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42 results on '"Skinner, Owen S."'

5. Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell.

Author

Mick, Eran, Titov, Denis V, Skinner, Owen S, Sharma, Rohit, Jourdain, Alexis A, and Mootha, Vamsi K

Subjects
ATF4, GCN2, genetics, genomics, human, human biology, integrated stress response, medicine, metabolism, mitochondria, mouse, p53, Biochemistry and Cell Biology
Abstract

Mitochondrial dysfunction is associated with activation of the integrated stress response (ISR) but the underlying triggers remain unclear. We systematically combined acute mitochondrial inhibitors with genetic tools for compartment-specific NADH oxidation to trace mechanisms linking different forms of mitochondrial dysfunction to the ISR in proliferating mouse myoblasts and in differentiated myotubes. In myoblasts, we find that impaired NADH oxidation upon electron transport chain (ETC) inhibition depletes asparagine, activating the ISR via the eIF2α kinase GCN2. In myotubes, however, impaired NADH oxidation following ETC inhibition neither depletes asparagine nor activates the ISR, reflecting an altered metabolic state. ATP synthase inhibition in myotubes triggers the ISR via a distinct mechanism related to mitochondrial inner-membrane hyperpolarization. Our work dispels the notion of a universal path linking mitochondrial dysfunction to the ISR, instead revealing multiple paths that depend both on the nature of the mitochondrial defect and on the metabolic state of the cell.

Published
2020

10. The biosynthesis of methanobactin

Author

Kenney, Grace E., Dassama, Laura M. K., Pandelia, Maria-Eirini, Gizzi, Anthony S., Martinie, Ryan J., Gao, Peng, DeHart, Caroline J., Schachner, Luis F., Skinner, Owen S., Ro, Soo Y., Zhu, Xiao, Sadek, Monica, Thomas, Paul M., Almo, Steven C., Bollinger, J. Martin, Krebs, Carsten, Kelleher, Neil L., and Rosenzweig, Amy C.

Published
2018

11. Metabolic regulation of species-specific developmental rates

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Diaz-Cuadros, Margarete, Miettinen, Teemu P, Skinner, Owen S, Sheedy, Dylan, Díaz-García, Carlos Manlio, Gapon, Svetlana, Hubaud, Alexis, Yellen, Gary, Manalis, Scott R, Oldham, William M, Pourquié, Olivier, Massachusetts Institute of Technology. Department of Biological Engineering, Diaz-Cuadros, Margarete, Miettinen, Teemu P, Skinner, Owen S, Sheedy, Dylan, Díaz-García, Carlos Manlio, Gapon, Svetlana, Hubaud, Alexis, Yellen, Gary, Manalis, Scott R, Oldham, William M, and Pourquié, Olivier

Abstract

Animals display substantial inter-species variation in the rate of embryonic development despite a broad conservation of the overall sequence of developmental events. Differences in biochemical reaction rates, including the rates of protein production and degradation, are thought to be responsible for species-specific rates of development1-3. However, the cause of differential biochemical reaction rates between species remains unknown. Here, using pluripotent stem cells, we have established an in vitro system that recapitulates the twofold difference in developmental rate between mouse and human embryos. This system provides a quantitative measure of developmental speed as revealed by the period of the segmentation clock, a molecular oscillator associated with the rhythmic production of vertebral precursors. Using this system, we show that mass-specific metabolic rates scale with the developmental rate and are therefore higher in mouse cells than in human cells. Reducing these metabolic rates by inhibiting the electron transport chain slowed down the segmentation clock by impairing the cellular NAD+/NADH redox balance and, further downstream, lowering the global rate of protein synthesis. Conversely, increasing the NAD+/NADH ratio in human cells by overexpression of the Lactobacillus brevis NADH oxidase LbNOX increased the translation rate and accelerated the segmentation clock. These findings represent a starting point for the manipulation of developmental rate, with multiple translational applications including accelerating the differentiation of human pluripotent stem cells for disease modelling and cell-based therapies.

Published
2023

14. Circulating markers of NADH-reductive stress correlate with mitochondrial disease severity

Author

Sharma, Rohit, Reinstadler, Bryn, Engelstad, Kristin, Skinner, Owen S., Stackowitz, Erin, Haller, Ronald G., Clish, Clary B., Pierce, Kerry, Walker, Melissa A., Fryer, Robert, Oglesbee, Devin, Mao, Xiangling, Shungu, Dikoma C., Khatri, Ashok, Hirano, Michio, De Vivo, Darryl C., and Mootha, Vamsi K.

