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Mello DF, Perez L, Bergemann CM, Morton KS, Ryde IT, Meyer JN. Comprehensive characterization of mitochondrial bioenergetics at different larval stages reveals novel insights about the developmental metabolism of Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600841. [PMID: 38979262 PMCID: PMC11230424 DOI: 10.1101/2024.06.26.600841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mitochondrial bioenergetic processes are fundamental to development, stress responses, and health. Caenorhabditis elegans is widely used to study developmental biology, mitochondrial disease, and mitochondrial toxicity. Oxidative phosphorylation generally increases during development in many species, and genetic and environmental factors may alter this normal trajectory. Altered mitochondrial function during development can lead to both drastic, short-term responses including arrested development and death, and subtle consequences that may persist throughout life and into subsequent generations. Understanding normal and altered developmental mitochondrial biology in C. elegans is currently constrained by incomplete and conflicting reports on how mitochondrial bioenergetic parameters change during development in this species. We used a Seahorse XFe24 Extracellular Flux (XF) Analyzer to carry out a comprehensive analysis of mitochondrial and non-mitochondrial oxygen consumption rates (OCR) throughout larval development in C. elegans. We optimized and describe conditions for analysis of basal OCR, basal mitochondrial OCR, ATP-linked OCR, spare and maximal respiratory capacity, proton leak, and non-mitochondrial OCR. A key consideration is normalization, and we present and discuss results as normalized per individual worm, protein content, worm volume, mitochondrial DNA (mtDNA) count, nuclear DNA (ncDNA) count, and mtDNA:ncDNA ratio. Which normalization process is best depends on the question being asked, and differences in normalization explain some of the discrepancies in previously reported developmental changes in OCR in C. elegans. Broadly, when normalized to worm number, our results agree with previous reports in showing dramatic increases in OCR throughout development. However, when normalized to total protein, worm volume, or ncDNA or mtDNA count, after a significant 2-3-fold increase from L1 to L2 stages, we found small or no changes in most OCR parameters from the L2 to the L4 stage, other than a marginal increase at L3 in spare and maximal respiratory capacity. Overall, our results indicate an earlier cellular shift to oxidative metabolism than suggested in most previous literature.
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Affiliation(s)
- Danielle F Mello
- Nicholas School of the Environment, Duke University, Box 90328, Durham, NC, 27708-0328 United States of America
| | - Luiza Perez
- Nicholas School of the Environment, Duke University, Box 90328, Durham, NC, 27708-0328 United States of America
| | - Christina M Bergemann
- Nicholas School of the Environment, Duke University, Box 90328, Durham, NC, 27708-0328 United States of America
| | - Katherine S Morton
- Nicholas School of the Environment, Duke University, Box 90328, Durham, NC, 27708-0328 United States of America
| | - Ian T Ryde
- Nicholas School of the Environment, Duke University, Box 90328, Durham, NC, 27708-0328 United States of America
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Box 90328, Durham, NC, 27708-0328 United States of America
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Giovannetti M, Rodríguez-Palero MJ, Fabrizio P, Nicolle O, Bedet C, Michaux G, Witting M, Artal-Sanz M, Palladino F. SIN-3 transcriptional coregulator maintains mitochondrial homeostasis and polyamine flux. iScience 2024; 27:109789. [PMID: 38746662 PMCID: PMC11091686 DOI: 10.1016/j.isci.2024.109789] [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] [Received: 08/14/2023] [Revised: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 06/05/2024] Open
Abstract
Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays a role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear-encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals revealed a mitochondria stress signature and deregulation of methionine flux, resulting in decreased S-adenosyl methionine (SAM) and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.
