable interest in super-resolution, live-cell imaging because of its low light dose and high imaging speed. Obtaining a high-quality reconstruction image in SIM depends on the precise determination of the parameters of the fringe illumination pattern. The image recombination transform (IRT) algorithm is superior to other algorithms in obtaining the precise initial phase without any approximation, which is promising to provide a considerable solution to address the difficulty of initial phase estimation at low-modulation-depth conditions. However, the IRT algorithm only considers a phase shift of π∕2, which limits its applications in general scenarios. In this letter, we present a general form of IRT algorithm suitable for arbitrary phase shifts, providing a powerful tool for parameter estimation in low signal-to-noise cases. To demonstrate the effectiveness of the enhanced IRT algorithm, we constructed a multicolor, structured illumination microscope and studied at super-resolution, the cargo traffic in HRPE cells, and monitored the movement of mitochondrial structures and microtubules in COS-7 cells. The custom SIM system using the enhanced IRT algorithm allows multicolor capability and a low excitation intensity fluorescence imaging less than 1 W/cm2. High-quality super-resolution images are obtained, which demonstrates the utility of this approach in imaging in the life sciences.
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Affiliation(s)
- Tianyu Zhao
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an, Shaanxi 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Authors contributed equally to this work
| | - Huiwen Hao
- State Key Laboratory of Membrane Biology & Biomedical Pioneer Innovation Center (BIOPIC) & School of Life Sciences, Peking University, Beijing 100871, China
- Authors contributed equally to this work
| | - Zhaojun Wang
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yansheng Liang
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Kun Feng
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Minru He
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an, Shaanxi 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Yun
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Piero R. Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yujie Sun
- State Key Laboratory of Membrane Biology & Biomedical Pioneer Innovation Center (BIOPIC) & School of Life Sciences, Peking University, Beijing 100871, China
| | - Baoli Yao
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an, Shaanxi 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Lei
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Zhang H, Cao X, Tang M, Zhong G, Si Y, Li H, Zhu F, Liao Q, Li L, Zhao J, Feng J, Li S, Wang C, Kaulich M, Wang F, Chen L, Li L, Xia Z, Liang T, Lu H, Feng XH, Zhao B. A subcellular map of the human kinome. eLife 2021; 10:64943. [PMID: 33988507 PMCID: PMC8175086 DOI: 10.7554/elife.64943] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
The human kinome comprises 538 kinases playing essential functions by catalyzing protein phosphorylation. Annotation of subcellular distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 cellular compartments. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a similar condition. KA revealed kinase family-enriched subcellular localizations and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other structures. Furthermore, KA demonstrated the role of liquid-liquid phase separation in formation of kinase condensates. Identification of MOK as a mitochondrial kinase revealed its function in cristae dynamics, respiration, and oxidative stress response. Although limited by possible mislocalization due to overexpression or epitope tagging, this subcellular map of the kinome can be used to refine regulatory mechanisms involving protein phosphorylation.
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Affiliation(s)
- Haitao Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Xiaolei Cao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Mei Tang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Guoxuan Zhong
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yuan Si
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haidong Li
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Feifeng Zhu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qinghua Liao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Liuju Li
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jianhui Zhao
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jia Feng
- Department of Ophthalmology, The Children's Hospital, School of Medicine, and National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, China
| | - Shuaifeng Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chenliang Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, Frankfurt, Germany
| | - Fangwei Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Li Li
- Institute of Aging Research, Hangzhou Normal University, Hangzhou, China
| | - Zongping Xia
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Tingbo Liang
- Cancer Center, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huasong Lu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Bin Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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11
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Uno K, Sugimoto N, Sato Y. N-aryl pyrido cyanine derivatives are nuclear and organelle DNA markers for two-photon and super-resolution imaging. Nat Commun 2021; 12:2650. [PMID: 33976192 PMCID: PMC8113587 DOI: 10.1038/s41467-021-23019-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
Live cell imaging using fluorescent DNA markers are an indispensable molecular tool in various biological and biomedical fields. It is a challenge to develop DNA probes that avoid UV light photo-excitation, have high specificity for DNA, are cell-permeable and are compatible with cutting-edge imaging techniques such as super-resolution microscopy. Herein, we present N-aryl pyrido cyanine (N-aryl-PC) derivatives as a class of long absorption DNA markers with absorption in the wide range of visible light. The high DNA specificity and membrane permeability allow the staining of both organelle DNA as well as nuclear DNA, in various cell types, including plant tissues, without the need for washing post-staining. N-aryl-PC dyes are also highly compatible with a separation of photon by lifetime tuning method in stimulated emission depletion microscopy (SPLIT-STED) for super-resolution imaging as well as two-photon microscopy for deep tissue imaging, making it a powerful tool in the life sciences.
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Affiliation(s)
- Kakishi Uno
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nagisa Sugimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya, Japan
| | - Yoshikatsu Sato
- Graduate School of Science, Nagoya University, Nagoya, Japan.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya, Japan.
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12
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Liput M, Magliaro C, Kuczynska Z, Zayat V, Ahluwalia A, Buzanska L. Tools and approaches for analyzing the role of mitochondria in health, development and disease using human cerebral organoids. Dev Neurobiol 2021; 81:591-607. [PMID: 33725382 DOI: 10.1002/dneu.22818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/16/2022]
Abstract
Mitochondria are cellular organelles involved in generating energy to power various processes in the cell. Although the pivotal role of mitochondria in neurogenesis was demonstrated (first in animal models), very little is known about their role in human embryonic neurodevelopment and its pathology. In this respect human-induced pluripotent stem cells (hiPSC)-derived cerebral organoids provide a tractable, alternative model system of the early neural development and disease that is responsive to pharmacological and genetic manipulations, not possible to apply in humans. Although the involvement of mitochondria in the pathogenesis and progression of neurodegenerative diseases and brain dysfunction has been demonstrated, the precise role they play in cell life and death remains unknown, compromising the development of new mitochondria-targeted approaches to treat human diseases. The cerebral organoid model of neurogenesis and disease in vitro provides an unprecedented opportunity to answer some of the most fundamental questions about mitochondrial function in early human neurodevelopment and neural pathology. Largely an unexplored territory due to the lack of tools and approaches, this review focuses on recent technological advancements in fluorescent and molecular tools, imaging systems, and computational approaches for quantitative and qualitative analyses of mitochondrial structure and function in three-dimensional cellular assemblies-cerebral organoids. Future developments in this direction will further facilitate our understanding of the important role or mitochondrial dynamics and energy requirements during early embryonic development. This in turn will provide a further understanding of how dysfunctional mitochondria contribute to disease processes.
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Affiliation(s)
- Michał Liput
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Chiara Magliaro
- Research Centre "E. Piaggio", and Department of Information Engineering, University of Pisa, Pisa, Italy
| | - Zuzanna Kuczynska
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Valery Zayat
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Arti Ahluwalia
- Research Centre "E. Piaggio", and Department of Information Engineering, University of Pisa, Pisa, Italy
| | - Leonora Buzanska
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
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13
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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14
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Zhu T, Yang G, Liu X, Xiang P, Yang Z, Zhang S, Chen J, Wang H, Campos de Souza S, Zhang Z, Zhang R, Tian Y, Wu J, Tian X. Live cell mitochondrial 3-dimensional dynamic ultrastructures under oxidative phosphorylation revealed by a Pyridine-BODIPY probe. Biosens Bioelectron 2021; 178:113036. [PMID: 33548656 DOI: 10.1016/j.bios.2021.113036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 02/05/2023]
Abstract
Recent advancements in super-resolution nanoscopy allowed the study of mitochondrial biology at nanoscale and boosted the understanding its correlated cellular processes those were previously poorly understood. Nevertheless, studying mitochondrial ultrastructure remains a challenge due to the lack of probes that could target specific mitochondrial substances (e.g. cristae or mtDNA) and survive under harsh super-resolution optical conditions. Herein, in this work, we have rationally constructed a pyridine-BODIPY (Py-BODIPY) derivative that could target mitochondrial membrane in living cells without interfering its physiological microenvironments. Furthermore, we found Py-BODIPY is a membrane potential independent probe, hence it is not limit to live-cell staining but also showed a strong internalization into pre-fixed and stimulus disrupted sample. Importantly, its cristae specificity and superb photostability allow the observation of mitochondrial dynamic nano-structures with an unprecedented resolution, allow demonstrating how mitochondrial 3D ultrastructure evolved under oxidative phosphorylation condition.