Subjects
NAD (Coenzyme) -- Physiological aspects -- Health aspects, Mitochondrial diseases -- Genetic aspects -- Development and progression, Biological markers -- Identification and classification -- Health aspects, Oxidation-reduction reaction -- Health aspects, Health care industry
Abstract

Mitochondrial disorders represent a large collection of rare syndromes that are difficult to manage both because we do not fully understand biochemical pathogenesis and because we currently lack facile markers of severity. The m.3243A>G variant is the most common heteroplasmic mitochondrial DNA mutation and underlies a spectrum of diseases, notably mitochondrial encephalomyopathy lactic acidosis and stroke-like episodes (MELAS). To identify robust circulating markers of m.3243A>G disease, we first performed discovery proteomics, targeted metabolomics, and untargeted metabolomics on plasma from a deeply phenotyped cohort (102 patients, 32 controls). In a validation phase, we measured concentrations of prioritized metabolites in an independent cohort using distinct methods. We validated 20 analytes (1 protein, 19 metabolites) that distinguish patients with MELAS from controls. The collection includes classic (lactate, alanine) and more recently identified (GDF-15, [alpha]-hydroxybutyrate) mitochondrial markers. By mining untargeted mass-spectra we uncovered 3 less well- studied metabolite families: N-lactoyl-amino acids, [beta]-hydroxy acylcarnitines, and [beta]-hydroxy fatty acids. Many of these 20 analytes correlate strongly with established measures of severity, including Karnofsky status, and mechanistically, nearly all markers are attributable to an elevated NADH/NA[D.sup.+] ratio, or NADH-reductive stress. Our work defines a panel of organelle function tests related to NADH-reductive stress that should enable classification and monitoring of mitochondrial disease., Introduction With the initial detection of the mitochondrial respiratory chain, it was anticipated that its dysfunction would lead to metabolic perturbations and disease (1). There is now widespread appreciation that [...]

Published
2021
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17. A natural fusion of flavodiiron, rubredoxin, and NADH:rubredoxin oxidoreductase domains is the highly efficient water-forming oxidase of T. vaginalis

Author

Abdulaziz, Evana N., primary, Bell, Tristan A., additional, Rashid, Bazlur, additional, Heacock, Mina L., additional, Skinner, Owen S., additional, Yaseen, Mohammad A., additional, Chao, Luke H., additional, Mootha, Vamsi K., additional, Pierik, Antonio J., additional, and Cracan, Valentin, additional

Published
2022
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22. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations

Author

Rath, Sneha, primary, Sharma, Rohit, additional, Gupta, Rahul, additional, Ast, Tslil, additional, Chan, Connie, additional, Durham, Timothy J, additional, Goodman, Russell P, additional, Grabarek, Zenon, additional, Haas, Mary E, additional, Hung, Wendy H W, additional, Joshi, Pallavi R, additional, Jourdain, Alexis A, additional, Kim, Sharon H, additional, Kotrys, Anna V, additional, Lam, Stephanie S, additional, McCoy, Jason G, additional, Meisel, Joshua D, additional, Miranda, Maria, additional, Panda, Apekshya, additional, Patgiri, Anupam, additional, Rogers, Robert, additional, Sadre, Shayan, additional, Shah, Hardik, additional, Skinner, Owen S, additional, To, Tsz-Leung, additional, Walker, Melissa A, additional, Wang, Hong, additional, Ward, Patrick S, additional, Wengrod, Jordan, additional, Yuan, Chen-Ching, additional, Calvo, Sarah E, additional, and Mootha, Vamsi K, additional

Published
2020
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26. β-Glucocerebrosidase Modulators Promote Dimerization of β-Glucocerebrosidase and Reveal an Allosteric Binding Site

Author

Zheng, Jianbin, primary, Chen, Long, additional, Skinner, Owen S., additional, Ysselstein, Daniel, additional, Remis, Jonathan, additional, Lansbury, Peter, additional, Skerlj, Renato, additional, Mrosek, Michael, additional, Heunisch, Ursula, additional, Krapp, Stephan, additional, Charrow, Joel, additional, Schwake, Michael, additional, Kelleher, Neil L., additional, Silverman, Richard B., additional, and Krainc, Dimitri, additional

Published
2018
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31. Native Electron Capture Dissociation Maps to Iron-Binding Channels in Horse Spleen Ferritin

Author

Skinner, Owen S., McAnally, Michael O., Van Duyne, Richard P., Schatz, George C., Breuker, Kathrin, Compton, Philip D., and Kelleher, Neil L.