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Affiliation(s)
- Marina Giovannetti
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - María-Jesús Rodríguez-Palero
- Andalusian Centre for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide and Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Paola Fabrizio
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ophélie Nicolle
- University Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, 35000 Rennes, France
| | - Cécile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Grégoire Michaux
- University Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, 35000 Rennes, France
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 2, 85354 Freising, Weihenstephan, Germany
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide and Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
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Sleiman A, Lalanne K, Vianna F, Perrot Y, Richaud M, SenGupta T, Cardot-Martin M, Pedini P, Picard C, Nilsen H, Galas S, Adam-Guillermin C. Targeted Central Nervous System Irradiation with Proton Microbeam Induces Mitochondrial Changes in Caenorhabditis elegans. BIOLOGY 2023; 12:839. [PMID: 37372124 DOI: 10.3390/biology12060839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Fifty percent of all patients with cancer worldwide require radiotherapy. In the case of brain tumors, despite the improvement in the precision of radiation delivery with proton therapy, studies have shown structural and functional changes in the brains of treated patients with protons. The molecular pathways involved in generating these effects are not completely understood. In this context, we analyzed the impact of proton exposure in the central nervous system area of Caenorhabditis elegans with a focus on mitochondrial function, which is potentially implicated in the occurrence of radiation-induced damage. To achieve this objective, the nematode C. elegans were micro-irradiated with 220 Gy of protons (4 MeV) in the nerve ring (head region) using the proton microbeam, MIRCOM. Our results show that protons induce mitochondrial dysfunction, characterized by an immediate dose-dependent loss of the mitochondrial membrane potential (ΔΨm) associated with oxidative stress 24 h after irradiation, which is itself characterized by the induction of the antioxidant proteins in the targeted region, observed using SOD-1::GFP and SOD-3::GFP strains. Moreover, we demonstrated a two-fold increase in the mtDNA copy number in the targeted region 24 h after irradiation. In addition, using the GFP::LGG-1 strain, an induction of autophagy in the irradiated region was observed 6 h following the irradiation, which is associated with the up-regulation of the gene expression of pink-1 (PTEN-induced kinase) and pdr-1 (C. elegans parkin homolog). Furthermore, our data showed that micro-irradiation of the nerve ring region did not impact the whole-body oxygen consumption 24 h following the irradiation. These results indicate a global mitochondrial dysfunction in the irradiated region following proton exposure. This provides a better understanding of the molecular pathways involved in radiation-induced side effects and may help in finding new therapies.
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Affiliation(s)
- Ahmad Sleiman
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, PSE-SANTE/SDOS/LMDN, Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Kévin Lalanne
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, PSE-SANTE/SDOS/LMDN, Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - François Vianna
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, PSE-SANTE/SDOS/LMDN, Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, PSE-SANTE/SDOS/LDRI, 92262 Fontenay-aux-Roses, France
| | - Myriam Richaud
- IBMM, University of Montpellier, CNRS, ENSCM, 34093 Montpellier, France
| | - Tanima SenGupta
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Mikaël Cardot-Martin
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, PSE-SANTE/SDOS/LMDN, Cadarache, 13115 Saint-Paul-lez-Durance, France
| | - Pascal Pedini
- Aix Marseille University, CNRS, EFS, ADES, 13288 Marseille, France
| | | | - Hilde Nilsen
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
| | - Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, 34093 Montpellier, France
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, PSE-SANTE/SDOS/LMDN, Cadarache, 13115 Saint-Paul-lez-Durance, France
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Santos CS, Macedo F, Kowaltowski AJ, Bertotti M, Unwin PR, Marques da Cunha F, Meloni GN. Unveiling the contribution of the reproductive system of individual Caenorhabditis elegans on oxygen consumption by single-point scanning electrochemical microscopy measurements. Anal Chim Acta 2021; 1146:88-97. [PMID: 33461723 PMCID: PMC7836392 DOI: 10.1016/j.aca.2020.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/03/2023]
Abstract
Metabolic analysis in animals is usually either evaluated as whole-body measurements or in isolated tissue samples. To reveal tissue specificities in vivo, this study uses scanning electrochemical microscopy (SECM) to provide localized oxygen consumption rates (OCRs) in different regions of single adult Caenorhabditis elegans individuals. This is achieved by measuring the oxygen reduction current at the SECM tip electrode and using a finite element method model of the experiment that defines oxygen concentration and flux at the surface of the organism. SECM mapping measurements uncover a marked heterogeneity of OCR along the worm, with high respiration rates at the reproductive system region. To enable sensitive and quantitative measurements, a self-referencing approach is adopted, whereby the oxygen reduction current at the SECM tip is measured at a selected point on the worm and in bulk solution (calibration). Using genetic and pharmacological approaches, our SECM measurements indicate that viable eggs in the reproductive system are the main contributors in the total oxygen consumption of adult Caenorhabditis elegans. The finding that large regional differences in OCR exist within the animal provides a new understanding of oxygen consumption and metabolic measurements, paving the way for tissue-specific metabolic analyses and toxicity evaluation within single organisms.