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Affiliation(s)
- Tong Zhu
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, 610041, China; School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Guanqing Yang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Xiaolu Liu
- School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Pan Xiang
- School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Zhenghui Yang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Sijing Zhang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Juan Chen
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Hong Wang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Senio Campos de Souza
- Department of Chemistry, University College London, London University College London, Gower Street, London, WC1E 6BT, UK
| | - Zhongping Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China; CAS Center for Excellence in Nanoscience, Institute of Intelligent Machines, Chinese Academy of Science, Hefei, China
| | - Ruilong Zhang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Yupeng Tian
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Jieying Wu
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Xiaohe Tian
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, 610041, China; School of Life Science, Anhui University, Hefei, 230601, PR China; Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China; Department of Chemistry, University College London, London University College London, Gower Street, London, WC1E 6BT, UK.
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15
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Li W, Pan W, Huang M, Yang Z, He Y, Zhang W, Zhang J, Gu Z, Zhang D, Yan W, Qu J. Disulfide-Reduction-Triggered Spontaneous Photoblinking Cy5 Probe for Nanoscopic Imaging of Mitochondrial Dynamics in Live Cells. Anal Chem 2021; 93:2596-2602. [PMID: 33464055 DOI: 10.1021/acs.analchem.0c04658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria are highly dynamic organelles with interconnected tubule structures that are sensitive to environmental stress and light illumination. Super-resolution optical imaging of mitochondrial dynamics is of significance for understanding such biological events. Direct stochastic optical reconstruction microscopy has the advantages of a high spatial resolution, low phototoxicity in live-cell imaging, and the capacity to incorporate smart fluorescent probes. However, dSTORM imaging in live cells is challenging because of the requirement for an imaging buffer and a low temporal resolution. In this work, we achieved dSTORM imaging of mitochondrial dynamics in live cells with a disulfide-substituted Cy5 probe without using any toxic imaging buffer. Under the illumination of very low laser power, the probe exhibited spontaneous photoblinking triggered by disulfide-bond reduction in mitochondria of live cells. The obtained thiol attacked nearby carbon to form a six-membered ring and the reversible opening/closing of the ring produced spontaneous photoblinking behavior. With this new STORM strategy, we achieved observation of mitochondrial dynamics for more than 3 min, which provides a promising tool for further studies of mitochondria with an ultrafine structure.
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Affiliation(s)
- Wen Li
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenhui Pan
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Meina Huang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhigang Yang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ying He
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jianguo Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhenyu Gu
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Dan Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Yan
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Junle Qu
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
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16
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Zorkau M, Proctor-Kent Y, Berlinguer-Palmini R, Hamilton A, Chrzanowska-Lightowlers ZM, Lightowlers RN. Visualizing Mitochondrial Ribosomal RNA and Mitochondrial Protein Synthesis in Human Cell Lines. Methods Mol Biol 2021; 2192:159-181. [PMID: 33230773 DOI: 10.1007/978-1-0716-0834-0_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Human mitochondria contain their own DNA (mtDNA) that encodes 13 proteins all of which are core subunits of oxidative phosphorylation (OXPHOS) complexes. To form functional complexes, these 13 components need to be correctly assembled with approximately 70 nuclear-encoded subunits that are imported following synthesis in the cytosol. How this complicated coordinated translation and assembly is choreographed is still not clear. Methods are being developed to determine whether all members of a particular complex are translated in close proximity, whether protein synthesis is clustered in submitochondrial factories, whether these align with incoming polypeptides, and if there is evidence for co-translational translation that is regulated and limited by the interaction of the incoming proteins with synthesis of their mtDNA-encoded partners. Two methods are described in this chapter to visualize the distribution of mitochondrial ribosomal RNAs in conjunction with newly synthesized mitochondrial proteins. The first combines RNA Fluorescent In Situ Hybridization (FISH) and super-resolution immunocytochemistry to pinpoint mitochondrial ribosomal RNA. The second localizes nascent translation within the mitochondrial network through non-canonical amino acid labeling, click chemistry and fluorescent microscopy.
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Affiliation(s)
- Matthew Zorkau
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK
| | - Yasmin Proctor-Kent
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK
| | | | - Andrew Hamilton
- School of Medicine, Dentistry and Nursing, Glasgow University, Glasgow, UK
| | - Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK.
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Newcastle University, Medical School, Newcastle Upon Tyne, UK.
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17
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Smirnova A, Richert L, Smirnov A, Mély Y, Tarassov I. Suborganellar Localization of Mitochondrial Proteins and Transcripts in Human Cells. Methods Mol Biol 2021; 2277:157-173. [PMID: 34080151 DOI: 10.1007/978-1-0716-1270-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondria have complex ultrastructure which includes continuous subcompartments, such as matrix, intermembrane space, and two membranes, as well as focal structures, such as nucleoids, RNA granules, and mitoribosomes. Comprehensive studies of the spatial distribution of proteins and RNAs inside the mitochondria are necessary to understand organellar gene expression processes and macromolecule targeting pathways. Here we give examples of distribution analysis of mitochondrial proteins and transcripts by conventional microscopy and the super-resolution technique 3D STORM. We provide detailed protocols and discuss limitations of immunolabeling of mitochondrial proteins and newly synthesized mitochondrial RNAs by bromouridine incorporation and single-molecule RNA FISH in hepatocarcinoma cells.
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Affiliation(s)
- Anna Smirnova
- UMR 7156 - Molecular Genetics, Genomics, Microbiology (GMGM), University of Strasbourg/CNRS, Strasbourg, France
| | - Ludovic Richert
- UMR 7021 - Laboratory of Biophotonics and Pharmacology (LBP), University of Strasbourg/CNRS, Illkirch, France
| | - Alexandre Smirnov
- UMR 7156 - Molecular Genetics, Genomics, Microbiology (GMGM), University of Strasbourg/CNRS, Strasbourg, France
| | - Yves Mély
- UMR 7021 - Laboratory of Biophotonics and Pharmacology (LBP), University of Strasbourg/CNRS, Illkirch, France
| | - Ivan Tarassov
- UMR 7156 - Molecular Genetics, Genomics, Microbiology (GMGM), University of Strasbourg/CNRS, Strasbourg, France.
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18
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Duranova H, Valkova V, Knazicka Z, Olexikova L, Vasicek J. Mitochondria: A worthwhile object for ultrastructural qualitative characterization and quantification of cells at physiological and pathophysiological states using conventional transmission electron microscopy. Acta Histochem 2020; 122:151646. [PMID: 33128989 DOI: 10.1016/j.acthis.2020.151646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022]
Abstract
Mitochondria are highly dynamic intracellular organelles with ultrastructural heterogeneity reflecting the behaviour and functions of the cells. The ultrastructural remodelling, performed by the counteracting active processes of mitochondrial fusion and fission, enables the organelles to respond to diverse cellular requirements and cues. It is also an important part of mechanisms underlying adaptation of mitochondria to pathophysiological conditions that challenge the cell homeostasis. However, if the stressor is constantly acting, the adaptive capacity of the cell can be exceeded and defective changes in mitochondrial morphology (indicating the insufficient functionality of mitochondria or development of mitochondrial disorders) may appear. Beside qualitative description of mitochondrial ultrastructure, stereological principles concerning the estimation of alterations in mitochondrial volume density or surface density are invaluable approaches for unbiased quantification of cells under physiological or pathophysiological conditions. In order to improve our understanding of cellular functions and dysfunctions, transmission electron microscopy (TEM) still remains a gold standard for qualitative and quantitative ultrastructural examination of mitochondria from various cell types, as well as from those experienced to different stimuli or toxicity-inducing factors. In the current study, general morphological and functional features of mitochondria, and their ultrastructural heterogeneity related to physiological and pathophysiological states of the cells are reviewed. Moreover, stereological approaches for accurate quantification of mitochondrial ultrastructure from electron micrographs taken from TEM are described in detail.
