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Handley S, Anwer AG, Knab A, Bhargava A, Goldys EM. AutoMitoNetwork: Software for analyzing mitochondrial networks in autofluorescence images to enable label-free cell classification. Cytometry A 2024. [PMID: 39078083 DOI: 10.1002/cyto.a.24889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/31/2024]
Abstract
High-resolution mitochondria imaging in combination with image analysis tools have significantly advanced our understanding of cellular function in health and disease. However, most image analysis tools for mitochondrial studies have been designed to work with fluorescently labeled images only. Additionally, efforts to integrate features describing mitochondrial networks with machine learning techniques for the differentiation of cell types have been limited. Herein, we present AutoMitoNetwork software for image-based assessment of mitochondrial networks in label-free autofluorescence images using a range of interpretable morphological, intensity, and textural features. To demonstrate its utility, we characterized unstained mitochondrial networks in healthy retinal cells and in retinal cells exposed to two types of treatments: rotenone, which directly inhibited mitochondrial respiration and ATP production, and iodoacetic acid, which had a milder impact on mitochondrial networks via the inhibition of anaerobic glycolysis. For both cases, our multi-dimensional feature analysis combined with a support vector machine classifier distinguished between healthy cells and those treated with rotenone or iodoacetic acid. Subtle changes in morphological features were measured including increased fragmentation in the treated retinal cells, pointing to an association with metabolic mechanisms. AutoMitoNetwork opens new options for image-based machine learning in label-free imaging, diagnostics, and mitochondrial disease drug development.
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Affiliation(s)
- Shannon Handley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), University of New South Wales, Sydney, New South Wales, Australia
- The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Ayad G Anwer
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), University of New South Wales, Sydney, New South Wales, Australia
- The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Aline Knab
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), University of New South Wales, Sydney, New South Wales, Australia
- The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Akanksha Bhargava
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), University of New South Wales, Sydney, New South Wales, Australia
- The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Ewa M Goldys
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), University of New South Wales, Sydney, New South Wales, Australia
- The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
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2
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Vicente JJ, Khan K, Tillinghast G, McFaline-Figueroa JL, Sancak Y, Stella N. The microtubule targeting agent ST-401 triggers cell death in interphase and prevents the formation of polyploid giant cancer cells. J Transl Med 2024; 22:441. [PMID: 38730481 PMCID: PMC11084142 DOI: 10.1186/s12967-024-05234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Microtubule targeting agents (MTAs) are commonly prescribed to treat cancers and predominantly kill cancer cells in mitosis. Significantly, some MTA-treated cancer cells escape death in mitosis, exit mitosis and become malignant polyploid giant cancer cells (PGCC). Considering the low number of cancer cells undergoing mitosis in tumor tissues, killing them in interphase may represent a favored antitumor approach. We discovered that ST-401, a mild inhibitor of microtubule (MT) assembly, preferentially kills cancer cells in interphase as opposed to mitosis, a cell death mechanism that avoids the development of PGCC. Single cell RNA sequencing identified mRNA transcripts regulated by ST-401, including mRNAs involved in ribosome and mitochondrial functions. Accordingly, ST-401 induces a transient integrated stress response, reduces energy metabolism, and promotes mitochondria fission. This cell response may underly death in interphase and avoid the development of PGCC. Considering that ST-401 is a brain-penetrant MTA, we validated these results in glioblastoma cell lines and found that ST-401 also reduces energy metabolism and promotes mitochondria fission in GBM sensitive lines. Thus, brain-penetrant mild inhibitors of MT assembly, such as ST-401, that induce death in interphase through a previously unanticipated antitumor mechanism represent a potentially transformative new class of therapeutics for the treatment of GBM.
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Affiliation(s)
- Juan Jesus Vicente
- Department of Physiology and Biophysics, University of Washington, Health Sciences Building G424, 1705 NE Pacific Str., Seattle, WA, 98195-7280, USA.
| | - Kainat Khan
- Department of Pharmacology, University of Washington, Health Sciences Center F404A, 1959 NE Pacific Str., Seattle, WA, 98195-7280, USA
| | - Grant Tillinghast
- Department of Biomedical Engineering, Columbia University, New York, NY, 10025, USA
| | | | - Yasemin Sancak
- Department of Pharmacology, University of Washington, Health Sciences Center F404A, 1959 NE Pacific Str., Seattle, WA, 98195-7280, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Health Sciences Center F404A, 1959 NE Pacific Str., Seattle, WA, 98195-7280, USA.
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA.
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3
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Hultgren NW, Zhou T, Williams DS. Machine learning-based 3D segmentation of mitochondria in polarized epithelial cells. Mitochondrion 2024; 76:101882. [PMID: 38599302 DOI: 10.1016/j.mito.2024.101882] [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: 04/25/2023] [Revised: 03/18/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Mitochondria are dynamic organelles that alter their morphological characteristics in response to functional needs. Therefore, mitochondrial morphology is an important indicator of mitochondrial function and cellular health. Reliable segmentation of mitochondrial networks in microscopy images is a crucial initial step for further quantitative evaluation of their morphology. However, 3D mitochondrial segmentation, especially in cells with complex network morphology, such as in highly polarized cells, remains challenging. To improve the quality of 3D segmentation of mitochondria in super-resolution microscopy images, we took a machine learning approach, using 3D Trainable Weka, an ImageJ plugin. We demonstrated that, compared with other commonly used methods, our approach segmented mitochondrial networks effectively, with improved accuracy in different polarized epithelial cell models, including differentiated human retinal pigment epithelial (RPE) cells. Furthermore, using several tools for quantitative analysis following segmentation, we revealed mitochondrial fragmentation in bafilomycin-treated RPE cells.
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Affiliation(s)
- Nan W Hultgren
- Department of Ophthalmology and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA.
| | - Tianli Zhou
- Department of Ophthalmology and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - David S Williams
- Department of Ophthalmology and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA; Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, CA 90095, USA.
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4
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Martins TS, Correia M, Pinheiro D, Lemos C, Mendes MV, Pereira C, Costa V. Sit4 Genetically Interacts with Vps27 to Regulate Mitochondrial Function and Lifespan in Saccharomyces cerevisiae. Cells 2024; 13:655. [PMID: 38667270 PMCID: PMC11049076 DOI: 10.3390/cells13080655] [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: 01/06/2024] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The Sit4 protein phosphatase plays a key role in orchestrating various cellular processes essential for maintaining cell viability during aging. We have previously shown that SIT4 deletion promotes vacuolar acidification, mitochondrial derepression, and oxidative stress resistance, increasing yeast chronological lifespan. In this study, we performed a proteomic analysis of isolated vacuoles and yeast genetic interaction analysis to unravel how Sit4 influences vacuolar and mitochondrial function. By employing high-resolution mass spectrometry, we show that sit4Δ vacuolar membranes were enriched in Vps27 and Hse1, two proteins that are part of the endosomal sorting complex required for transport-0. In addition, SIT4 exhibited a negative genetic interaction with VPS27, as sit4∆vps27∆ double mutants had a shortened lifespan compared to sit4∆ and vps27∆ single mutants. Our results also show that Vps27 did not increase sit4∆ lifespan by improving protein trafficking or vacuolar sorting pathways. However, Vps27 was critical for iron homeostasis and mitochondrial function in sit4∆ cells, as sit4∆vps27∆ double mutants exhibited high iron levels and impaired mitochondrial respiration. These findings show, for the first time, cross-talk between Sit4 and Vps27, providing new insights into the mechanisms governing chronological lifespan.
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Affiliation(s)
- Telma S. Martins
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Miguel Correia
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Denise Pinheiro
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Carolina Lemos
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marta Vaz Mendes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Clara Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vítor Costa
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
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5
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Liu D, Webber HC, Bian F, Xu Y, Prakash M, Feng X, Yang M, Yang H, You IJ, Li L, Liu L, Liu P, Huang H, Chang CY, Liu L, Shah SH, Torre AL, Welsbie DS, Sun Y, Duan X, Goldberg JL, Braun M, Lansky Z, Hu Y. Optineurin-facilitated axonal mitochondria delivery promotes neuroprotection and axon regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587832. [PMID: 38617277 PMCID: PMC11014509 DOI: 10.1101/2024.04.02.587832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Optineurin (OPTN) mutations are linked to amyotrophic lateral sclerosis (ALS) and normal tension glaucoma (NTG), but a relevant animal model is lacking, and the molecular mechanisms underlying neurodegeneration are unknown. We found that OPTN C-terminus truncation (OPTN∆C) causes late-onset neurodegeneration of retinal ganglion cells (RGCs), optic nerve (ON), and spinal cord motor neurons, preceded by a striking decrease of axonal mitochondria. Surprisingly, we discover that OPTN directly interacts with both microtubules and the mitochondrial transport complex TRAK1/KIF5B, stabilizing them for proper anterograde axonal mitochondrial transport, in a C-terminus dependent manner. Encouragingly, overexpressing OPTN/TRAK1/KIF5B reverses not only OPTN truncation-induced, but also ocular hypertension-induced neurodegeneration, and promotes striking ON regeneration. Therefore, in addition to generating new animal models for NTG and ALS, our results establish OPTN as a novel facilitator of the microtubule-dependent mitochondrial transport necessary for adequate axonal mitochondria delivery, and its loss as the likely molecular mechanism of neurodegeneration.
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Affiliation(s)
- Dong Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hannah C. Webber
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Fuyun Bian
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yangfan Xu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Manjari Prakash
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Xue Feng
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Ming Yang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hang Yang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - In-Jee You
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Liang Li
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Liping Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Pingting Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Haoliang Huang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Chien-Yi Chang
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Liang Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sahil H Shah
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA; USA
| | - Derek S. Welsbie
- Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA; USA
| | - Yang Sun
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xin Duan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA; USA
| | - Jeffrey Louis Goldberg
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Marcus Braun
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Yang Hu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
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6
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Blick E, Mormino M, Siewers V, Nygård Y. Development of an Haa1-Based Biosensor for Acetic Acid Sensing in Saccharomyces cerevisiae. Methods Mol Biol 2024; 2844:221-238. [PMID: 39068343 DOI: 10.1007/978-1-0716-4063-0_15] [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] [Indexed: 07/30/2024]
Abstract
Transcription factor (TF)-based biosensors are important tools in strain development and screening as they can allow accurate monitoring of intracellular concentrations of a molecule. Acetic acid is one of the main inhibitors in lignocellulosic biomass and a major challenge when using yeast cell factories for biorefinery applications. Thus, developing acetic acid tolerant strains is of great importance. The acetic acid sensing biosensor developed relies on the endogenous Saccharomyces cerevisiae TF Haa1 that upon binding of acetic acid translocates to the nucleus. The acetic acid biosensor can be used as a tool for strain development and evaluation, as well as for screening of acetic acid-producing strains and for dynamic monitoring of acetic acid accumulation. This chapter describes a methodology for developing a TF-based biosensor for acetic acid sensing. Protocols for design considerations, part construction, and characterization procedures are included. The approach can potentially be adapted to any molecule where a suitable TF can be identified.