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Affiliation(s)
- Carla S Santos
- Departamento de Química Fundamental, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil.
| | - Felipe Macedo
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua três de Maio, 100, 04044-020, São Paulo, Brazil
| | - Alicia J Kowaltowski
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Mauro Bertotti
- Departamento de Química Fundamental, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Patrick R Unwin
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom; Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua três de Maio, 100, 04044-020, São Paulo, Brazil
| | - Gabriel N Meloni
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom; Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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Sleep Analysis in Adult C. elegans Reveals State-Dependent Alteration of Neural and Behavioral Responses. J Neurosci 2021; 41:1892-1907. [PMID: 33446520 PMCID: PMC7939084 DOI: 10.1523/jneurosci.1701-20.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 01/26/2023] Open
Abstract
Sleep, a state of quiescence associated with growth and restorative processes, is conserved across species. Invertebrates including the nematode Caenorhabditis elegans exhibit sleep-like states during development, satiety, and stress. Here, we describe behavior and neural activity during sleep and awake states in adult C. elegans hermaphrodites using new microfluidic methods. We observed effects of fluid flow, oxygen, feeding, odors, and genetic perturbations on long-term sleep behavior over 12 h. We developed a closed-loop sleep detection system to automatically deliver chemical stimuli to assess sleep-dependent changes to evoked neural responses in individual animals. Sleep increased the arousal threshold to aversive stimulation, yet the associated sensory neuron and first-layer interneuron responses were unchanged. This localizes adult sleep-dependent neuromodulation within interneurons presynaptic to the premotor interneurons, rather than afferent sensory circuits. However, sleep prolonged responses in appetitive chemosensory neurons, suggesting that sleep modulates responsiveness specifically across sensory systems rather than broadly damping global circuit activity. SIGNIFICANCE STATEMENT Much is known about molecular mechanisms that facilitate sleep control. However, it is unclear how these pathways modulate neural circuit-level sensory processing or how misregulation of neural activity contributes to sleep disorders. The nematode Caenorhabditis elegans provides the ability to study neural circuitry with single-neuron resolution, and recent studies examined sleep states between developmental stages and when stressed. Here, we examine an additional form of spontaneous sleep in adult C. elegans at the behavioral and neural activity levels. Using a closed-loop system, we show that delayed behavioral responses to aversive chemical stimulation during sleep arise from sleep-dependent sensorimotor modulation localized presynaptic to the premotor circuit, rather than early sensory circuits.
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A Miniature Intermittent-Flow Respirometry System with a 3D-Printed, Palm-Sized Zebrafish Treadmill for Measuring Rest and Activity Metabolic Rates. SENSORS 2020; 20:s20185088. [PMID: 32906794 PMCID: PMC7570584 DOI: 10.3390/s20185088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022]
Abstract
Zebrafish are a preferred vertebrate model for evaluating metabolism during development, and for toxicity studies. However, commercially available intermittent-flow respirometry systems (IFRS) do not provide a suitable zebrafish-scaled swimming tunnel with a low water volume and proper flow velocities. We developed a miniature IFRS (mIFRS) with a 3D-printed, palm-sized zebrafish treadmill for measuring the swimming ability and metabolic rate of a single one- or three-month-old zebrafish with and without toxicity treatment. The 3D-printed zebrafish treadmill consists of discrete components assembled together which enables the provision of a temporary closed circulating water flow. The results showed that three-month-old zebrafish of normal physiological status had higher energetic efficiency and could swim at a higher critical swimming speed (Ucrit) of 16.79 cm/s with a lower cost of transport (COTopt) of 0.11 μmol g−1m−1. However, for a single three-month-old zebrafish treated with an antibacterial agent, Ucrit decreased to 45% of normal zebrafish and the COTopt increased to 0.24 μmol g−1m−1, due to the impairment of mitochondria. Our mIFRS provides a low-cost, portable, and readily adaptable tool for studying the swimming performance and energetic metabolism of zebrafish.