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Affiliation(s)
- Hana Duranova
- AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Veronika Valkova
- AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic
| | - Zuzana Knazicka
- Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic
| | - Lucia Olexikova
- Institute of Farm Animal Genetics and Reproduction, NPPC - Research Institute for Animal Production in Nitra, Hlohovecká 2, 951 41 Lužianky, Slovak Republic
| | - Jaromir Vasicek
- Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic; Institute of Farm Animal Genetics and Reproduction, NPPC - Research Institute for Animal Production in Nitra, Hlohovecká 2, 951 41 Lužianky, Slovak Republic
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19
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Ould Amer Y, Hebert-Chatelain E. Insight into the Interactome of Intramitochondrial PKA Using Biotinylation-Proximity Labeling. Int J Mol Sci 2020; 21:ijms21218283. [PMID: 33167377 PMCID: PMC7663848 DOI: 10.3390/ijms21218283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are fully integrated in cell signaling. Reversible phosphorylation is involved in adjusting mitochondrial physiology to the cellular needs. Protein kinase A (PKA) phosphorylates several substrates present at the external surface of mitochondria to maintain cellular homeostasis. However, few targets of PKA located inside the organelle are known. The aim of this work was to characterize the impact and the interactome of PKA located inside mitochondria. Our results show that the overexpression of intramitochondrial PKA decreases cellular respiration and increases superoxide levels. Using proximity-dependent biotinylation, followed by LC-MS/MS analysis and in silico phospho-site prediction, we identified 21 mitochondrial proteins potentially targeted by PKA. We confirmed the interaction of PKA with TIM44 using coimmunoprecipitation and observed that TIM44-S80 is a key residue for the interaction between the protein and the kinase. These findings provide insights into the interactome of intramitochondrial PKA and suggest new potential mechanisms in the regulation of mitochondrial functions.
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Affiliation(s)
- Yasmine Ould Amer
- Department of Biology, University of Moncton, Moncton, NB E1A 3E9, Canada;
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, University of Moncton, Moncton, NB E1A 3E9, Canada
| | - Etienne Hebert-Chatelain
- Department of Biology, University of Moncton, Moncton, NB E1A 3E9, Canada;
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, University of Moncton, Moncton, NB E1A 3E9, Canada
- Correspondence:
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20
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Haas KT, Rivière M, Wightman R, Peaucelle A. Multitarget Immunohistochemistry for Confocal and Super-resolution Imaging of Plant Cell Wall Polysaccharides. Bio Protoc 2020; 10:e3783. [PMID: 33659438 PMCID: PMC7842508 DOI: 10.21769/bioprotoc.3783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/21/2020] [Accepted: 08/17/2020] [Indexed: 11/02/2022] Open
Abstract
The plant cell wall (PCW) is a pecto-cellulosic extracellular matrix that envelopes the plant cell. By integrating extra-and intra-cellular cues, PCW mediates a plethora of essential physiological functions. Notably, it permits controlled and oriented tissue growth by tuning its local mechano-chemical properties. To refine our knowledge of these essential properties of PCW, we need an appropriate tool for the accurate observation of the native (in muro) structure of the cell wall components. The label-free techniques, such as AFM, EM, FTIR, and Raman microscopy, are used; however, they either do not have the chemical or spatial resolution. Immunolabeling with electron microscopy allows observation of the cell wall nanostructure, however, it is mostly limited to single and, less frequently, multiple labeling. Immunohistochemistry (IHC) is a versatile tool to analyze the distribution and localization of multiple biomolecules in the tissue. The subcellular resolution of chemical changes in the cell wall component can be observed with standard diffraction-limited optical microscopy. Furthermore, novel chemical imaging tools such as multicolor 3D dSTORM (Three-dimensional, direct Stochastic Optical Reconstruction Microscopy) nanoscopy makes it possible to resolve the native structure of the cell wall polymers with nanometer precision and in three dimensions. Here we present a protocol for preparing multi-target immunostaining of the PCW components taking as example Arabidopsis thaliana, Star fruit (Averrhoa carambola), and Maize thin tissue sections. This protocol is compatible with the standard confocal microscope, dSTORM nanoscope, and can also be implemented for other optical nanoscopy such as STED (Stimulated Emission Depletion Microscopy). The protocol can be adapted for any other subcellular compartments, plasma membrane, cytoplasmic, and intracellular organelles.
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Affiliation(s)
- Kalina T. Haas
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Methieu Rivière
- Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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21
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Song Y, Zhang X, Shen Z, Yang W, Wei J, Li S, Wang X, Li X, He Q, Zhang S, Zhang Q, Gao B. Improving Brightness and Stability of Si-Rhodamine for Super-Resolution Imaging of Mitochondria in Living Cells. Anal Chem 2020; 92:12137-12144. [PMID: 32844652 DOI: 10.1021/acs.analchem.9b04926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photostable and bright organic dyes emitting in the near-infrared region are highly desirable for long-term dynamic bioimaging. Herein, we report a synthetic approach to build novel methoxy modified Si-rhodamine (SiRMO) dyes by introducing the methoxybenzene on the xanthene moiety. The brightness of SiRMO increased from 2300 M-1 cm-1 (SiRMO-0) to 49000 M-1 cm-1 (SiRMO-2) when the substituent 2,5-dimethoxybenzene was replaced with 2,6-dimethoxybenzene. Moreover, the stability of SiRMO-2 was significantly improved due to the steric hindrance protection of the two methoxy groups on the ninth carbon atom of the xanthene. After fast cellular uptake, the SiRMO dyes selectively stained the mitochondria with a low background in live cultured cells and primary neurons. The high brightness and stability of SiRMO-2 significantly improved the capability of monitoring mitochondria dynamic processes in living cells under super-resolution conditions. Moreover, with the fluorescence nanoscopy techniques, we observed the structure of mitochondrial cristae and mitochondria fission, fusion, and apoptosis with a high temporal resolution. Under two-photon illumination, SiRMO-2 showed also enhanced two-photon brightness and stability, which are important for imaging in thick tissue.
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Affiliation(s)
- Yifang Song
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Xue Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Zixin Shen
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Wei Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Juandi Wei
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Shiyi Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Xu Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Xinwei Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qihua He
- Peking University Health Science Center, Beijing 100191, China
| | - Shuchen Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qisheng Zhang
- Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Baoxiang Gao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
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22
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Yang X, Yang Z, Wu Z, He Y, Shan C, Chai P, Ma C, Tian M, Teng J, Jin D, Yan W, Das P, Qu J, Xi P. Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe. Nat Commun 2020; 11:3699. [PMID: 32709877 PMCID: PMC7382495 DOI: 10.1038/s41467-020-17546-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria play a critical role in generating energy to support the entire lifecycle of biological cells, yet it is still unclear how their morphological structures evolve to regulate their functionality. Conventional fluorescence microscopy can only provide ~300 nm resolution, which is insufficient to visualize mitochondrial cristae. Here, we developed an enhanced squaraine variant dye (MitoESq-635) to study the dynamic structures of mitochondrial cristae in live cells with a superresolution technique. The low saturation intensity and high photostability of MitoESq-635 make it ideal for long-term, high-resolution (stimulated emission depletion) STED nanoscopy. We performed time-lapse imaging of the mitochondrial inner membrane over 50 min (3.9 s per frame, with 71.5 s dark recovery) in living HeLa cells with a resolution of 35.2 nm. The forms of the cristae during mitochondrial fusion and fission can be clearly observed. Our study demonstrates the emerging capability of optical STED nanoscopy to investigate intracellular physiological processes with nanoscale resolution for an extended period of time.