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Affiliation(s)
- Elin Blick
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Maurizio Mormino
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Yvonne Nygård
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
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7
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Banerjee R, Mukherjee A, Adhikary A, Sharma S, Hussain MS, Ali ME, Nagotu S. Insights into the role of the conserved GTPase domain residues T62 and S277 in yeast Dnm1. Int J Biol Macromol 2023; 253:127381. [PMID: 37838106 DOI: 10.1016/j.ijbiomac.2023.127381] [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: 06/08/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Mitochondrial division is a highly regulated process. The master regulator of this process is the multi-domain, conserved protein called Dnm1 in yeast. In this study, we systematically analyzed two residues, T62 and S277, reported to be putatively phosphorylated in the GTPase domain of the protein. These residues lie in the G2 and G5 motifs of the GTPase domain. Both residues are important for the function of the protein, as evident from in vivo and in vitro analysis of the non-phosphorylatable and phosphomimetic variants. Dnm1T62A/D and Dnm1S277A/D showed differences with respect to the protein localization and puncta dynamics in vivo, albeit both were non-functional as assessed by mitochondrial morphology and GTPase activity. Overall, the secondary structure of the protein variants was unaltered, but local conformational changes were observed. Interestingly, both Dnm1T62A/D and Dnm1S277A/D exhibited dominant-negative behavior when expressed in cells containing endogenous Dnm1. To our knowledge, we report for the first time a single residue (S277) change that does not alter the localization of Dnm1 but makes it non-functional in a dominant-negative manner. Intriguingly, the two residues analyzed in this study are present in the same domain but exhibit variable effects when mutated to alanine or aspartic acid.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ankita Adhikary
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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8
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Megarioti AH, Esch BM, Athanasopoulos A, Koulouris D, Makridakis M, Lygirou V, Samiotaki M, Zoidakis J, Sophianopoulou V, André B, Fröhlich F, Gournas C. Ferroptosis-protective membrane domains in quiescence. Cell Rep 2023; 42:113561. [PMID: 38096056 DOI: 10.1016/j.celrep.2023.113561] [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: 04/09/2023] [Revised: 11/02/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Quiescence is a common cellular state, required for stem cell maintenance and microorganismal survival under stress conditions or starvation. However, the mechanisms promoting quiescence maintenance remain poorly known. Plasma membrane components segregate into distinct microdomains, yet the role of this compartmentalization in quiescence remains unexplored. Here, we show that flavodoxin-like proteins (FLPs), ubiquinone reductases of the yeast eisosome membrane compartment, protect quiescent cells from lipid peroxidation and ferroptosis. Eisosomes and FLPs expand specifically in respiratory-active quiescent cells, and mutants lacking either show accelerated aging and defective quiescence maintenance and accumulate peroxidized phospholipids with monounsaturated or polyunsaturated fatty acids (PUFAs). FLPs are essential for the extramitochondrial regeneration of the lipophilic antioxidant ubiquinol. FLPs, alongside the Gpx1/2/3 glutathione peroxidases, prevent iron-driven, PUFA-dependent ferroptotic cell death. Our work describes ferroptosis-protective mechanisms in yeast and introduces plasma membrane compartmentalization as an important factor in the long-term survival of quiescent cells.
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Affiliation(s)
- Amalia H Megarioti
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece; Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece
| | - Bianca M Esch
- Bioanalytical Chemistry Section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Alexandros Athanasopoulos
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece
| | - Dimitrios Koulouris
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece
| | - Manousos Makridakis
- Biotechnology Division, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming," 16672 Vari, Greece
| | - Jerome Zoidakis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece; Biotechnology Division, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vicky Sophianopoulou
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece
| | - Bruno André
- Molecular Physiology of the Cell Laboratory, Université Libre de Bruxelles (ULB), IBMM, 6041 Gosselies, Belgium
| | - Florian Fröhlich
- Bioanalytical Chemistry Section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany; Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany.
| | - Christos Gournas
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15341 Agia Paraskevi, Greece.
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9
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Wong W, Bravo P, Yunker PJ, Ratcliff WC, Burnetti AJ. Examining the role of oxygen-binding proteins on the early evolution of multicellularity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569647. [PMID: 38106219 PMCID: PMC10723371 DOI: 10.1101/2023.12.01.569647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Oxygen availability is a key factor in the evolution of multicellularity, as larger and more sophisticated organisms often require mechanisms allowing efficient oxygen delivery to their tissues. One such mechanism is the presence of oxygen-binding proteins, such as globins and hemerythrins, which arose in the ancestor of bilaterian animals. Despite their importance, the precise mechanisms by which oxygen-binding proteins influenced the early stages of multicellular evolution under varying environmental oxygen levels are not yet clear. We addressed this knowledge gap by heterologously expressing the oxygen binding proteins myoglobin and myohemerythrin in snowflake yeast, a model system of simple, undifferentiated multicellularity. These proteins increased the depth and rate of oxygen diffusion, increasing the fitness of snowflake yeast growing aerobically. Experiments show that, paradoxically, oxygen-binding proteins confer a greater fitness benefit for larger organisms under high, not low, O2 conditions. We show via biophysical modeling that this is because facilitated diffusion is more efficient when oxygen is abundant, transporting a greater quantity of O2 which can be used for metabolism. By alleviating anatomical diffusion limitations to oxygen consumption, the evolution of O2-binding proteins in the oxygen-rich Neoproterozoic may have been a key breakthrough enabling the evolution of increasingly large, complex multicellular metazoan lineages.
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Affiliation(s)
- Whitney Wong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pablo Bravo
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony J Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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10
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Charrasse S, Poquillon T, Saint-Omer C, Pastore M, Bordignon B, Frye RE, Reynes C, Racine V, Aouacheria A. Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity. Comput Struct Biotechnol J 2023; 21:5609-5619. [PMID: 38047232 PMCID: PMC10690410 DOI: 10.1016/j.csbj.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Mitochondria are essential organelles that play crucial roles in cellular energy metabolism, calcium signaling and apoptosis. Their importance in tissue homeostasis and stress responses, combined to their ability to transition between various structural and functional states, make them excellent organelles for monitoring cellular health. Quantitative assessment of mitochondrial morphology can therefore provide valuable insights into environmentally-induced cell damage. High-content screening (HCS) provides a powerful tool for analyzing organelles and cellular substructures. We developed a fully automated and miniaturized HCS wet-plus-dry pipeline (MITOMATICS) exploiting mitochondrial morphology as a marker for monitoring cellular health or damage. MITOMATICS uses an in-house, proprietary software (MitoRadar) to enable fast, exhaustive and cost-effective analysis of mitochondrial morphology and its inherent diversity in live cells. We applied our pipeline and big data analytics software to assess the mitotoxicity of selected chemicals, using the mitochondrial uncoupler CCCP as an internal control. Six different pesticides (inhibiting complexes I, II and III of the mitochondrial respiratory chain) were tested as individual compounds and five other pesticides present locally in Occitanie (Southern France) were assessed in combination to determine acute mitotoxicity. Our results show that the assayed pesticides exhibit specific signatures when used as single compounds or chemical mixtures and that they function synergistically to impact mitochondrial architecture. Study of environment-induced mitochondrial damage has the potential to open new fields in mechanistic toxicology, currently underexplored by regulatory toxicology and exposome research. Such exploration could inform health policy guidelines and foster pharmacological intervention, water, air and soil pollution control and food safety.
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Affiliation(s)
- Sophie Charrasse
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
| | - Titouan Poquillon
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
- QuantaCell SAS, Hôpital Saint Eloi, IRMB, 80 avenue Augustin Fliche, 34090 Montpellier, France
| | - Charlotte Saint-Omer
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
| | - Manuela Pastore
- STATABIO BioCampus, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Benoit Bordignon
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Christelle Reynes
- STATABIO BioCampus, Univ. Montpellier, CNRS, INSERM, Montpellier, France
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Victor Racine
- QuantaCell SAS, Hôpital Saint Eloi, IRMB, 80 avenue Augustin Fliche, 34090 Montpellier, France
| | - Abdel Aouacheria
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
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11
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Vicente JJ, Khan K, Tillinghast G, McFaline-Figueroa JL, Sancak Y, Stella N. Mitosis exit followed by death in interphase prevents the development of polyploid giant cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555795. [PMID: 37693393 PMCID: PMC10491223 DOI: 10.1101/2023.08.31.555795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Microtubule targeting agents ( MTAs ) are commonly prescribed to treat cancers and predominantly kill cancer cells in mitosis. Significantly, some MTA-treated cancer cells can escape death in mitosis and exit mitosis, and become malignant polyploid giant cancer cells ( PGCC ). Considering the low number of malignant cells undergoing mitosis in tumor tissue, killing these cells in interphase may represent a favored antitumor approach. We discovered that ST-401, a mild inhibitor of microtubule assembly, preferentially kills cancer cells in interphase as opposed to mitosis, and avoids the development of PGCC. Single cell RNA sequencing identified mRNA transcripts regulated by ST-401, including mRNAs involved in ribosome and mitochondrial functions. Accordingly, ST-401 induces an integrated stress response and promotes mitochondria fission accompanied by a reduction in energy metabolism. This cell response may underly death in interphase and avoid the development of PGCC.
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12
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Paukštytė J, López Cabezas RM, Feng Y, Tong K, Schnyder D, Elomaa E, Gregorova P, Doudin M, Särkkä M, Sarameri J, Lippi A, Vihinen H, Juutila J, Nieminen A, Törönen P, Holm L, Jokitalo E, Krisko A, Huiskonen J, Sarin LP, Hietakangas V, Picotti P, Barral Y, Saarikangas J. Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity. Mol Cell 2023; 83:3360-3376.e11. [PMID: 37699397 DOI: 10.1016/j.molcel.2023.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/18/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
Aging is associated with progressive phenotypic changes. Virtually all cellular phenotypes are produced by proteins, and their structural alterations can lead to age-related diseases. However, we still lack comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contributions to age-related phenotypes. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry (LiP-MS). The results, compiled in online ProtAge catalog, unraveled age-related functional changes in regulators of translation, protein folding, and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging, causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction, and led to lifespan extension. Altogether, this comprehensive map of protein structural changes enables identifying mechanisms of age-related phenotypes and offers opportunities for their reversal.