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Lewallen M, Burggren W. Metabolic physiology of the freshwater planaria Girardia dorotocephela and Schmidtea mediterranea: reproductive mode, specific dynamic action, and temperature. Am J Physiol Regul Integr Comp Physiol 2020; 319:R428-R438. [PMID: 32783687 DOI: 10.1152/ajpregu.00099.2020] [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] [Indexed: 11/22/2022]
Abstract
Planarians are widely used animal models for studies in regeneration, developmental biology, neurobiology, and behavior. However, surprisingly little is known about other aspects of their basic biology, even though such information might help validate these flatworms as a general animal model. We hypothesized that planaria, although dependent on simple diffusion of O2 across the integument for O2 uptake, would nonetheless show changes in oxygen consumption (V̇o2) associated with reproductive mode (sexual or asexual), feeding (specific dynamic action; SDA), temperature (Q10 values), and photoperiod typical of those responses of more complex invertebrates. In the current experiments, routine V̇o2 was measured over the range of 13-28°C in Schmidtea mediterranea and Girardia dorotocephala. At the long-term maintenance temperature of 18°C, routine V̇o2 was ~13 µL O2·g-1·h-1 in the two asexual strains, but approximately twice as high (27 µL O2·g-1·h-1) in the sexual strain of S. mediterranea, suggesting a metabolic cost for sexual reproduction. Metabolic temperature sensitivity, measured by Q10, was about one to three for all three groups. All three groups showed a large (~2- to 3-fold) increase in V̇o2 within a day following feeding, suggesting a large SDA effect. Starvation, causing "degrowth" in some planaria, resulted in a loss of one-third of body mass in sexual S. mediterranea but no body mass loss in either asexual strains. Collectively, these data indicate that, while being a relatively simple flatworm with no dedicated respiratory or circulatory system, their metabolic physiological responses are quite similar to those shown by more complex invertebrates and vertebrates, contributing to their validation as an animal model.
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Affiliation(s)
- Melissa Lewallen
- Developmental Integrative Biology, Department of Biological Sciences, University of North Texas, Denton, Texas
| | - Warren Burggren
- Developmental Integrative Biology, Department of Biological Sciences, University of North Texas, Denton, Texas
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Krenger R, Cornaglia M, Lehnert T, Gijs MAM. Microfluidic system for Caenorhabditis elegans culture and oxygen consumption rate measurements. LAB ON A CHIP 2020; 20:126-135. [PMID: 31729516 DOI: 10.1039/c9lc00829b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mitochondrial respiration is a key signature for the assessment of mitochondrial functioning and mitochondrial dysfunction is related to many diseases including metabolic syndrome and aging-associated conditions. Here, we present a microfluidic Caenorhabditis elegans culture system with integrated luminescence-based oxygen sensing. The material used for the fabrication of the microfluidic chip is off-stoichiometry dual-cure thiol-ene-epoxy (OSTE+), which is well-suited for reliably recording on-chip oxygen consumption rates (OCR) due to its low gas permeability. With our microfluidic approach, it was possible to confine a single nematode in a culture chamber, starting from the L4 stage and studying it over a time span of up to 6 days. An automated protocol for successive worm feeding and OCR measurements during worm development was applied. We found an increase of OCR values from the L4 larval stage to adulthood, and a continuous decrease as the worm further ages. In addition, we performed a C. elegans metabolic assay in which exposure to the mitochondrial uncoupling agent FCCP increased the OCR by a factor of about two compared to basal respiration rates. Subsequent treatment with sodium azide inhibited completely mitochondrial respiration.
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Affiliation(s)
- Roger Krenger
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Matteo Cornaglia
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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To TL, Cuadros AM, Shah H, Hung WHW, Li Y, Kim SH, Rubin DHF, Boe RH, Rath S, Eaton JK, Piccioni F, Goodale A, Kalani Z, Doench JG, Root DE, Schreiber SL, Vafai SB, Mootha VK. A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering. Cell 2019; 179:1222-1238.e17. [PMID: 31730859 PMCID: PMC7053407 DOI: 10.1016/j.cell.2019.10.032] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/12/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022]
Abstract
Mitochondrial dysfunction is associated with a spectrum of human conditions, ranging from rare, inborn errors of metabolism to the aging process. To identify pathways that modify mitochondrial dysfunction, we performed genome-wide CRISPR screens in the presence of small-molecule mitochondrial inhibitors. We report a compendium of chemical-genetic interactions involving 191 distinct genetic modifiers, including 38 that are synthetic sick/lethal and 63 that are suppressors. Genes involved in glycolysis (PFKP), pentose phosphate pathway (G6PD), and defense against lipid peroxidation (GPX4) scored high as synthetic sick/lethal. A surprisingly large fraction of suppressors are pathway intrinsic and encode mitochondrial proteins. A striking example of such "intra-organelle" buffering is the alleviation of a chemical defect in complex V by simultaneous inhibition of complex I, which benefits cells by rebalancing redox cofactors, increasing reductive carboxylation, and promoting glycolysis. Perhaps paradoxically, certain forms of mitochondrial dysfunction may best be buffered with "second site" inhibitors to the organelle.