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Affiliation(s)
- Xusan Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
- School of Applied and Engineering Physics, Cornell University, Ithaca, 14853, USA.
| | - Zhigang Yang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Zhaoyang Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Ying He
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Chunyan Shan
- School of Life Sciences, Peking University, Beijing, 100871, China
- National Center for Protein Sciences, Peking University, Beijing, 100871, China
| | - Peiyuan Chai
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chenshuo Ma
- Material Science and Engineering, Rutgers University, Piscataway, NJ, 08854, USA
| | - Mi Tian
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Junlin Teng
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dayong Jin
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Yan
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Pintu Das
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Peng Xi
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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23
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Kunz TC, Götz R, Gao S, Sauer M, Kozjak-Pavlovic V. Using Expansion Microscopy to Visualize and Characterize the Morphology of Mitochondrial Cristae. Front Cell Dev Biol 2020; 8:617. [PMID: 32760723 PMCID: PMC7373753 DOI: 10.3389/fcell.2020.00617] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are double membrane bound organelles indispensable for biological processes such as apoptosis, cell signaling, and the production of many important metabolites, which includes ATP that is generated during the process known as oxidative phosphorylation (OXPHOS). The inner membrane contains folds called cristae, which increase the membrane surface and thus the amount of membrane-bound proteins necessary for the OXPHOS. These folds have been of great interest not only because of their importance for energy conversion, but also because changes in morphology have been linked to a broad range of diseases from cancer, diabetes, neurodegenerative diseases, to aging and infection. With a distance between opposing cristae membranes often below 100 nm, conventional fluorescence imaging cannot provide a resolution sufficient for resolving these structures. For this reason, various highly specialized super-resolution methods including dSTORM, PALM, STED, and SIM have been applied for cristae visualization. Expansion Microscopy (ExM) offers the possibility to perform super-resolution microscopy on conventional confocal microscopes by embedding the sample into a swellable hydrogel that is isotropically expanded by a factor of 4–4.5, improving the resolution to 60–70 nm on conventional confocal microscopes, which can be further increased to ∼ 30 nm laterally using SIM. Here, we demonstrate that the expression of the mitochondrial creatine kinase MtCK linked to marker protein GFP (MtCK-GFP), which localizes to the space between the outer and the inner mitochondrial membrane, can be used as a cristae marker. Applying ExM on mitochondria labeled with this construct enables visualization of morphological changes of cristae and localization studies of mitochondrial proteins relative to cristae without the need for specialized setups. For the first time we present the combination of specific mitochondrial intermembrane space labeling and ExM as a tool for studying internal structure of mitochondria.
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Affiliation(s)
- Tobias C Kunz
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ralph Götz
- Department of Biotechnology and Biophysics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Shiqiang Gao
- Department of Botany I, Julius-Maximilans-Universität Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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24
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Yang G, Liu Z, Zhang R, Tian X, Chen J, Han G, Liu B, Han X, Fu Y, Hu Z, Zhang Z. A Multi‐responsive Fluorescent Probe Reveals Mitochondrial Nucleoprotein Dynamics with Reactive Oxygen Species Regulation through Super‐resolution Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Guanqing Yang
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
| | - Zhengjie Liu
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
| | - Ruilong Zhang
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education Hefei Anhui 230601 China
| | - Xiaohe Tian
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
| | - Juan Chen
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
| | - Guangmei Han
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
| | - Bianhua Liu
- Institute of Intelligent Machines Chinese Academy of Sciences Hefei Anhui 230031 China
| | - Xinya Han
- School of Chemistry and Chemical Engineering Anhui University of Technology Ma'anshan Anhui 243032 China
| | - Yao Fu
- Department of Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Zhongping Zhang
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology Anhui University Hefei Anhui 230601 China
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education Hefei Anhui 230601 China
- Institute of Intelligent Machines Chinese Academy of Sciences Hefei Anhui 230031 China
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25
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Yang G, Liu Z, Zhang R, Tian X, Chen J, Han G, Liu B, Han X, Fu Y, Hu Z, Zhang Z. A Multi-responsive Fluorescent Probe Reveals Mitochondrial Nucleoprotein Dynamics with Reactive Oxygen Species Regulation through Super-resolution Imaging. Angew Chem Int Ed Engl 2020; 59:16154-16160. [PMID: 32573047 DOI: 10.1002/anie.202005959] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Indexed: 11/06/2022]
Abstract
Understanding the biomolecular interactions in a specific organelle has been a long-standing challenge because it requires super-resolution imaging to resolve the spatial locations and dynamic interactions of multiple biomacromolecules. Two key difficulties are the scarcity of suitable probes for super-resolution nanoscopy and the complications that arise from the use of multiple probes. Herein, we report a quinolinium derivative probe that is selectively enriched in mitochondria and switches on in three different fluorescence modes in response to hydrogen peroxide (H2 O2 ), proteins, and nucleic acids, enabling the visualization of mitochondrial nucleoprotein dynamics. STED nanoscopy reveals that the proteins localize at mitochondrial cristae and largely fuse with nucleic acids to form nucleoproteins, whereas increasing H2 O2 level leads to disassociation of nucleic acid-protein complexes.
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Affiliation(s)
- Guanqing Yang
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Zhengjie Liu
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Ruilong Zhang
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China.,Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University), Ministry of Education, Hefei, Anhui, 230601, China
| | - Xiaohe Tian
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Juan Chen
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Guangmei Han
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Bianhua Liu
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Xinya Han
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma'anshan, Anhui, 243032, China
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, 58183, Sweden
| | - Zhongping Zhang
- School of Chemistry and Chemical Engineering and Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China.,Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University), Ministry of Education, Hefei, Anhui, 230601, China.,Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
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26
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Segawa M, Wolf DM, Hultgren NW, Williams DS, van der Bliek AM, Shackelford DB, Liesa M, Shirihai OS. Quantification of cristae architecture reveals time-dependent characteristics of individual mitochondria. Life Sci Alliance 2020; 3:e201900620. [PMID: 32499316 PMCID: PMC7283135 DOI: 10.26508/lsa.201900620] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
Recent breakthroughs in live-cell imaging have enabled visualization of cristae, making it feasible to investigate the structure-function relationship of cristae in real time. However, quantifying live-cell images of cristae in an unbiased way remains challenging. Here, we present a novel, semi-automated approach to quantify cristae, using the machine-learning Trainable Weka Segmentation tool. Compared with standard techniques, our approach not only avoids the bias associated with manual thresholding but more efficiently segments cristae from Airyscan and structured illumination microscopy images. Using a cardiolipin-deficient cell line, as well as FCCP, we show that our approach is sufficiently sensitive to detect perturbations in cristae density, size, and shape. This approach, moreover, reveals that cristae are not uniformly distributed within the mitochondrion, and sites of mitochondrial fission are localized to areas of decreased cristae density. After a fusion event, individual cristae from the two mitochondria, at the site of fusion, merge into one object with distinct architectural values. Overall, our study shows that machine learning represents a compelling new strategy for quantifying cristae in living cells.