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Affiliation(s)
- Jurgita Paukštytė
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Rosa María López Cabezas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Ellinoora Elomaa
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Pavlina Gregorova
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Matteo Doudin
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Meeri Särkkä
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Jesse Sarameri
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helena Vihinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anni Nieminen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Törönen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Liisa Holm
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Juha Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - L Peter Sarin
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland.
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13
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Chelius X, Bartosch V, Rausch N, Haubner M, Schramm J, Braun RJ, Klecker T, Westermann B. Selective retention of dysfunctional mitochondria during asymmetric cell division in yeast. PLoS Biol 2023; 21:e3002310. [PMID: 37721958 PMCID: PMC10538663 DOI: 10.1371/journal.pbio.3002310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
Decline of mitochondrial function is a hallmark of cellular aging. To counteract this process, some cells inherit mitochondria asymmetrically to rejuvenate daughter cells. The molecular mechanisms that control this process are poorly understood. Here, we made use of matrix-targeted D-amino acid oxidase (Su9-DAO) to selectively trigger oxidative damage in yeast mitochondria. We observed that dysfunctional mitochondria become fusion-incompetent and immotile. Lack of bud-directed movements is caused by defective recruitment of the myosin motor, Myo2. Intriguingly, intact mitochondria that are present in the same cell continue to move into the bud, establishing that quality control occurs directly at the level of the organelle in the mother. The selection of healthy organelles for inheritance no longer works in the absence of the mitochondrial Myo2 adapter protein Mmr1. Together, our data suggest a mechanism in which the combination of blocked fusion and loss of motor protein ensures that damaged mitochondria are retained in the mother cell to ensure rejuvenation of the bud.
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Affiliation(s)
- Xenia Chelius
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | | | | | | | - Jana Schramm
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Ralf J. Braun
- Department Medizin, Fakultät Medizin/Zahnmedizin, Danube Private University, Krems, Austria
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
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14
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Leite AC, Martins TS, Cesário RR, Teixeira V, Costa V, Pereira C. Mitochondrial respiration promotes Cdc37-dependent stability of the Cdk1 homolog Cdc28. J Cell Sci 2023; 136:286215. [PMID: 36594787 DOI: 10.1242/jcs.260279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/25/2022] [Indexed: 01/04/2023] Open
Abstract
Cdc28, the homolog of mammalian Cdk1, is a conserved key regulatory kinase for all major cell cycle transitions in yeast. We have found that defects in mitochondrial respiration (including deletion of ATP2, an ATP synthase subunit) inhibit growth of cells carrying a degron allele of Cdc28 (cdc28td) or Cdc28 temperature-sensitive mutations (cdc28-1 and cdc28-1N) at semi-permissive temperatures. Loss of cell proliferation in the atp2Δcdc28td double mutant is associated with aggravated cell cycle arrest and mitochondrial dysfunction, including mitochondrial hyperpolarization and fragmentation. Unexpectedly, in mutants defective in mitochondrial respiration, steady-state protein levels of mutant cdc28 are strongly reduced, accounting for the aggravated growth defects. Stability of Cdc28 is promoted by the Hsp90-Cdc37 chaperone complex. Our results show that atp2Δcdc28td double-mutant cells, but not single mutants, are sensitive to chemical inhibition of the Hsp90-Cdc37 complex, and exhibit reduced levels of additional Hsp90-Cdc37 client kinases, suggesting an inhibition of this complex. In agreement, overexpression of CDC37 improved atp2Δcdc28td cell growth and Cdc28 levels. Overall, our study shows that simultaneous disturbance of mitochondrial respiration and Cdc28 activity reduces the capacity of Cdc37 to chaperone client kinases, leading to growth arrest.
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Affiliation(s)
- Ana Cláudia Leite
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Telma S Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Rute R Cesário
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vitor Teixeira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vítor Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Clara Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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15
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Ciliary neurotrophic factor-mediated neuroprotection involves enhanced glycolysis and anabolism in degenerating mouse retinas. Nat Commun 2022; 13:7037. [PMID: 36396639 PMCID: PMC9672129 DOI: 10.1038/s41467-022-34443-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Ciliary neurotrophic factor (CNTF) acts as a potent neuroprotective cytokine in multiple models of retinal degeneration. To understand mechanisms underlying its broad neuroprotective effects, we have investigated the influence of CNTF on metabolism in a mouse model of photoreceptor degeneration. CNTF treatment improves the morphology of photoreceptor mitochondria, but also leads to reduced oxygen consumption and suppressed respiratory chain activities. Molecular analyses show elevated glycolytic pathway gene transcripts and active enzymes. Metabolomics analyses detect significantly higher levels of ATP and the energy currency phosphocreatine, elevated glycolytic pathway metabolites, increased TCA cycle metabolites, lipid biosynthetic pathway intermediates, nucleotides, and amino acids. Moreover, CNTF treatment restores the key antioxidant glutathione to the wild type level. Therefore, CNTF significantly impacts the metabolic status of degenerating retinas by promoting aerobic glycolysis and augmenting anabolic activities. These findings reveal cellular mechanisms underlying enhanced neuronal viability and suggest potential therapies for treating retinal degeneration.
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16
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Hu K, Yan TM, Cao KY, Li F, Ma XR, Lai Q, Liu JC, Pan Y, Kou JP, Jiang ZH. A tRNA-derived fragment of ginseng protects heart against ischemia/reperfusion injury via targeting the lncRNA MIAT/VEGFA pathway. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:672-688. [PMID: 36090756 PMCID: PMC9440274 DOI: 10.1016/j.omtn.2022.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Traditional Chinese medicines (TCMs) have been widely used for treating ischemic heart disease (IHD), and secondary metabolites are generally regarded as their pharmacologically active components. However, the effects of nucleic acids in TCMs remain unclear. We reported for the first time that a 22-mer double-strand RNA consisting of HC83 (a tRNA-derived fragment [tRF] from the 3' end of tRNAGln(UUG) of ginseng) and its complementary sequence significantly promoted H9c2 cell survival after hypoxia/reoxygenation (H/R) in vitro. HC83_mimic could also significantly improve cardiac function by maintaining both cytoskeleton integrity and mitochondrial function of cardiomyocytes. Further in vivo investigations revealed that HC83_mimic is more potent than metoprolol by >500-fold against myocardial ischemia/reperfusion (MI/R) injury. In-depth studies revealed that HC83 directly downregulated a lncRNA known as myocardial infarction-associated transcript (MIAT) that led to a subsequent upregulation of VEGFA expression. These findings provided the first evidence that TCM-derived tRFs can exert miRNA-like functions in mammalian systems, therefore supporting the idea that TCM-derived tRFs are promising RNA drug candidates shown to have extraordinarily potent effects. In summary, this study provides a novel strategy not only for discovering pharmacologically active tRFs from TCMs but also for efficiently exploring new therapeutic targets for various diseases.
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Affiliation(s)
- Kua Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Kai-Yue Cao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Fang Li
- Department of Complex Prescription of TCM, China Pharmaceutical University, Nanjing 211198, China
| | - Xiao-Rong Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Qiong Lai
- Department of Complex Prescription of TCM, China Pharmaceutical University, Nanjing 211198, China
| | - Jin-Cheng Liu
- Department of Complex Prescription of TCM, China Pharmaceutical University, Nanjing 211198, China
| | - Yu Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Jun-Ping Kou
- Department of Complex Prescription of TCM, China Pharmaceutical University, Nanjing 211198, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
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17
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Yu JSL, Correia-Melo C, Zorrilla F, Herrera-Dominguez L, Wu MY, Hartl J, Campbell K, Blasche S, Kreidl M, Egger AS, Messner CB, Demichev V, Freiwald A, Mülleder M, Howell M, Berman J, Patil KR, Alam MT, Ralser M. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance. Nat Microbiol 2022; 7:542-555. [PMID: 35314781 PMCID: PMC8975748 DOI: 10.1038/s41564-022-01072-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic–prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically. Using microbiome data analysis and a self-establishing metabolically cooperating yeast community model, the authors show that the presence of auxotrophs in a microbial community increases metabolic interactions between cells and fosters antimicrobial drug tolerance.
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Affiliation(s)
- Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Francisco Zorrilla
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucia Herrera-Dominguez
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Mary Y Wu
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Johannes Hartl
- Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marco Kreidl
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vadim Demichev
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité University Medicine, Berlin, Germany.,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Howell
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Kiran R Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE. .,Warwick Medical School, University of Warwick, Coventry, UK.
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK. .,Department of Biochemistry, Charité University Medicine, Berlin, Germany. .,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany.
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18
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Vowinckel J, Hartl J, Marx H, Kerick M, Runggatscher K, Keller MA, Mülleder M, Day J, Weber M, Rinnerthaler M, Yu JSL, Aulakh SK, Lehmann A, Mattanovich D, Timmermann B, Zhang N, Dunn CD, MacRae JI, Breitenbach M, Ralser M. The metabolic growth limitations of petite cells lacking the mitochondrial genome. Nat Metab 2021; 3:1521-1535. [PMID: 34799698 PMCID: PMC7612105 DOI: 10.1038/s42255-021-00477-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022]
Abstract
Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.
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Affiliation(s)
- Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Biognosys AG, Schlieren, Switzerland
| | - Johannes Hartl
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Hans Marx
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Martin Kerick
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Parasitology and Biomedicine 'López-Neyra' (IPBLN, CSIC), Granada, Spain
| | - Kathrin Runggatscher
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Manuela Weber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Andrea Lehmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Nianshu Zhang
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Turkey
| | - James I MacRae
- Metabolomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany.