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Affiliation(s)
- Tsz-Leung To
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Hardik Shah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wendy H W Hung
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Yang Li
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sharon H Kim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel H F Rubin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ryan H Boe
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sneha Rath
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John K Eaton
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zohra Kalani
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Scott B Vafai
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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10
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Maglioni S, Mello DF, Schiavi A, Meyer JN, Ventura N. Mitochondrial bioenergetic changes during development as an indicator of C. elegans health-span. Aging (Albany NY) 2019; 11:6535-6554. [PMID: 31454791 PMCID: PMC6738431 DOI: 10.18632/aging.102208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/07/2019] [Indexed: 11/25/2022]
Abstract
Mild suppression of mitochondrial activity has beneficial effects across species. The nematode Caenorhabditis elegans is a versatile, genetically tractable model organism widely employed for aging studies, which has led to the identification of many of the known evolutionarily conserved mechanisms regulating lifespan. In C. elegans the pro-longevity effect of reducing mitochondrial function, for example by RNA interference, is only achieved if mitochondrial stress is applied during larval development. Surprisingly, a careful analysis of changes in mitochondrial functions resulting from such treatments during the developmental windows in which pro-longevity signals are programmed has never been carried out. Thus, although the powerful C. elegans genetics have led to the identification of different molecular mechanisms causally involved in mitochondrial stress control of longevity, specific functional mitochondrial biomarkers indicative or predictive of lifespan remain to be identified. To fill this gap, we systematically characterized multiple mitochondrial functional parameters at an early developmental stage in animals that are long-lived due to mild knockdown of twelve different mitochondrial proteins and correlated these parameters with animals’ lifespan. We found that basal oxygen consumption rate and ATP-linked respiration positively correlate with lifespan extension and propose the testable hypothesis that the Bioenergetic Health Index can be used as a proxy to predict health-span outcomes.
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Affiliation(s)
- Silvia Maglioni
- IUF-Leibniz Research Institute for Environmental Medicine, 40225 Duesseldorf, Germany
| | - Danielle F Mello
- Nicholas School of the Environment and Integrated Toxicology and Environmental Health Program, Duke University, Durham, NC 27708, USA
| | - Alfonso Schiavi
- IUF-Leibniz Research Institute for Environmental Medicine, 40225 Duesseldorf, Germany.,Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty of the Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Joel N Meyer
- Nicholas School of the Environment and Integrated Toxicology and Environmental Health Program, Duke University, Durham, NC 27708, USA
| | - Natascia Ventura
- IUF-Leibniz Research Institute for Environmental Medicine, 40225 Duesseldorf, Germany.,Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty of the Heinrich Heine University, 40225 Duesseldorf, Germany
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Ng LF, Gruber J. Measurement of Respiration Rate in Live Caenorhabditis elegans. Bio Protoc 2019; 9:e3243. [PMID: 33654770 DOI: 10.21769/bioprotoc.3243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/21/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial function and dysfunction are at the core of aging and involved in many age-dependent diseases. Rate of oxygen consumption is a measure of mitochondrial function and energy production rate. The nematode Caenorhabditis elegans (C. elegans) offers an opportunity to study "living" mitochondria without the need for mitochondrial extraction, purification and associated artifacts. Oxygen consumption rate (OCR) is traditionally measured using single-chamber Clark electrodes with or without the addition of metabolic modulators. More recently, multi-well oxygen electrodes with automated injection system have been developed to enable rapid measurement of OCR under different conditions. Here, we describe a detailed protocol that we have adapted from existing protocols to measure coupled and uncoupled mitochondrial respiration (with and without metabolic modulators) in live respiring nematodes using a Seahorse XFe96 extracellular flux analyzer. We present details on our protocol, including preparation of nematode culture, use of metabolic modulators, execution of Seahorse XF assay as well as post-experimental data analysis. As a reference, we provide results of a series of experiments in which the metabolic activity of N2 wild-type nematodes was compared to N2 nematode treated with paraquat, a compound that generates reactive oxygen species (ROS), thus causing oxidative damage and mitochondrial dysfunction. These data illustrate the kind of insights that can be obtained even using a low number of nematodes (10 animals only per well).
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Affiliation(s)
- Li Fang Ng
- Ageing Research Laboratory, Science Division, Yale-NUS College, Singapore
| | - Jan Gruber
- Ageing Research Laboratory, Science Division, Yale-NUS College, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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