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Affiliation(s)
- Mayuko Segawa
- Department of Medicine, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Dane M Wolf
- Department of Medicine, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Graduate Program in Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Nan W Hultgren
- Departments of Ophthalmology and Neurobiology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - David S Williams
- Departments of Ophthalmology and Neurobiology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander M van der Bliek
- Molecular Biology Institute at University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - David B Shackelford
- Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marc Liesa
- Department of Medicine, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Orian S Shirihai
- Department of Medicine, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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27
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Szalai AM, Lopez LF, Morales-Vásquez MÁ, Stefani FD, Aramendía PF. Analysis of sparse molecular distributions in fibrous arrangements based on the distance to the first neighbor in single molecule localization microscopy. NANOSCALE 2020; 12:9495-9506. [PMID: 32313910 DOI: 10.1039/c9nr10805j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single Molecule Localization Microscopy (SMLM) currently attains a lateral resolution of around 10 nm approaching molecular size. Together with increasingly specific fluorescent labeling, it opens the possibility to quantitatively analyze molecular organization. When the labeling density is high enough, SMLM provides clear images of the molecular organization. However, either due to limited labeling efficiency or due to intrinsically low molecular abundance, SMLM delivers a small set of sparse and highly precise localizations. In this work, we introduce a correlation analysis of molecular locations based on the functional dependence of the complementary cumulative distribution function (CCDF) of the distance to the first neighbor (r1). We demonstrate that the log(-log(CCDF(r1))) vs. log(r1) is characterized by a scaling exponent n that takes extreme values of 2 for a random 2D distribution and 1 for a strictly linear arrangement, and find that n is a robust and sensitive metric to distinguish characteristics of the underlying structure responsible for the molecular distribution, even at a very low labeling density. The method enables the detection of fibrillary organization and the estimation of the diameter of host fibers under conditions where a visual inspection provides no clue.
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Affiliation(s)
- Alan M Szalai
- Centro de Investigaciones en Bionanociencias "Elizabeth Jares-Erijman" (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
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28
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Wolf DM, Segawa M, Shirihai OS, Liesa M. Method for live-cell super-resolution imaging of mitochondrial cristae and quantification of submitochondrial membrane potentials. Methods Cell Biol 2020; 155:545-555. [PMID: 32183976 PMCID: PMC7216778 DOI: 10.1016/bs.mcb.2019.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The emergence of diffraction-unlimited live-cell imaging technologies has enabled the examination of mitochondrial form and function in unprecedented detail. We recently developed an approach for visualizing the inner mitochondrial membrane and determined that cristae membranes possess distinct mitochondrial membrane potentials, representing unique bioenergetic subdomains within the same organelle. Here, we outline a methodology for resolving cristae and inner boundary membranes using the LSM880 with Airyscan. Furthermore, we demonstrate how to analyze TMRE fluorescence intensity using the Nernst equation to calculate membrane potentials of individual cristae. Altogether, using these new techniques to study the electrochemical properties of the cristae can help to gain deeper insight into the still elusive nature of the mitochondrion.
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Affiliation(s)
- Dane M Wolf
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Graduate Program in Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, United States
| | - Mayuko Segawa
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States.
| | - Marc Liesa
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States.
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29
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Sánchez MI, Vida Y, Pérez-Inestrosa E, Mascareñas JL, Vázquez ME, Sugiura A, Martínez-Costas J. MitoBlue as a tool to analyze the mitochondria-lysosome communication. Sci Rep 2020; 10:3528. [PMID: 32103132 PMCID: PMC7044336 DOI: 10.1038/s41598-020-60573-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/13/2020] [Indexed: 11/25/2022] Open
Abstract
MitoBlue is a fluorescent bisamidine that can be used to easily monitor the changes in mitochondrial degradation processes in different cells and cellular conditions. MitoBlue staining pattern is exceptional among mitochondrial dyes and recombinant fluorescent probes, allowing the dynamic study of mitochondrial recycling in a variety of situations in living cells. MitoBlue is a unique tool for the study of these processes that will allow the detailed characterization of communication between mitochondria and lysosomes.
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Affiliation(s)
- Mateo I Sánchez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de, Compostela, Spain
| | - Yolanda Vida
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND. Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, 29590, Campanillas, Málaga, Spain.,Universidad de Málaga-IBIMA, Departamento de Química Orgánica. Campus de Teatinos s/n, 29071, Málaga, Spain
| | - Ezequiel Pérez-Inestrosa
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND. Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, 29590, Campanillas, Málaga, Spain.,Universidad de Málaga-IBIMA, Departamento de Química Orgánica. Campus de Teatinos s/n, 29071, Málaga, Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de, Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de, Compostela, Spain
| | - Ayumu Sugiura
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada. .,Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, 15782, Santiago de, Compostela, Spain.
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30
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Evolving mtDNA populations within cells. Biochem Soc Trans 2020; 47:1367-1382. [PMID: 31484687 PMCID: PMC6824680 DOI: 10.1042/bst20190238] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular mtDNA populations, changing cell-to-cell distributions, means, and variances of mutant mtDNA load over time. As mtDNA mutant load has nonlinear effects on cell functionality, and cell functionality has nonlinear effects on tissue performance, these statistics of cellular mtDNA populations play vital roles in health, disease, and inheritance. This mini review will describe some of the better-known ways in which these populations change over time in different organisms, highlighting the importance of quantitatively understanding both mutant load mean and variance. Due to length constraints, we cannot attempt to be comprehensive but hope to provide useful links to some of the many excellent studies on these topics.
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31
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Hornak I, Rieger H. Stochastic Model of T Cell Repolarization during Target Elimination I. Biophys J 2020; 118:1733-1748. [PMID: 32130873 DOI: 10.1016/j.bpj.2020.01.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cytotoxic T lymphocytes (T) and natural killer cells are the main cytotoxic killer cells of the human body to eliminate pathogen-infected or tumorigenic cells (i.e., target cells). Once a natural killer or T cell has identified a target cell, they form a tight contact zone, the immunological synapse (IS). One then observes a repolarization of the cell involving the rotation of the microtubule (MT) cytoskeleton and a movement of the MT organizing center (MTOC) to a position that is just underneath the plasma membrane at the center of the IS. Concomitantly, a massive relocation of organelles attached to MTs is observed, including the Golgi apparatus, lytic granules, and mitochondria. Because the mechanism of this relocation is still elusive, we devise a theoretical model for the molecular-motor-driven motion of the MT cytoskeleton confined between plasma membrane and nucleus during T cell polarization. We analyze different scenarios currently discussed in the literature, the cortical sliding and capture-shrinkage mechanisms, and compare quantitative predictions about the spatiotemporal evolution of MTOC position and MT cytoskeleton morphology with experimental observations. The model predicts the experimentally observed biphasic nature of the repositioning due to an interplay between MT cytoskeleton geometry and motor forces and confirms the dominance of the capture-shrinkage over the cortical sliding mechanism when the MTOC and IS are initially diametrically opposed. We also find that the two mechanisms act synergistically, thereby reducing the resources necessary for repositioning. Moreover, it turns out that the localization of dyneins in the peripheral supramolecular activation cluster facilitates their interaction with the MTs. Our model also opens a way to infer details of the dynein distribution from the experimentally observed features of the MT cytoskeleton dynamics. In a subsequent publication, we will address the issue of general initial configurations and situations in which the T cell established two ISs.
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Affiliation(s)
- Ivan Hornak
- Center for Biophysics (ZBP) and Department of Theoretical Physics, Saarland University, Saarbrücken, Germany
| | - Heiko Rieger
- Center for Biophysics (ZBP) and Department of Theoretical Physics, Saarland University, Saarbrücken, Germany.