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
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19
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Bouwknegt J, Koster CC, Vos AM, Ortiz-Merino RA, Wassink M, Luttik MAH, van den Broek M, Hagedoorn PL, Pronk JT. Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis. Fungal Biol Biotechnol 2021; 8:10. [PMID: 34656184 PMCID: PMC8520639 DOI: 10.1186/s40694-021-00117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD. Results Heterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9. Conclusions Activity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure–function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-021-00117-4.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Aurin M Vos
- Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mats Wassink
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter L Hagedoorn
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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20
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Bakare AB, Meshrkey F, Lowe B, Molder C, Rao RR, Zhan J, Iyer S. MitoCellPhe reveals mitochondrial morphologies in single fibroblasts and clustered stem cells. Am J Physiol Cell Physiol 2021; 321:C735-C748. [PMID: 34469204 PMCID: PMC8560386 DOI: 10.1152/ajpcell.00231.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/27/2021] [Accepted: 08/16/2021] [Indexed: 11/22/2022]
Abstract
Mitochondria are dynamic organelles that differ significantly in their morphologies across cell types, reflecting specific cellular needs and stages in development. Despite the wide biological significance in disease and in health, delineating mitochondrial morphologies in complex systems remains challenging. Here, we present the Mitochondrial Cellular Phenotype (MitoCellPhe) tool developed for quantifying mitochondrial morphologies and demonstrate its utility in delineating differences in mitochondrial morphologies in a human fibroblast and human induced pluripotent stem cell (hiPSC) line. MitoCellPhe generates 24 parameters, allowing for a comprehensive analysis of mitochondrial structures and importantly allows for quantification to be performed on mitochondria in images containing single cells or clusters of cells. With this tool, we were able to validate previous findings that show networks of mitochondria in healthy fibroblast cell lines and a more fragmented morphology in hiPSCs. Using images generated from control and diseased fibroblasts and hiPSCs, we also demonstrate the efficacy of the toolset in delineating differences in morphologies between healthy and the diseased state in both stem cell (hiPSC) and differentiated fibroblast cells. Our results demonstrate that MitoCellPhe enables high-throughput, sensitive, detailed, and quantitative mitochondrial morphological assessment and thus enables better biological insights into mitochondrial dynamics in health and disease.
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Affiliation(s)
- Ajibola B Bakare
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Fibi Meshrkey
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas
- Department of Histology and Cell Biology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Benjamin Lowe
- Department of Computer Science and Computer Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Carson Molder
- Department of Computer Science and Computer Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Raj R Rao
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Justin Zhan
- Department of Computer Science and Computer Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas
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21
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Corso D, Chemello F, Alessio E, Urso I, Ferrarese G, Bazzega M, Romualdi C, Lanfranchi G, Sales G, Cagnin S. MyoData: An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle. Comput Struct Biotechnol J 2021; 19:4142-4155. [PMID: 34527188 PMCID: PMC8342900 DOI: 10.1016/j.csbj.2021.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression through non-coding RNAs at single myofiber and nucleus resolution. Reinterpretation of KEGG pathways with microRNA and long non-coding RNA activities. miR-149, -214, and let-7e alter mitochondrial shape. The long non-coding RNA Pvt1 is a sponge for miR-27a. miR-208b regulates Sox6; miR-214 regulates both Sox6 and Slc16a3.
Non-coding RNAs represent the largest part of transcribed mammalian genomes and prevalently exert regulatory functions. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) can modulate the activity of each other. Skeletal muscle is the most abundant tissue in mammals. It is composed of different cell types with myofibers that represent the smallest complete contractile system. Considering that lncRNAs and miRNAs are more cell type-specific than coding RNAs, to understand their function it is imperative to evaluate their expression and action within single myofibers. In this database, we collected gene expression data for coding and non-coding genes in single myofibers and used them to produce interaction networks based on expression correlations. Since biological pathways are more informative than networks based on gene expression correlation, to understand how altered genes participate in the studied phenotype, we integrated KEGG pathways with miRNAs and lncRNAs. The database also integrates single nucleus gene expression data on skeletal muscle in different patho-physiological conditions. We demonstrated that these networks can serve as a framework from which to dissect new miRNA and lncRNA functions to experimentally validate. Some interactions included in the database have been previously experimentally validated using high throughput methods. These can be the basis for further functional studies. Using database information, we demonstrate the involvement of miR-149, -214 and let-7e in mitochondria shaping; the ability of the lncRNA Pvt1 to mitigate the action of miR-27a via sponging; and the regulatory activity of miR-214 on Sox6 and Slc16a3. The MyoData is available at https://myodata.bio.unipd.it.
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Affiliation(s)
- Davide Corso
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Francesco Chemello
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Enrico Alessio
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Ilenia Urso
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Giulia Ferrarese
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Martina Bazzega
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.,CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
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22
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Mormino M, Siewers V, Nygård Y. Development of an Haa1-based biosensor for acetic acid sensing in Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6363685. [PMID: 34477863 PMCID: PMC8435060 DOI: 10.1093/femsyr/foab049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022] Open
Abstract
Acetic acid is one of the main inhibitors of lignocellulosic hydrolysates and acetic acid tolerance is crucial for the development of robust cell factories for conversion of biomass. As a precursor of acetyl-coenzyme A, it also plays an important role in central carbon metabolism. Thus, monitoring acetic acid levels is a crucial aspect when cultivating yeast. Transcription factor-based biosensors represent useful tools to follow metabolite concentrations. Here, we present the development of an acetic acid biosensor based on the Saccharomyces cerevisiae transcription factor Haa1 that upon binding to acetic acid relocates to the nucleus. In the biosensor, a synthetic transcription factor consisting of Haa1 and BM3R1 from Bacillus megaterium was used to control expression of a reporter gene under a promoter containing BM3R1 binding sites. The biosensor did not drive expression under a promoter containing Haa1 binding sites and responded to acetic acid over a linear range spanning from 10 to 60 mM. To validate its applicability, the biosensor was integrated into acetic acid-producing strains. A direct correlation between biosensor output and acetic acid production was detected. The developed biosensor enables high-throughput screening of strains producing acetic acid and could also be used to investigate acetic acid-tolerant strain libraries.
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Affiliation(s)
- Maurizio Mormino
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Yvonne Nygård
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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23
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Banerjee R, Kumar A, Satpati P, Nagotu S. Mimicking human Drp1 disease-causing mutations in yeast Dnm1 reveals altered mitochondrial dynamics. Mitochondrion 2021; 59:283-295. [PMID: 34157431 DOI: 10.1016/j.mito.2021.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022]
Abstract
The dynamin-related protein 1 (Drp1) and its homologs in various eukaryotes are essential to maintain mitochondrial morphology and regulate mitochondrial division. Several mutations in different domains of Drp1 have been reported, which result in debilitating conditions. Four such disease-causing mutations of the middle domain of Drp1 were mimicked in the yeast dynamin-related GTPase (Dnm1) and were characterized in this study. Mitochondrial morphology and protein function were observed to be altered to a variable extent in cells expressing the mutated variants of Dnm1. Several aspects related to the protein such as punctate formation, localization to mitochondria, dynamic behavior and structure were analyzed by microscopy, biochemical studies and molecular dynamics simulations. Significant effects on the protein structure and function were observed in cells expressing A430D and G397D mutations. Overall, our data provide insight into the molecular and cellular alterations resulting from middle domain mutations in Dnm1.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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24
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Hemel IMGM, Engelen BPH, Luber N, Gerards M. A hitchhiker's guide to mitochondrial quantification. Mitochondrion 2021; 59:216-224. [PMID: 34102326 DOI: 10.1016/j.mito.2021.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/21/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022]
Abstract
The variety of available mitochondrial quantification tools makes it difficult to select the most reliable and accurate quantification tool. Here, we performed elaborate analyses on five open source ImageJ tools. Excessive clustering of mitochondrial structures was observed in four tools, caused by the global thresholding applied by these tools. The Mitochondrial Analyzer, which uses adaptive thresholding, outperformed the other examined tools, with accurate structural segregation and identification. Additionally, we showed that the Mitochondrial Analyzer successfully identifies mitochondrial morphology differences. Based on the observed performance, we consider the Mitochondrial Analyzer the best open source tool for mitochondrial network morphology quantification.
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Affiliation(s)
- Irene M G M Hemel
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Bob P H Engelen
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Nicole Luber
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Mike Gerards
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands.
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25
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Bozdag GO, Libby E, Pineau R, Reinhard CT, Ratcliff WC. Oxygen suppression of macroscopic multicellularity. Nat Commun 2021; 12:2838. [PMID: 33990594 PMCID: PMC8121917 DOI: 10.1038/s41467-021-23104-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/14/2021] [Indexed: 02/04/2023] Open
Abstract
Atmospheric oxygen is thought to have played a vital role in the evolution of large, complex multicellular organisms. Challenging the prevailing theory, we show that the transition from an anaerobic to an aerobic world can strongly suppress the evolution of macroscopic multicellularity. Here we select for increased size in multicellular 'snowflake' yeast across a range of metabolically-available O2 levels. While yeast under anaerobic and high-O2 conditions evolved to be considerably larger, intermediate O2 constrained the evolution of large size. Through sequencing and synthetic strain construction, we confirm that this is due to O2-mediated divergent selection acting on organism size. We show via mathematical modeling that our results stem from nearly universal evolutionary and biophysical trade-offs, and thus should apply broadly. These results highlight the fact that oxygen is a double-edged sword: while it provides significant metabolic advantages, selection for efficient use of this resource may paradoxically suppress the evolution of macroscopic multicellular organisms.
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Affiliation(s)
- G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Eric Libby
- Integrated Science Lab, Umeå University, Umeå, Sweden
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- Santa Fe Institute, Santa Fe, NM, USA
| | - Rozenn Pineau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Georgia, USA
| | - Christopher T Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Riverside, CA, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- NASA Astrobiology Institute, Reliving the Past Team, Atlanta, GA, USA.
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26
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Ihenacho UK, Meacham KA, Harwig MC, Widlansky ME, Hill RB. Mitochondrial Fission Protein 1: Emerging Roles in Organellar Form and Function in Health and Disease. Front Endocrinol (Lausanne) 2021; 12:660095. [PMID: 33841340 PMCID: PMC8027123 DOI: 10.3389/fendo.2021.660095] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial fission protein 1 (Fis1) was identified in yeast as being essential for mitochondrial division or fission and subsequently determined to mediate human mitochondrial and peroxisomal fission. Yet, its exact functions in humans, especially in regard to mitochondrial fission, remains an enigma as genetic deletion of Fis1 elongates mitochondria in some cell types, but not others. Fis1 has also been identified as an important component of apoptotic and mitophagic pathways suggesting the protein may have multiple, essential roles. This review presents current perspectives on the emerging functions of Fis1 and their implications in human health and diseases, with an emphasis on Fis1's role in both endocrine and neurological disorders.