Abstract

Native electron capture dissociation (NECD) is a process during which proteins undergo fragmentation similar to that from radical dissociation methods, but without the addition of exogenous electrons. However, after three initial reports of NECD from the cytochrome cdimer complex, no further evidence of the effect has been published. Here, we report NECD behavior from horse spleen ferritin, a ∼490 kDa protein complex ∼20-fold larger than the previously studied cytochrome cdimer. Application of front-end infrared excitation (FIRE) in conjunction with low- and high-m/zquadrupole isolation and collisionally activated dissociation (CAD) provides new insights into the NECD mechanism. Additionally, activation of the intact complex in either the electrospray droplet or the gas phase produced c-type fragment ions. Similar to the previously reported results on cytochrome c, these fragment ions form near residues known to interact with iron atoms in solution. By mapping the location of backbone cleavages associated with c-type ions onto the crystal structure, we are able to characterize two distinct iron binding channels that facilitate iron ion transport into the core of the complex. The resulting pathways are in good agreement with previously reported results for iron binding sites in mammalian ferritin.

Published
2024
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34. An informatic framework for decoding protein complexes by top-down mass spectrometry

Author

Skinner, Owen S, primary, Havugimana, Pierre C, additional, Haverland, Nicole A, additional, Fornelli, Luca, additional, Early, Bryan P, additional, Greer, Joseph B, additional, Fellers, Ryan T, additional, Durbin, Kenneth R, additional, Do Vale, Luis H F, additional, Melani, Rafael D, additional, Seckler, Henrique S, additional, Nelp, Micah T, additional, Belov, Mikhail E, additional, Horning, Stevan R, additional, Makarov, Alexander A, additional, LeDuc, Richard D, additional, Bandarian, Vahe, additional, Compton, Philip D, additional, and Kelleher, Neil L, additional

Published
2016
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37. Applying Label-Free Quantitation to Top Down Proteomics

Author

Ntai, Ioanna, primary, Kim, Kyunggon, additional, Fellers, Ryan T., additional, Skinner, Owen S., additional, Smith, Archer D., additional, Early, Bryan P., additional, Savaryn, John P., additional, LeDuc, Richard D., additional, Thomas, Paul M., additional, and Kelleher, Neil L., additional

Published
2014
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40. Top-down characterization of endogenous protein complexes with native proteomics

Author

Skinner, Owen S, Haverland, Nicole A, Fornelli, Luca, Melani, Rafael D, Do Vale, Luis H F, Seckler, Henrique S, Doubleday, Peter F, Schachner, Luis F, Srzentić, Kristina, Kelleher, Neil L, and Compton, Philip D

Abstract

Protein complexes exhibit great diversity in protein membership, post-translational modifications and noncovalent cofactors, enabling them to function as the actuators of many important biological processes. The exposition of these molecular features using current methods lacks either throughput or molecular specificity, ultimately limiting the use of protein complexes as direct analytical targets in a wide range of applications. Here, we apply native proteomics, enabled by a multistage tandem MS approach, to characterize 125 intact endogenous complexes and 217 distinct proteoforms derived from mouse heart and human cancer cell lines in discovery mode. The native conditions preserved soluble protein–protein interactions, high-stoichiometry noncovalent cofactors, covalent modifications to cysteines, and, remarkably, superoxide ligands bound to the metal cofactor of superoxide dismutase 2. These data enable precise compositional analysis of protein complexes as they exist in the cell and demonstrate a new approach that uses MS as a bridge to structural biology.

Published
2018
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42. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations.

Author

Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW, Joshi PR, Jourdain AA, Kim SH, Kotrys AV, Lam SS, McCoy JG, Meisel JD, Miranda M, Panda A, Patgiri A, Rogers R, Sadre S, Shah H, Skinner OS, To TL, Walker MA, Wang H, Ward PS, Wengrod J, Yuan CC, Calvo SE, and Mootha VK

Subjects
Animals, Bayes Theorem, DNA, Mitochondrial genetics, DNA, Mitochondrial metabolism, Datasets as Topic, Humans, Internet, Machine Learning, Mass Spectrometry, Mice, Mitochondria genetics, Mitochondrial Membranes metabolism, Mitochondrial Proteins classification, Mitochondrial Proteins genetics, Proteome classification, Proteome genetics, Software, Databases, Protein, Mitochondria metabolism, Mitochondrial Proteins metabolism, Molecular Sequence Annotation, Proteome metabolism
Abstract

The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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