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32
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Fuchs P, Rugen N, Carrie C, Elsässer M, Finkemeier I, Giese J, Hildebrandt TM, Kühn K, Maurino VG, Ruberti C, Schallenberg-Rüdinger M, Steinbeck J, Braun HP, Eubel H, Meyer EH, Müller-Schüssele SJ, Schwarzländer M. Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:420-441. [PMID: 31520498 DOI: 10.1111/tpj.14534] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/23/2019] [Accepted: 08/28/2019] [Indexed: 05/14/2023]
Abstract
Mitochondria host vital cellular functions, including oxidative phosphorylation and co-factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we explore the protein composition of an individual average plant mitochondrion to deduce principles of functional and structural organisation. We perform proteomics on purified mitochondria from cultured heterotrophic Arabidopsis cells with intensity-based absolute quantification and scale the dataset to the single organelle based on criteria that are justified by experimental evidence and theoretical considerations. We estimate that a total of 1.4 million protein molecules make up a single Arabidopsis mitochondrion on average. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40 000 for Voltage-Dependent Anion Channel 1 to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat proteins that modify mitochondrial transcripts. For our analysis, we consider the physical and chemical constraints of the single organelle and discuss prominent features of mitochondrial architecture, protein biogenesis, oxidative phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, and dynamics. While assessing the limitations of our considerations, we exemplify how our understanding of biochemical function and structural organization of plant mitochondria can be connected in order to obtain global and specific insights into how organelles work.
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Affiliation(s)
- Philippe Fuchs
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
- Institut für Nutzpflanzenforschung und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Nils Rugen
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Chris Carrie
- Department Biologie I - Botanik, Ludwig-Maximilians-Universität München, Grosshadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Marlene Elsässer
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
- Institut für Nutzpflanzenforschung und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
- Institut für Zelluläre und Molekulare Botanik (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Iris Finkemeier
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
| | - Jonas Giese
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
| | - Tatjana M Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 10, 06120, Halle/Saale, Germany
| | - Veronica G Maurino
- Institute of Developmental and Molecular Biology of Plants, and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Cristina Ruberti
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
| | - Mareike Schallenberg-Rüdinger
- Institut für Zelluläre und Molekulare Botanik (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Janina Steinbeck
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Etienne H Meyer
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 10, 06120, Halle/Saale, Germany
| | - Stefanie J Müller-Schüssele
- Institut für Nutzpflanzenforschung und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Markus Schwarzländer
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität, Schlossplatz 7-8, 48143, Münster, Germany
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Abstract
AbstractCentrosome is the main microtubule-organizing center in most animal cells. Its core structure, centriole, also assembles cilia and flagella that have important sensing and motility functions. Centrosome has long been recognized as a highly conserved organelle in eukaryotic species. Through electron microscopy, its ultrastructure was revealed to contain a beautiful nine-symmetrical core 60 years ago, yet its molecular basis has only been unraveled in the past two decades. The emergence of super-resolution microscopy allows us to explore the insides of a centrosome, which is smaller than the diffraction limit of light. Super-resolution microscopy also enables the compartmentation of centrosome proteins into different zones and the identification of their molecular interactions and functions. This paper compiles the centrosome architecture knowledge that has been revealed in recent years and highlights the power of several super-resolution techniques.
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34
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Jaiswal A, Hoerth CH, Zúñiga Pereira AM, Lorenz H. Improved spatial resolution by induced live cell and organelle swelling in hypotonic solutions. Sci Rep 2019; 9:12911. [PMID: 31501484 PMCID: PMC6733880 DOI: 10.1038/s41598-019-49408-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Induced morphology changes of cells and organelles are by far the easiest way to determine precise protein sub-locations and organelle quantities in light microscopy. By using hypotonic solutions to swell mammalian cell organelles we demonstrate that precise membrane, lumen or matrix protein locations within the endoplasmic reticulum, Golgi and mitochondria can reliably be established. We also show the benefit of this approach for organelle quantifications, especially for clumped or intertwined organelles like peroxisomes and mitochondria. Since cell and organelle swelling is reversible, it can be applied to live cells for successive high-resolution analyses. Our approach outperforms many existing imaging modalities with respect to resolution, ease-of-use and cost-effectiveness without excluding any co-utilization with existing optical (super)resolution techniques.
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Affiliation(s)
- Astha Jaiswal
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Christian H Hoerth
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Ana M Zúñiga Pereira
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.,Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Holger Lorenz
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.
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35
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Live-cell STED nanoscopy of mitochondrial cristae. Sci Rep 2019; 9:12419. [PMID: 31455826 PMCID: PMC6712041 DOI: 10.1038/s41598-019-48838-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are highly dynamic organelles that exhibit a complex inner architecture. They exhibit a smooth outer membrane and a highly convoluted inner membrane that forms invaginations called cristae. Imaging cristae in living cells poses a formidable challenge for super-resolution light microscopy. Relying on a cell line stably expressing the mitochondrial protein COX8A fused to the SNAP-tag and using STED (stimulated emission depletion) nanoscopy, we demonstrate the visualization of cristae dynamics in cultivated human cells. We show that in human HeLa cells lamellar cristae are often arranged in groups separated by voids that are generally occupied by mitochondrial nucleoids.
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36
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37
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Mitochondria as playmakers of apoptosis, autophagy and senescence. Semin Cell Dev Biol 2019; 98:139-153. [PMID: 31154010 DOI: 10.1016/j.semcdb.2019.05.022] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022]
Abstract
Mitochondria are the key energy-producing organelles and cellular source of reactive species. They are responsible for managing cell life and death by a balanced homeostasis passing through a network of structures, regulated principally via fission and fusion. Herein we discuss about the most advanced findings considering mitochondria as dynamic biophysical systems playing compelling roles in the regulation of energy metabolism in both physiologic and pathologic processes controlling cell death and survival. Precisely, we focus on the mitochondrial commitment to the onset, maintenance and counteraction of apoptosis, autophagy and senescence in the bioenergetic reprogramming of cancer cells. In this context, looking for a pharmacological manipulation of cell death processes as a successful route for future targeted therapies, there is major biotechnological challenge in underlining the location, function and molecular mechanism of mitochondrial proteins. Based on the critical role of mitochondrial functions for cellular health, a better knowledge of the main molecular players in mitochondria disfunction could be decisive for the therapeutical control of degenerative diseases, including cancer.
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38
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Abstract
Significance: In addition to their classical role in cellular ATP production, mitochondria are of key relevance in various (patho)physiological mechanisms including second messenger signaling, neuro-transduction, immune responses and death induction. Recent Advances: Within cells, mitochondria are motile and display temporal changes in internal and external structure ("mitochondrial dynamics"). During the last decade, substantial empirical and in silico evidence was presented demonstrating that mitochondrial dynamics impacts on mitochondrial function and vice versa. Critical Issues: However, a comprehensive and quantitative understanding of the bidirectional links between mitochondrial external shape, internal structure and function ("morphofunction") is still lacking. The latter particularly hampers our understanding of the functional properties and behavior of individual mitochondrial within single living cells. Future Directions: In this review we discuss the concept of mitochondrial morphofunction in mammalian cells, primarily using experimental evidence obtained within the last decade. The topic is introduced by briefly presenting the central role of mitochondria in cell physiology and the importance of the mitochondrial electron transport chain (ETC) therein. Next, we summarize in detail how mitochondrial (ultra)structure is controlled and discuss empirical evidence regarding the equivalence of mitochondrial (ultra)structure and function. Finally, we provide a brief summary of how mitochondrial morphofunction can be quantified at the level of single cells and mitochondria, how mitochondrial ultrastructure/volume impacts on mitochondrial bioreactions and intramitochondrial protein diffusion, and how mitochondrial morphofunction can be targeted by small molecules.