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Affiliation(s)
| | - Kelsey A. Meacham
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Megan Cleland Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael E. Widlansky
- Department of Medicine, Division of Cardiovascular Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - R. Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
- *Correspondence: R. Blake Hill,
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27
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Sidarala V, Pearson GL, Parekh VS, Thompson B, Christen L, Gingerich MA, Zhu J, Stromer T, Ren J, Reck EC, Chai B, Corbett JA, Mandrup-Poulsen T, Satin LS, Soleimanpour SA. Mitophagy protects β cells from inflammatory damage in diabetes. JCI Insight 2020; 5:141138. [PMID: 33232298 PMCID: PMC7819751 DOI: 10.1172/jci.insight.141138] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
Inflammatory damage contributes to β cell failure in type 1 and 2 diabetes (T1D and T2D, respectively). Mitochondria are damaged by inflammatory signaling in β cells, resulting in impaired bioenergetics and initiation of proapoptotic machinery. Hence, the identification of protective responses to inflammation could lead to new therapeutic targets. Here, we report that mitophagy serves as a protective response to inflammatory stress in both human and rodent β cells. Utilizing in vivo mitophagy reporters, we observed that diabetogenic proinflammatory cytokines induced mitophagy in response to nitrosative/oxidative mitochondrial damage. Mitophagy-deficient β cells were sensitized to inflammatory stress, leading to the accumulation of fragmented dysfunctional mitochondria, increased β cell death, and hyperglycemia. Overexpression of CLEC16A, a T1D gene and mitophagy regulator whose expression in islets is protective against T1D, ameliorated cytokine-induced human β cell apoptosis. Thus, mitophagy promotes β cell survival and prevents diabetes by countering inflammatory injury. Targeting this pathway has the potential to prevent β cell failure in diabetes and may be beneficial in other inflammatory conditions.
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Affiliation(s)
- Vaibhav Sidarala
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and
| | - Gemma L Pearson
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and
| | - Vishal S Parekh
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Benjamin Thompson
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lisa Christen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morgan A Gingerich
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and.,Program in Biological Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jie Zhu
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and
| | - Tracy Stromer
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and
| | - Jianhua Ren
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emma C Reck
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and
| | - Biaoxin Chai
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and
| | - John A Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Leslie S Satin
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and.,Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Scott A Soleimanpour
- Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine, and.,VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
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28
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Guldner IH, Wang Q, Yang L, Golomb SM, Zhao Z, Lopez JA, Brunory A, Howe EN, Zhang Y, Palakurthi B, Barron M, Gao H, Xuei X, Liu Y, Li J, Chen DZ, Landreth GE, Zhang S. CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10. Cell 2020; 183:1234-1248.e25. [PMID: 33113353 PMCID: PMC7704908 DOI: 10.1016/j.cell.2020.09.064] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 08/25/2020] [Accepted: 09/28/2020] [Indexed: 12/30/2022]
Abstract
Brain metastasis (br-met) develops in an immunologically unique br-met niche. Central nervous system-native myeloid cells (CNS-myeloids) and bone-marrow-derived myeloid cells (BMDMs) cooperatively regulate brain immunity. The phenotypic heterogeneity and specific roles of these myeloid subsets in shaping the br-met niche to regulate br-met outgrowth have not been fully revealed. Applying multimodal single-cell analyses, we elucidated a heterogeneous but spatially defined CNS-myeloid response during br-met outgrowth. We found Ccr2+ BMDMs minimally influenced br-met while CNS-myeloid promoted br-met outgrowth. Additionally, br-met-associated CNS-myeloid exhibited downregulation of Cx3cr1. Cx3cr1 knockout in CNS-myeloid increased br-met incidence, leading to an enriched interferon response signature and Cxcl10 upregulation. Significantly, neutralization of Cxcl10 reduced br-met, while rCxcl10 increased br-met and recruited VISTAHi PD-L1+ CNS-myeloid to br-met lesions. Inhibiting VISTA- and PD-L1-signaling relieved immune suppression and reduced br-met burden. Our results demonstrate that loss of Cx3cr1 in CNS-myeloid triggers a Cxcl10-mediated vicious cycle, cultivating a br-met-promoting, immune-suppressive niche.
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Affiliation(s)
- Ian H Guldner
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA
| | - Qingfei Wang
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA
| | - Lin Yang
- Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Department of Computer Science and Engineering, College of Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Samantha M Golomb
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA
| | - Zhuo Zhao
- Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Department of Computer Science and Engineering, College of Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jacqueline A Lopez
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Abigail Brunory
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA
| | - Erin N Howe
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA
| | - Yizhe Zhang
- Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Department of Computer Science and Engineering, College of Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Bhavana Palakurthi
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA
| | - Martin Barron
- Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Jun Li
- Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Danny Z Chen
- Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Department of Computer Science and Engineering, College of Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gary E Landreth
- Indiana University School of Medicine Stark Neuroscience Research Institute, Indianapolis, IN 46202, USA
| | - Siyuan Zhang
- Department of Biological Sciences, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA; Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA.
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Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology. Sci Rep 2020; 10:18941. [PMID: 33144635 PMCID: PMC7642274 DOI: 10.1038/s41598-020-75899-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.
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Walden EA, Fong RY, Pham TT, Knill H, Laframboise SJ, Huard S, Harper ME, Baetz K. Phenomic screen identifies a role for the yeast lysine acetyltransferase NuA4 in the control of Bcy1 subcellular localization, glycogen biosynthesis, and mitochondrial morphology. PLoS Genet 2020; 16:e1009220. [PMID: 33253187 PMCID: PMC7728387 DOI: 10.1371/journal.pgen.1009220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/10/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cellular metabolism is tightly regulated by many signaling pathways and processes, including lysine acetylation of proteins. While lysine acetylation of metabolic enzymes can directly influence enzyme activity, there is growing evidence that lysine acetylation can also impact protein localization. As the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 has been implicated in a variety of metabolic processes, we have explored whether NuA4 controls the localization and/or protein levels of metabolic proteins. We performed a high-throughput microscopy screen of over 360 GFP-tagged metabolic proteins and identified 23 proteins whose localization and/or abundance changed upon deletion of the NuA4 scaffolding subunit, EAF1. Within this, three proteins were required for glycogen synthesis and 14 proteins were associated with the mitochondria. We determined that in eaf1Δ cells the transcription of glycogen biosynthesis genes is upregulated resulting in increased proteins and glycogen production. Further, in the absence of EAF1, mitochondria are highly fused, increasing in volume approximately 3-fold, and are chaotically distributed but remain functional. Both the increased glycogen synthesis and mitochondrial elongation in eaf1Δ cells are dependent on Bcy1, the yeast regulatory subunit of PKA. Surprisingly, in the absence of EAF1, Bcy1 localization changes from being nuclear to cytoplasmic and PKA activity is altered. We found that NuA4-dependent localization of Bcy1 is dependent on a lysine residue at position 313 of Bcy1. However, the glycogen accumulation and mitochondrial elongation phenotypes of eaf1Δ, while dependent on Bcy1, were not fully dependent on Bcy1-K313 acetylation state and subcellular localization of Bcy1. As NuA4 is highly conserved with the human Tip60 complex, our work may inform human disease biology, revealing new avenues to investigate the role of Tip60 in metabolic diseases.
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Affiliation(s)
- Elizabeth A. Walden
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Roger Y. Fong
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Trang T. Pham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Hana Knill
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sylvain Huard
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
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31
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Picture perfect: Imaging mitochondrial membrane potential changes in retina slices with minimal stray fluorescence. Exp Eye Res 2020; 202:108318. [PMID: 33091432 DOI: 10.1016/j.exer.2020.108318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/24/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022]
Abstract
Mitochondrial membrane potential (Ψm) is a critical parameter that can be used to determine cellular well-being. As it is a direct measure of the cell's ATP generating capability, in recent years, this key component in cell biology has been the subject of thousands of biochemical and biophysical investigations. Membrane-permeant fluorescent dyes, like tetramethylrhodamine ethyl ester (TMRE), have been predominantly employed to monitor ΔΨm in cells. These dyes are typically lipophilic cationic compounds that equilibrate across membranes in a Nernstian fashion, thus accumulating into the mitochondrial membrane matrix space in inverse proportion to Ψm. However, the bath loading method practiced for labelling tissue slices with these cationic dyes poses limitations in the form of non-specificity and low signal to noise ratio, which compromises the precision of the results. Therefore, we introduce an alternative way for TMRE loading to image the ΔΨm in tissue slices by utilizing a low resistance glass pipette attached to a pressure injector. This method shows highly precise fluorescent dye labelling of the mitochondria and offers maximum output intensity, in turn enhancing signal to noise ratio.
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Chemello F, Grespi F, Zulian A, Cancellara P, Hebert-Chatelain E, Martini P, Bean C, Alessio E, Buson L, Bazzega M, Armani A, Sandri M, Ferrazza R, Laveder P, Guella G, Reggiani C, Romualdi C, Bernardi P, Scorrano L, Cagnin S, Lanfranchi G. Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle. Cell Rep 2020; 26:3784-3797.e8. [PMID: 30917329 DOI: 10.1016/j.celrep.2019.02.105] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/29/2018] [Accepted: 02/26/2019] [Indexed: 12/27/2022] Open
Abstract
Skeletal muscle is composed of different myofiber types that preferentially use glucose or lipids for ATP production. How fuel preference is regulated in these post-mitotic cells is largely unknown, making this issue a key question in the fields of muscle and whole-body metabolism. Here, we show that microRNAs (miRNAs) play a role in defining myofiber metabolic profiles. mRNA and miRNA signatures of all myofiber types obtained at the single-cell level unveiled fiber-specific regulatory networks and identified two master miRNAs that coordinately control myofiber fuel preference and mitochondrial morphology. Our work provides a complete and integrated mouse myofiber type-specific catalog of gene and miRNA expression and establishes miR-27a-3p and miR-142-3p as regulators of lipid use in skeletal muscle.
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Affiliation(s)
- Francesco Chemello
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Pasqua Cancellara
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Etienne Hebert-Chatelain
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Camilla Bean
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Enrico Alessio
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Martina Bazzega
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Marco Sandri
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Ruggero Ferrazza
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Paolo Laveder
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
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Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. Proc Natl Acad Sci U S A 2020; 117:7524-7535. [PMID: 32184324 PMCID: PMC7132131 DOI: 10.1073/pnas.1918216117] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This work offers a unique portrayal of yeast mitochondria through the characterization of its absolute proteome. The study of biophysical changes in the mitochondrial network associated with proteome profiling, throughout yeast growth and the transition from fermentative to respiratory metabolism, lays out the crucial role this organelle has in balancing the overall metabolic status of the cell. Using proteomic mass spectrometry, state of the art fluorescence microscopy, and lipidomics analysis, these data provide a highly quantitative description of key mitochondrial processes across three states of metabolism. In particular, the work highlights the significant contribution of functional and structural remodeling occurring during the diauxic shift of this subcellular organelle. Saccharomyces cerevisiae constitutes a popular eukaryal model for research on mitochondrial physiology. Being Crabtree-positive, this yeast has evolved the ability to ferment glucose to ethanol and respire ethanol once glucose is consumed. Its transition phase from fermentative to respiratory metabolism, known as the diauxic shift, is reflected by dramatic rearrangements of mitochondrial function and structure. To date, the metabolic adaptations that occur during the diauxic shift have not been fully characterized at the organelle level. In this study, the absolute proteome of mitochondria was quantified alongside precise parametrization of biophysical properties associated with the mitochondrial network using state-of-the-art optical-imaging techniques. This allowed the determination of absolute protein abundances at a subcellular level. By tracking the transformation of mitochondrial mass and volume, alongside changes in the absolute mitochondrial proteome allocation, we could quantify how mitochondria balance their dual role as a biosynthetic hub as well as a center for cellular respiration. Furthermore, our findings suggest that in the transition from a fermentative to a respiratory metabolism, the diauxic shift represents the stage where major structural and functional reorganizations in mitochondrial metabolism occur. This metabolic transition, initiated at the mitochondria level, is then extended to the rest of the yeast cell.
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Mitochondrial Fission and Fusion Dynamics Generate Efficient, Robust, and Evenly Distributed Network Topologies in Budding Yeast Cells. Cell Syst 2020; 10:287-297.e5. [PMID: 32105618 DOI: 10.1016/j.cels.2020.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 10/22/2019] [Accepted: 02/04/2020] [Indexed: 11/22/2022]
Abstract
The simplest configuration of mitochondria in a cell is as small separate organellar units. Instead, mitochondria often form a dynamic, intricately connected network. A basic understanding of the topological properties of mitochondrial networks, and their influence on cell function is lacking. We performed an extensive quantitative analysis of mitochondrial network topology, extracting mitochondrial networks in 3D from live-cell microscopic images of budding yeast cells. In the presence of fission and fusion, mitochondrial network structures exhibited certain topological properties similar to other real-world spatial networks. Fission and fusion dynamics were required to efficiently distribute mitochondria throughout the cell and generate highly interconnected networks that can facilitate efficient diffusive search processes. Thus, mitochondrial fission and fusion combine to regulate the underlying topology of mitochondrial networks, which may independently impact cell function.
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Whole-Genome Approach to Understanding the Mechanism of Action of a Histatin 5-Derived Peptide. Antimicrob Agents Chemother 2020; 64:AAC.01698-19. [PMID: 31843998 DOI: 10.1128/aac.01698-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022] Open
Abstract
The incidence of opportunistic fungal infections that threaten immunocompromised patients, along with the limited arsenal of antifungal drugs, calls for renewed efforts to develop novel antifungal therapies. Antimicrobial peptides have garnered interest as potential therapeutics. Among naturally occurring peptides, histatin 5 is a well-characterized 24-amino-acid peptide with strong antifungal activity. Our lab has identified a smaller histatin derivative, KM29, with stronger activity against multiple Candida spp., prompting us to investigate its fungicidal mechanism. A genetic screen was developed to test the Saccharomyces cerevisiae genomewide deletion collection for mutants with increased or decreased peptide sensitivity. The goal was to identify genes that would reveal insights into the mechanism of action of KM29, to be assessed in Candida albicans Several biological processes yielded increased sensitivity, with endosomal transport and vacuolar function appearing at high frequencies. Among the pathways involved in increased resistance, mitochondrial function showed the highest normalized genome frequency; hence, we focused on characterizing this pathway. KM29 localizes to mitochondria, and the killing activity depends on a functional electron transport chain. In addition, KM29 triggered reactive oxygen species (ROS) production, which was responsible for some cell death but insufficient to account for the complete killing activity. In agreement with this finding, we found that KM29 induced mitochondrial fragmentation and a mild loss of mitochondrial membrane potential. Furthermore, respiratory mutants exhibited severely diminished KM29 uptake. We confirmed this behavior in a C. albicans respiratory mutant. Taking our findings together, this work delineates the mitochondrial functions associated with KM29 fungicidal activity and provides additional pathways for further characterization in Candida spp.
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Larrea D, Pera M, Gonnelli A, Quintana-Cabrera R, Akman HO, Guardia-Laguarta C, Velasco KR, Area-Gomez E, Dal Bello F, De Stefani D, Horvath R, Shy ME, Schon EA, Giacomello M. MFN2 mutations in Charcot-Marie-Tooth disease alter mitochondria-associated ER membrane function but do not impair bioenergetics. Hum Mol Genet 2020; 28:1782-1800. [PMID: 30649465 PMCID: PMC6522073 DOI: 10.1093/hmg/ddz008] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/27/2018] [Accepted: 12/31/2018] [Indexed: 12/23/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) type 2A is a form of peripheral neuropathy, due almost exclusively to dominant mutations in the nuclear gene encoding the mitochondrial protein mitofusin-2 (MFN2). However, there is no understanding of the relationship of clinical phenotype to genotype. MFN2 has two functions: it promotes inter-mitochondrial fusion and mediates endoplasmic reticulum (ER)-mitochondrial tethering at mitochondria-associated ER membranes (MAM). MAM regulates a number of key cellular functions, including lipid and calcium homeostasis, and mitochondrial behavior. To date, no studies have been performed to address whether mutations in MFN2 in CMT2A patient cells affect MAM function, which might provide insight into pathogenesis. Using fibroblasts from three CMT2AMFN2 patients with different mutations in MFN2, we found that some, but not all, examined aspects of ER-mitochondrial connectivity and of MAM function were indeed altered, and correlated with disease severity. Notably, however, respiratory chain function in those cells was unimpaired. Our results suggest that CMT2AMFN2 is a MAM-related disorder but is not a respiratory chain-deficiency disease. The alterations in MAM function described here could also provide insight into the pathogenesis of other forms of CMT.
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Affiliation(s)
- Delfina Larrea
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Marta Pera
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | | | | | - H Orhan Akman
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | | | - Kevin R Velasco
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Estela Area-Gomez
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | | | | | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Michael E Shy
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Eric A Schon
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
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Chacko LA, Ananthanarayanan V. Quantification of Mitochondrial Dynamics in Fission Yeast. Bio Protoc 2019; 9:e3450. [PMID: 33654945 DOI: 10.21769/bioprotoc.3450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 11/02/2022] Open
Abstract
Mitochondria are double-membraned organelles responsible for several functions in the cell including energy production, calcium signaling, and cellular metabolism. An equilibrium between fission and fusion events of mitochondria is required for their proper functioning. Mitochondrial morphologies have been quantified in yeast using image processing modules such as MitoGraph and MitoLoc. However, the dynamics of mitochondrial fission and fusion have not been analyzed in these methods. Here, we present a method for measuring mitochondrial morphologies, as well as estimation of fission and fusion frequencies of mitochondria in individual fission yeast cells whose mitochondria are fluorescently-tagged or stained. The latter relies on counting of individual mitochondria upon signal filtering in each frame of a time-lapse. Taken together, we present a simple protocol for analyzing mitochondrial dynamics, which can easily be adopted to other model systems.
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Affiliation(s)
- Leeba Ann Chacko
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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38
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Yan T, Zhao Y. Acetaldehyde induces phosphorylation of dynamin-related protein 1 and mitochondrial dysfunction via elevating intracellular ROS and Ca 2+ levels. Redox Biol 2019; 28:101381. [PMID: 31756635 PMCID: PMC6879985 DOI: 10.1016/j.redox.2019.101381] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/31/2019] [Accepted: 11/10/2019] [Indexed: 12/21/2022] Open
Abstract
Excessive alcohol consumption impairs brain function and has been associated with an earlier onset of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Acetaldehyde, the most toxic metabolite of alcohol, has been speculated to mediate the neurotoxicity induced by alcohol abuse. However, the precise mechanisms by which acetaldehyde induces neurotoxicity remain elusive. In this study, it was found that acetaldehyde treatment induced excessive mitochondrial fragmentation, impaired mitochondrial function and caused cytotoxicity in cortical neurons and SH-SY5Y cells. Further analyses showed that acetaldehyde induced the phosphorylation of mitochondrial fission related protein dynamin-related protein 1 (Drp1) at Ser616 and promoted its translocation to mitochondria. The elevation of Drp1 phosphorylation was partly dependent on the reactive oxygen species (ROS)-mediated activation of c-Jun-N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK), as N-acetyl-l-cysteine (NAC) pretreatment inhibited the activation of JNK and p38 MAPK while attenuating Drp1 phosphorylation in acetaldehyde-treated cells. In addition, acetaldehyde treatment elevated intracellular Ca2+ level and activated Ca2+/calmodulin-dependent protein kinase II (CaMKII). Pretreatment of CaMKII inhibitor prevented Drp1 phosphorylation in acetaldehyde-treated cells and ameliorated acetaldehyde-induced cytotoxicity, suggesting that CaMKII was a key effector mediating acetaldehyde-induced Drp1 phosphorylation and mitochondrial dysfunction. Taken together, acetaldehyde induced cytotoxicity by promoting excessive Drp1 phosphorylation and mitochondrial fragmentation. Both ROS and Ca2+-mediated signaling pathways played important roles in acetaldehyde-induced Drp1 phosphorylation. The results also suggested that prevention of oxidative stress by antioxidants might be beneficial for preventing neurotoxicity associated with acetaldehyde and alcohol abuse.
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Affiliation(s)
- Tingting Yan
- Department of Bioengineering, Harbin Institute of Technology, Weihai, 264209, Shandong, China
| | - Yan Zhao
- Department of Bioengineering, Harbin Institute of Technology, Weihai, 264209, Shandong, China.