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Affiliation(s)
- Elianne P. Bulthuis
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Merel J.W. Adjobo-Hermans
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter H.G.M. Willems
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Werner J.H. Koopman
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Address correspondence to: Dr. Werner J.H. Koopman, Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, P.O. Box 9101, Nijmegen NL-6500 HB, The Netherlands
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39
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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40
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Son T, Lee D, Lee C, Moon G, Ha GE, Lee H, Kwak H, Cheong E, Kim D. Superlocalized Three-Dimensional Live Imaging of Mitochondrial Dynamics in Neurons Using Plasmonic Nanohole Arrays. ACS NANO 2019; 13:3063-3074. [PMID: 30802028 DOI: 10.1021/acsnano.8b08178] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigated the transport of neuronal mitochondria using superlocalized near-fields with plasmonic nanohole arrays (PNAs). Compared to traditional imaging techniques, PNAs create a massive array of superlocalized light beams and allow 3D mitochondrial dynamics to be sampled and extracted almost in real time. In this work, mitochondrial fluorescence excited by the PNAs was captured by an optical microscope using dual objective lenses, which produced superlocalized dynamics while minimizing light scattering by the plasmonic substrate. It was found that mitochondria move with an average velocity 0.33 ± 0.26 μm/s, a significant part of which, by almost 50%, was contributed by the movement along the depth axis ( z-axis). Mitochondrial positions were acquired with superlocalized precision (σ x = 5.7 nm and σ y = 11.8 nm) in the lateral plane and σ z = 78.7 nm in the z-axis, which presents an enhancement by 12.7-fold in resolution compared to confocal fluorescence microscopy. The approach is expected to serve as a way to provide 3D information on molecular dynamics in real time.
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41
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Jeandard D, Smirnova A, Tarassov I, Barrey E, Smirnov A, Entelis N. Import of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches. Cells 2019; 8:E286. [PMID: 30917553 PMCID: PMC6468882 DOI: 10.3390/cells8030286] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/26/2023] Open
Abstract
Mitochondria harbor their own genetic system, yet critically depend on the import of a number of nuclear-encoded macromolecules to ensure their expression. In all eukaryotes, selected non-coding RNAs produced from the nuclear genome are partially redirected into the mitochondria, where they participate in gene expression. Therefore, the mitochondrial RNome represents an intricate mixture of the intrinsic transcriptome and the extrinsic RNA importome. In this review, we summarize and critically analyze data on the nuclear-encoded transcripts detected in human mitochondria and outline the proposed molecular mechanisms of their mitochondrial import. Special attention is given to the various experimental approaches used to study the mitochondrial RNome, including some recently developed genome-wide and in situ techniques.
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Affiliation(s)
- Damien Jeandard
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Anna Smirnova
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Ivan Tarassov
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Eric Barrey
- GABI-UMR1313, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | | | - Nina Entelis
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
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42
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Scott GR, Guo KH, Dawson NJ. The Mitochondrial Basis for Adaptive Variation in Aerobic Performance in High-Altitude Deer Mice. Integr Comp Biol 2019; 58:506-518. [PMID: 29873740 DOI: 10.1093/icb/icy056] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondria play a central role in aerobic performance. Studies aimed at elucidating how evolved variation in mitochondrial physiology contributes to adaptive variation in aerobic performance can therefore provide a unique and powerful lens to understanding the evolution of complex physiological traits. Here, we review our ongoing work on the importance of changes in mitochondrial quantity and quality to adaptive variation in aerobic performance in high-altitude deer mice. Whole-organism aerobic capacity in hypoxia (VO2max) increases in response to hypoxia acclimation in this species, but high-altitude populations have evolved consistently greater VO2max than populations from low altitude. The evolved increase in VO2max in highlanders is associated with an evolved increase in the respiratory capacity of the gastrocnemius muscle. This appears to result from highlanders having more mitochondria in this tissue, attributed to a higher proportional abundance of oxidative fiber-types and a greater mitochondrial volume density within oxidative fibers. The latter is primarily caused by an over-abundance of subsarcolemmal mitochondria in high-altitude mice, which is likely advantageous for mitochondrial O2 supply because more mitochondria are situated adjacent to the cell membrane and close to capillaries. Evolved changes in gastrocnemius phenotype appear to be underpinned by population differences in the expression of genes involved in energy metabolism, muscle development, and vascular development. Hypoxia acclimation has relatively little effect on respiratory capacity of the gastrocnemius, but it increases respiratory capacity of the diaphragm. However, the mechanisms responsible for this increase differ between populations: lowlanders appear to adjust mitochondrial quantity and quality (i.e., increases in citrate synthase [CS] activity, and mitochondrial respiration relative to CS activity) and they exhibit higher rates of mitochondrial release of reactive oxygen species, whereas highlanders only increase mitochondrial quantity in response to hypoxia acclimation. In contrast to the variation in skeletal muscles, the respiratory capacity of cardiac muscle does not appear to be affected by hypoxia acclimation and varies little between populations. Therefore, evolved changes in mitochondrial quantity and quality make important tissue-specific contributions to adaptive variation in aerobic performance in high-altitude deer mice.
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Affiliation(s)
- Graham R Scott
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Kevin H Guo
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Neal J Dawson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
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43
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Pyrihová E, Motycková A, Voleman L, Wandyszewska N, Fišer R, Seydlová G, Roger A, Kolísko M, Doležal P. A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes. Genome Biol Evol 2018; 10:2813-2822. [PMID: 30265292 PMCID: PMC6200312 DOI: 10.1093/gbe/evy215] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anoxia. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondria and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist, Giardia intestinalis, one of the few experimental models for mitosome biology. Here, we present the identification of a single G. intestinalis Tim17 protein (GiTim17), made possible only by the implementation of a metamonad-specific hidden Markov model. While very divergent in primary sequence and in predicted membrane topology, experimental data suggest that GiTim17 is an inner membrane mitosomal protein, forming a disulphide-linked dimer. We suggest that the peculiar GiTim17 sequence reflects adaptation to the unusual, detergent resistant, inner mitosomal membrane. Specific pull-down experiments indicate interaction of GiTim17 with mitosomal Tim44, the tethering component of the import motor complex. Analysis of TIM complexes across eukaryote diversity suggests that a "single Tim" translocase is a convergent adaptation of mitosomes in anaerobic protists, with Tim22 and Tim17 (but not Tim23), providing the protein backbone.
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Affiliation(s)
- Eva Pyrihová
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Alžbeta Motycková
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Natalia Wandyszewska
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Radovan Fišer
- Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic
| | - Gabriela Seydlová
- Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic
| | - Andrew Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Martin Kolísko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Biology Centre CAS, České Budějovice, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
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Lia D, Reyes A, de Melo Campos JTA, Piolot T, Baijer J, Radicella JP, Campalans A. Mitochondrial maintenance under oxidative stress depends on mitochondrially localised α-OGG1. J Cell Sci 2018; 131:jcs.213538. [PMID: 29848661 DOI: 10.1242/jcs.213538] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/21/2018] [Indexed: 12/18/2022] Open
Abstract
Accumulation of 8-oxoguanine (8-oxoG) in mitochondrial DNA and mitochondrial dysfunction have been observed in cells deficient for the DNA glycosylase OGG1 when exposed to oxidative stress. In human cells, up to eight mRNAs for OGG1 can be generated by alternative splicing and it is still unclear which of them codes for the protein that ensures the repair of 8-oxoG in mitochondria. Here, we show that the α-OGG1 isoform, considered up to now to be exclusively nuclear, has a functional mitochondrial-targeting sequence and is imported into mitochondria. We analyse the sub-mitochondrial localisation of α-OGG1 with unprecedented resolution and show that this DNA glycosylase is associated with DNA in mitochondrial nucleoids. We show that the presence of α-OGG1 inside mitochondria and its enzymatic activity are required to preserve the mitochondrial network in cells exposed to oxidative stress. Altogether, these results unveil a new role of α-OGG1 in the mitochondria and indicate that the same isoform ensures the repair of 8-oxoG in both nuclear and mitochondrial genomes. The activity of α-OGG1 in mitochondria is sufficient for the recovery of organelle function after oxidative stress.