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Musa M, Perić M, Bou Dib P, Sobočanec S, Šarić A, Lovrić A, Rudan M, Nikolić A, Milosević I, Vlahoviček K, Raimundo N, Kriško A. Heat-induced longevity in budding yeast requires respiratory metabolism and glutathione recycling. Aging (Albany NY) 2019; 10:2407-2427. [PMID: 30227387 PMCID: PMC6188503 DOI: 10.18632/aging.101560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/13/2018] [Indexed: 01/04/2023]
Abstract
Heat-induced hormesis is a well-known conserved phenomenon in aging, traditionally attributed to the benefits conferred by increased amounts of heat shock (HS) proteins. Here we find that the key event for the HS-induced lifespan extension in budding yeast is the switch from glycolysis to respiratory metabolism. The resulting increase in reactive oxygen species activates the antioxidant response, supported by the redirection of glucose from glycolysis to the pentose phosphate pathway, increasing the production of NADPH. This sequence of events culminates in replicative lifespan (RLS) extension, implying decreased mortality per generation that persists even after the HS has finished. We found that switching to respiratory metabolism, and particularly the consequent increase in glutathione levels, were essential for the observed RLS extension. These results draw the focus away solely from the HS response and demonstrate that the antioxidant response has a key role in heat-induced hormesis. Our findings underscore the importance of the changes in cellular metabolic activity for heat-induced longevity in budding yeast.
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Affiliation(s)
- Marina Musa
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Matea Perić
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Peter Bou Dib
- University Medical Center Göttingen, Institute of Cellular Biochemistry, Göttingen, Germany
| | - Sandra Sobočanec
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Ana Šarić
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Anita Lovrić
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Marina Rudan
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Andrea Nikolić
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Ira Milosević
- European Neuroscience Institute, University Medical Center Göttingen, Göttingen, Germany
| | - Kristian Vlahoviček
- University of Zagreb, Faculty of Natural Sciences and Mathematics, Zagreb, Croatia
| | - Nuno Raimundo
- University Medical Center Göttingen, Institute of Cellular Biochemistry, Göttingen, Germany
| | - Anita Kriško
- Mediterranean Institute for Life Sciences, Split, Croatia
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40
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Montemurro L, Raieli S, Angelucci S, Bartolucci D, Amadesi C, Lampis S, Scardovi AL, Venturelli L, Nieddu G, Cerisoli L, Fischer M, Teti G, Falconi M, Pession A, Hrelia P, Tonelli R. A Novel MYCN-Specific Antigene Oligonucleotide Deregulates Mitochondria and Inhibits Tumor Growth in MYCN-Amplified Neuroblastoma. Cancer Res 2019; 79:6166-6177. [PMID: 31615807 DOI: 10.1158/0008-5472.can-19-0008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/10/2019] [Accepted: 10/07/2019] [Indexed: 11/16/2022]
Abstract
Approximately half of high-risk neuroblastoma is characterized by MYCN amplification. N-Myc promotes tumor progression by inducing cell growth and inhibiting differentiation. MYCN has also been shown to play an active role in mitochondrial metabolism, but this relationship is not well understood. Although N-Myc is a known driver of the disease, it remains a target for which no therapeutic drug exists. Here, we evaluated a novel MYCN-specific antigene PNA oligonucleotide (BGA002) in MYCN-amplified (MNA) or MYCN-expressing neuroblastoma and investigated the mechanism of its antitumor activity. MYCN mRNA and cell viability were reduced in a broad set of neuroblastoma cell lines following BGA002 treatment. Furthermore, BGA002 decreased N-Myc protein levels and apoptosis in MNA neuroblastoma. Analysis of gene expression data from patients with neuroblastoma revealed that MYCN was associated with increased reactive oxygen species (ROS), downregulated mitophagy, and poor prognosis. Inhibition of MYCN caused profound mitochondrial damage in MNA neuroblastoma cells through downregulation of the mitochondrial molecular chaperone TRAP1, which subsequently increased ROS. Correspondingly, inhibition of MYCN reactivated mitophagy. Systemic administration of BGA002 downregulated N-Myc and TRAP1, with a concomitant decrease in MNA neuroblastoma xenograft tumor weight. In conclusion, this study highlights the role of N-Myc in blocking mitophagy in neuroblastoma and in conferring protection to ROS in mitochondria through upregulation of TRAP1. BGA002 is a potently improved MYCN-specific antigene oligonucleotide that reverts N-Myc-dysregulated mitochondrial pathways, leading to loss of the protective effect of N-Myc against mitochondrial ROS. SIGNIFICANCE: A second generation antigene peptide oligonucleotide targeting MYCN induces mitochondrial damage and inhibits growth of MYCN-amplified neuroblastoma cells.
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Affiliation(s)
- Luca Montemurro
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | | | - Silvia Angelucci
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | - Damiano Bartolucci
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | | | | | | | | | | | | | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Gabriella Teti
- Department of Biomedical and Neuromotor Sciences-DBNS, University of Bologna, Bologna, Italy
| | - Mirella Falconi
- Department of Biomedical and Neuromotor Sciences-DBNS, University of Bologna, Bologna, Italy
| | - Andrea Pession
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Roberto Tonelli
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy.
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41
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Chakraborty J, von Stockum S, Marchesan E, Caicci F, Ferrari V, Rakovic A, Klein C, Antonini A, Bubacco L, Ziviani E. USP14 inhibition corrects an in vivo model of impaired mitophagy. EMBO Mol Med 2019; 10:emmm.201809014. [PMID: 30249595 PMCID: PMC6220287 DOI: 10.15252/emmm.201809014] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial autophagy or mitophagy is a key process that allows selective sequestration and degradation of dysfunctional mitochondria to prevent excessive reactive oxygen species, and activation of cell death. Recent studies revealed that ubiquitin–proteasome complex activity and mitochondrial membrane rupture are key steps preceding mitophagy, in combination with the ubiquitination of specific outer mitochondrial membrane (OMM) proteins. The deubiquitinating enzyme ubiquitin‐specific peptidase 14 (USP14) has been shown to modulate both proteasome activity and autophagy. Here, we report that genetic and pharmacological inhibition of USP14 promotes mitophagy, which occurs in the absence of the well‐characterised mediators of mitophagy, PINK1 and Parkin. Critical to USP14‐induced mitophagy is the exposure of the LC3 receptor Prohibitin 2 by mitochondrial fragmentation and mitochondrial membrane rupture. Genetic or pharmacological inhibition of USP14 in vivo corrected mitochondrial dysfunction and locomotion behaviour of PINK1/Parkin mutant Drosophila model of Parkinson's disease, an age‐related progressive neurodegenerative disorder that is correlated with diminished mitochondrial quality control. Our study identifies a novel therapeutic target that ameliorates mitochondrial dysfunction and in vivo PD‐related symptoms.
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Affiliation(s)
| | | | | | | | - Vanni Ferrari
- Department of Biology, University of Padova, Padova, Italy
| | | | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Angelo Antonini
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy .,Fondazione Ospedale San Camillo IRCCS, Venezia, Italia
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42
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Zhu C, Li M, Vincent T, Martin HL, Crouch BT, Martinez AF, Madonna MC, Palmer GM, Dewhirst MW, Ramanujam N. Simultaneous in vivo optical quantification of key metabolic and vascular endpoints reveals tumor metabolic diversity in murine breast tumor models. JOURNAL OF BIOPHOTONICS 2019; 12:e201800372. [PMID: 30565420 PMCID: PMC8744479 DOI: 10.1002/jbio.201800372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 05/24/2023]
Abstract
Therapeutically exploiting vascular and metabolic endpoints becomes critical to translational cancer studies because altered vascularity and deregulated metabolism are two important cancer hallmarks. The metabolic and vascular phenotypes of three sibling breast tumor lines with different metastatic potential are investigated in vivo with a newly developed quantitative spectroscopy system. All tumor lines have different metabolic and vascular characteristics compared to normal tissues, and there are strong positive correlations between metabolic (glucose uptake and mitochondrial membrane potential) and vascular (oxygen saturations and hemoglobin concentrations) parameters for metastatic (4T1) tumors but not for micrometastatic (4T07) and nonmetastatic (67NR) tumors. A longitudinal study shows that both vascular and metabolic endpoints of 4T1 tumors increased up to a specific tumor size threshold beyond which these parameters decreased. The synchronous changes between metabolic and vascular parameters, along with the strong positive correlations between these endpoints suggest that 4T1 tumors rely on strong oxidative phosphorylation in addition to glycolysis. This study illustrates the great potential of our optical technique to provide valuable dynamic information about the interplay between the metabolic and vascular status of tumors, with important implications for translational cancer investigations.
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Affiliation(s)
- Caigang Zhu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Martin Li
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Thomas Vincent
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Hannah L Martin
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Brian T Crouch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Amy F Martinez
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
- Office of Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Megan C Madonna
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Gregory M Palmer
- Department of Radiation Oncology, Duke University, Durham, North Carolina
| | - Mark W Dewhirst
- Department of Radiation Oncology, Duke University, Durham, North Carolina
| | - Nimmi Ramanujam
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
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43
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Alessio E, Buson L, Chemello F, Peggion C, Grespi F, Martini P, Massimino ML, Pacchioni B, Millino C, Romualdi C, Bertoli A, Scorrano L, Lanfranchi G, Cagnin S. Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Nucleic Acids Res 2019; 47:1653-1670. [PMID: 30649422 PMCID: PMC6393313 DOI: 10.1093/nar/gkz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.
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Affiliation(s)
- Enrico Alessio
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Beniamina Pacchioni
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, 35131 Padova, Italy
- Venetian Institute of Molecular Medicine, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
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44
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Nightingale DJ, Geladaki A, Breckels LM, Oliver SG, Lilley KS. The subcellular organisation of Saccharomyces cerevisiae. Curr Opin Chem Biol 2019; 48:86-95. [PMID: 30503867 PMCID: PMC6391909 DOI: 10.1016/j.cbpa.2018.10.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/06/2023]
Abstract
Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will therefore enhance our understanding of cellular function. Here we review recent developments in this field with regard to mass spectrometry, fluorescence microscopy and computational prediction methods. We highlight relative strengths and limitations of current methodologies focussing particularly on studies in the yeast Saccharomyces cerevisiae. We further present the first cell-wide spatial proteome map of S. cerevisiae, generated using hyperLOPIT, a mass spectrometry-based protein correlation profiling technique. We compare protein subcellular localisation assignments from this map, with two published fluorescence microscopy studies and show that confidence in localisation assignment is attained using multiple orthogonal methods that provide complementary data.