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Affiliation(s)
- Debora Lia
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Julliane Tamara Araújo de Melo Campos
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil
| | - Tristan Piolot
- Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France
| | - Jan Baijer
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - J Pablo Radicella
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - Anna Campalans
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France .,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
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Dlasková A, Engstová H, Špaček T, Kahancová A, Pavluch V, Smolková K, Špačková J, Bartoš M, Hlavatá LP, Ježek P. 3D super-resolution microscopy reflects mitochondrial cristae alternations and mtDNA nucleoid size and distribution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:829-844. [PMID: 29727614 DOI: 10.1016/j.bbabio.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
3D super-resolution microscopy based on the direct stochastic optical reconstruction microscopy (dSTORM) with primary Alexa-Fluor-647-conjugated antibodies is a powerful method for accessing changes of objects that could be normally resolved only by electron microscopy. Despite the fact that mitochondrial cristae yet to become resolved, we have indicated changes in cristae width and/or morphology by dSTORM of ATP-synthase F1 subunit α (F1α). Obtained 3D images were analyzed with the help of Ripley's K-function modeling spatial patterns or transferring them into distance distribution function. Resulting histograms of distances frequency distribution provide most frequent distances (MFD) between the localized single antibody molecules. In fasting state of model pancreatic β-cells, INS-1E, MFD between F1α were ~80 nm at 0 and 3 mM glucose, whereas decreased to 61 nm and 57 nm upon glucose-stimulated insulin secretion (GSIS) at 11 mM and 20 mM glucose, respectively. Shorter F1α interdistances reflected cristae width decrease upon GSIS, since such repositioning of F1α correlated to average 20 nm and 15 nm cristae width at 0 and 3 mM glucose, and 9 nm or 8 nm after higher glucose simulating GSIS (11, 20 mM glucose, respectively). Also, submitochondrial entities such as nucleoids of mtDNA were resolved e.g. after bromo-deoxyuridine (BrDU) pretreatment using anti-BrDU dSTORM. MFD in distances distribution histograms reflected an average nucleoid diameter (<100 nm) and average distances between nucleoids (~1000 nm). Double channel PALM/dSTORM with Eos-lactamase-β plus anti-TFAM dSTORM confirmed the latter average inter-nucleoid distance. In conclusion, 3D single molecule (dSTORM) microscopy is a reasonable tool for studying mitochondrion.
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Affiliation(s)
- Andrea Dlasková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Engstová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Špaček
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anežka Kahancová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vojtěch Pavluch
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarína Smolková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jitka Špačková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Bartoš
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic; Alef Ltd, Prague, Czech Republic
| | - Lydie Plecitá Hlavatá
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Ježek
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
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46
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Fast, long-term, super-resolution imaging with Hessian structured illumination microscopy. Nat Biotechnol 2018; 36:451-459. [PMID: 29644998 DOI: 10.1038/nbt.4115] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 03/01/2018] [Indexed: 01/13/2023]
Abstract
To increase the temporal resolution and maximal imaging time of super-resolution (SR) microscopy, we have developed a deconvolution algorithm for structured illumination microscopy based on Hessian matrixes (Hessian-SIM). It uses the continuity of biological structures in multiple dimensions as a priori knowledge to guide image reconstruction and attains artifact-minimized SR images with less than 10% of the photon dose used by conventional SIM while substantially outperforming current algorithms at low signal intensities. Hessian-SIM enables rapid imaging of moving vesicles or loops in the endoplasmic reticulum without motion artifacts and with a spatiotemporal resolution of 88 nm and 188 Hz. Its high sensitivity allows the use of sub-millisecond excitation pulses followed by dark recovery times to reduce photobleaching of fluorescent proteins, enabling hour-long time-lapse SR imaging of actin filaments in live cells. Finally, we observed the structural dynamics of mitochondrial cristae and structures that, to our knowledge, have not been observed previously, such as enlarged fusion pores during vesicle exocytosis.
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47
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Serricchio M, Vissa A, Kim PK, Yip CM, McQuibban GA. Cardiolipin synthesizing enzymes form a complex that interacts with cardiolipin-dependent membrane organizing proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:447-457. [DOI: 10.1016/j.bbalip.2018.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022]
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He H, Ye Z, Xiao Y, Yang W, Qian X, Yang Y. Super-Resolution Monitoring of Mitochondrial Dynamics upon Time-Gated Photo-Triggered Release of Nitric Oxide. Anal Chem 2018; 90:2164-2169. [PMID: 29316789 DOI: 10.1021/acs.analchem.7b04510] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nitric oxide (NO) potentially plays a regulatory role in mitochondrial fusion and fission, which are vital to cell survival and implicated in health, disease, and aging. Molecular tools facilitating the study of the relationship between NO and mitochondrial dynamics are in need. We have recently developed a novel NO donor (NOD550). Upon photoactivation, NOD550 decomposes to release two NO molecules and a fluorophore. The NO release could be spatially mapped with subdiffraction resolution and with a temporal resolution of 10 s. Due to the preferential localization of NOD550 at mitochondria, morphology and dynamics of mitochondria could be monitored upon NO release from NOD550.
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Affiliation(s)
- Haihong He
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology , Shanghai, 200237, China
| | - Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian, Liaoning 116024, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian, Liaoning 116024, China
| | - Wei Yang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian, Liaoning 116024, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology , Shanghai, 200237, China
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology , Shanghai, 200237, China
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Model MA, Petruccelli JC. Intracellular Macromolecules in Cell Volume Control and Methods of Their Quantification. CURRENT TOPICS IN MEMBRANES 2018; 81:237-289. [DOI: 10.1016/bs.ctm.2018.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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50
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Rocha S, Freitas A, Guimaraes SC, Vitorino R, Aroso M, Gomez-Lazaro M. Biological Implications of Differential Expression of Mitochondrial-Shaping Proteins in Parkinson's Disease. Antioxidants (Basel) 2017; 7:E1. [PMID: 29267236 PMCID: PMC5789311 DOI: 10.3390/antiox7010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/17/2022] Open
Abstract
It has long been accepted that mitochondrial function and morphology is affected in Parkinson's disease, and that mitochondrial function can be directly related to its morphology. So far, mitochondrial morphological alterations studies, in the context of this neurodegenerative disease, have been performed through microscopic methodologies. The goal of the present work is to address if the modifications in the mitochondrial-shaping proteins occurring in this disorder have implications in other cellular pathways, which might constitute important pathways for the disease progression. To do so, we conducted a novel approach through a thorough exploration of the available proteomics-based studies in the context of Parkinson's disease. The analysis provided insight into the altered biological pathways affected by changes in the expression of mitochondrial-shaping proteins via different bioinformatic tools. Unexpectedly, we observed that the mitochondrial-shaping proteins altered in the context of Parkinson's disease are, in the vast majority, related to the organization of the mitochondrial cristae. Conversely, in the studies that have resorted to microscopy-based techniques, the most widely reported alteration in the context of this disorder is mitochondria fragmentation. Cristae membrane organization is pivotal for mitochondrial ATP production, and changes in their morphology have a direct impact on the organization and function of the oxidative phosphorylation (OXPHOS) complexes. To understand which biological processes are affected by the alteration of these proteins we analyzed the binding partners of the mitochondrial-shaping proteins that were found altered in Parkinson's disease. We showed that the binding partners fall into seven different cellular components, which include mitochondria, proteasome, and endoplasmic reticulum (ER), amongst others. It is noteworthy that, by evaluating the biological process in which these modified proteins are involved, we showed that they are related to the production and metabolism of ATP, immune response, cytoskeleton alteration, and oxidative stress, amongst others. In summary, with our bioinformatics approach using the data on the modified proteins in Parkinson's disease patients, we were able to relate the alteration of mitochondrial-shaping proteins to modifications of crucial cellular pathways affected in this disease.
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Affiliation(s)
- Sara Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Ana Freitas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.
- FMUP-Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal.
| | - Sofia C Guimaraes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Rui Vitorino
- iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal.
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Universidade do Porto, 4200-319 Porto, Portugal.
| | - Miguel Aroso
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Maria Gomez-Lazaro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.
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