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Affiliation(s)
- Daniel Jh Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
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45
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Valente AJ, Fonseca J, Moradi F, Foran G, Necakov A, Stuart JA. Quantification of Mitochondrial Network Characteristics in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:183-196. [DOI: 10.1007/978-981-13-8367-0_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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46
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Maintenance of Mitochondrial Morphology in Cryptococcus neoformans Is Critical for Stress Resistance and Virulence. mBio 2018; 9:mBio.01375-18. [PMID: 30401774 PMCID: PMC6222134 DOI: 10.1128/mbio.01375-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
C. neoformans is a yeast that causes fatal brain infection in close to 200,000 people worldwide every year, mainly afflicting individuals with AIDS or others who are severely immunocompromised. One feature of this microbe that helps it cause disease is that it is able to withstand toxic molecules it encounters when host cells engulf it in their efforts to control the infection. Mitochondria are important organelles responsible for energy production and other key cellular processes. They typically exist in a complex network that changes morphology by fusing and dividing; these alterations also influence mitochondrial function. Using genetic approaches, we found that changes in mitochondrial morphology dramatically influence cryptococcal virulence. We showed that this occurs because the altered mitochondria are less able to eliminate the harmful molecules that host cells produce to kill invading microbes. These findings are important because they elucidate fundamental biology and virulence and may suggest avenues for therapy. Mitochondria are essential organelles that act in pathways including ATP production, β-oxidation, and clearance of reactive oxygen species. They occur as a complex reticular network that constantly undergoes fusion and fission, mediated by dynamin-related proteins (DRPs). DRPs include Fzo1, which mediates fusion, and Dnm1, Mdv1, and Fis1, which mediate fission. Mitochondrial morphology has been implicated in virulence in multiple fungi, as with the association between virulence and increased mitochondrial fusion in Cryptococcus gattii. This relationship, however, has not been studied in Cryptococcus neoformans, a related opportunistic pathogen. C. neoformans is an environmental yeast that can adapt to the human host environment, overcome the innate immune system, and eventually disseminate and cause lethal meningoencephalitis. We used gene deletion of key DRPs to study their role in mitochondrial morphology and pathogenesis of this yeast. Interestingly, increasing mitochondrial fusion did not increase resistance to oxidative stress, unlike in model yeast. Blocking mitochondrial fusion, however, yielded increased susceptibility to oxidative and nitrosative stresses as well as complete avirulence. This lack of virulence was not mediated by any effects of altered mitochondrial function on two major virulence factors, capsule and melanin. Instead, it was due to decreased survival within macrophages, which in turn was a consequence of increased susceptibility to oxidative and nitrosative stress. Supporting this conclusion, reactive oxygen species (ROS) scavengers rescued the ability of fusion mutants to survive intracellularly. These findings increase our understanding of cryptococcal biology and virulence and shed light on an important group of proteins and cellular processes in this pathogen.
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47
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Bellomo F, Signorile A, Tamma G, Ranieri M, Emma F, De Rasmo D. Impact of atypical mitochondrial cyclic-AMP level in nephropathic cystinosis. Cell Mol Life Sci 2018; 75:3411-3422. [PMID: 29549422 PMCID: PMC11105431 DOI: 10.1007/s00018-018-2800-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/20/2018] [Accepted: 03/14/2018] [Indexed: 02/06/2023]
Abstract
Nephropathic cystinosis (NC) is a rare disease caused by mutations in the CTNS gene encoding for cystinosin, a lysosomal transmembrane cystine/H+ symporter, which promotes the efflux of cystine from lysosomes to cytosol. NC is the most frequent cause of Fanconi syndrome (FS) in young children, the molecular basis of which is not well established. Proximal tubular cells have very high metabolic rate due to the active transport of many solutes. Not surprisingly, mitochondrial disorders are often characterized by FS. A similar mechanism may also apply to NC. Because cAMP has regulatory properties on mitochondrial function, we have analyzed cAMP levels and mitochondrial targets in CTNS-/- conditionally immortalized proximal tubular epithelial cells (ciPTEC) carrying the classical homozygous 57-kb deletion (delCTNS-/-) or with compound heterozygous loss-of-function mutations (mutCTNS-/-). Compared to wild-type cells, cystinotic cells had significantly lower mitochondrial cAMP levels (delCTNS-/- ciPTEC by 56% ± 10.5, P < 0.0001; mutCTNS-/- by 26% ± 4.3, P < 0.001), complex I and V activities, mitochondrial membrane potential, and SIRT3 protein levels, which were associated with increased mitochondrial fragmentation. Reduction of complex I and V activities was associated with lower expression of part of their subunits. Treatment with the non-hydrolysable cAMP analog 8-Br-cAMP restored mitochondrial potential and corrected mitochondria morphology. Treatment with cysteamine, which reduces the intra-lysosomal cystine, was able to restore mitochondrial cAMP levels, as well as most other abnormal mitochondrial findings. These observations were validated in CTNS-silenced HK-2 cells, indicating a pivotal role of mitochondrial cAMP in the proximal tubular dysfunction observed in NC.
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Affiliation(s)
- Francesco Bellomo
- Laboratory of Nephrology, Department of Rare Diseases, Bambino Gesù Children's Hospital, Viale di S. Paolo, 15, 00149, Rome, Italy.
| | - Anna Signorile
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", Policlinico, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Grazia Tamma
- Department of Bioscience, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Marianna Ranieri
- Department of Bioscience, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Emma
- Laboratory of Nephrology, Department of Rare Diseases, Bambino Gesù Children's Hospital, Viale di S. Paolo, 15, 00149, Rome, Italy
- Division of Nephrology, Department of Pediatric Subspecialties, Bambino Gesù Children's Hospital, Rome, Italy
| | - Domenico De Rasmo
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", Policlinico, Piazza G. Cesare, 11, 70124, Bari, Italy.
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council (CNR), Bari, Italy.
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48
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Fu D, Lippincott-Schwartz J. Monitoring the Effects of Pharmacological Reagents on Mitochondrial Morphology. ACTA ACUST UNITED AC 2018; 79:e45. [PMID: 29924486 DOI: 10.1002/cpcb.45] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This protocol describes how to apply appropriate pharmacological controls to induce mitochondrial fusion or fission in studies of mitochondria morphology for four different mammalian cell types, HepG2 human liver hepatocellular carcinoma cells, MCF7 human breast adenocarcinoma cells, HEK293 human embryonic kidney cells, and collagen sandwich culture of primary rat hepatocytes. The protocol provides methods of treating cells with these pharmacological controls, staining mitochondria with commercially available MitoTracker Green and TMRE dyes, and imaging the mitochondrial morphology in live cells using a confocal fluorescent microscope. It also describes the cell culture methods needed for this protocol. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Dong Fu
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina.,Faculty of Pharmacy, The University of Sydney, Sydney, Australia
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49
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Rudan M, Bou Dib P, Musa M, Kanunnikau M, Sobočanec S, Rueda D, Warnecke T, Kriško A. Normal mitochondrial function in Saccharomyces cerevisiae has become dependent on inefficient splicing. eLife 2018; 7:35330. [PMID: 29570052 PMCID: PMC5898908 DOI: 10.7554/elife.35330] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/19/2018] [Indexed: 11/28/2022] Open
Abstract
Self-splicing introns are mobile elements that have invaded a number of highly conserved genes in prokaryotic and organellar genomes. Here, we show that deletion of these selfish elements from the Saccharomyces cerevisiae mitochondrial genome is stressful to the host. A strain without mitochondrial introns displays hallmarks of the retrograde response, with altered mitochondrial morphology, gene expression and metabolism impacting growth and lifespan. Deletion of the complete suite of mitochondrial introns is phenocopied by overexpression of the splicing factor Mss116. We show that, in both cases, abnormally efficient transcript maturation results in excess levels of mature cob and cox1 host mRNA. Thus, inefficient splicing has become an integral part of normal mitochondrial gene expression. We propose that the persistence of S. cerevisiae self-splicing introns has been facilitated by an evolutionary lock-in event, where the host genome adapted to primordial invasion in a way that incidentally rendered subsequent intron loss deleterious.
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Affiliation(s)
- Marina Rudan
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Peter Bou Dib
- Institut für Zellbiochemie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Marina Musa
- Mediterranean Institute for Life Sciences, Split, Croatia
| | | | - Sandra Sobočanec
- Division of Molecular Medicine, Rudjer Boškovic Institute, Bijenička, Zagreb, Croatia
| | - David Rueda
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Molecular Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Anita Kriško
- Mediterranean Institute for Life Sciences, Split, Croatia
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50
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Martinez AF, McCachren SS, Lee M, Murphy HA, Zhu C, Crouch BT, Martin HL, Erkanli A, Rajaram N, Ashcraft KA, Fontanella AN, Dewhirst MW, Ramanujam N. Metaboloptics: Visualization of the tumor functional landscape via metabolic and vascular imaging. Sci Rep 2018. [PMID: 29520098 PMCID: PMC5843602 DOI: 10.1038/s41598-018-22480-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Many cancers adeptly modulate metabolism to thrive in fluctuating oxygen conditions; however, current tools fail to image metabolic and vascular endpoints at spatial resolutions needed to visualize these adaptations in vivo. We demonstrate a high-resolution intravital microscopy technique to quantify glucose uptake, mitochondrial membrane potential (MMP), and SO2 to characterize the in vivo phentoypes of three distinct murine breast cancer lines. Tetramethyl rhodamine, ethyl ester (TMRE) was thoroughly validated to report on MMP in normal and tumor-bearing mice. Imaging MMP or glucose uptake together with vascular endpoints revealed that metastatic 4T1 tumors maintained increased glucose uptake across all SO2 (“Warburg effect”), and also showed increased MMP relative to normal tissue. Non-metastatic 67NR and 4T07 tumor lines both displayed increased MMP, but comparable glucose uptake, relative to normal tissue. The 4T1 peritumoral areas also showed a significant glycolytic shift relative to the tumor regions. During a hypoxic stress test, 4T1 tumors showed significant increases in MMP with corresponding significant drops in SO2, indicative of intensified mitochondrial metabolism. Conversely, 4T07 and 67NR tumors shifted toward glycolysis during hypoxia. Our findings underscore the importance of imaging metabolic endpoints within the context of a living microenvironment to gain insight into a tumor’s adaptive behavior.
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Affiliation(s)
- Amy F Martinez
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | | | - Marianne Lee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Helen A Murphy
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Brian T Crouch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Hannah L Martin
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Alaattin Erkanli
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | - Nirmala Ramanujam
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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