Substrate- and Isoform-Specific Proteome Stability in Normal and Stressed Cardiac Mitochondria

Wang

Molecular & Cellular Proteomics

et al. 2012

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161

187

Mitochondrial dysfunction is associated with many human diseases. Mitochondrial damage is exacerbated by inadequate protein quality control and often further contributes to pathogenesis. The maintenance of mitochondrial functions requires a delicate balance of continuous protein synthesis and degradation, i.e. protein turnover. To understand mitochondrial protein dynamics in vivo, we designed a metabolic heavy water ( 2 H 2 O) labeling strategy customized to examine individual protein turnover in the mitochondria in a systematic fashion. Mice were fed with 2 H 2 O at a minimal level (<5% body water) without physiological impacts. Mitochondrial proteins were analyzed from 9 mice at each of the 13 time points between 0 and 90 days (d) of labeling. A novel multiparameter fitting approach computationally determined the normalized peak areas of peptide mass isotopomers at initial and steady-state time points and permitted the protein halflife to be determined without plateau-level 2 H incorporation. We characterized the turnover rates of 458 proteins in mouse cardiac and hepatic mitochondria and found median turnover rates of 0.0402 d ؊1 and 0.163 d ؊1 , respectively, corresponding to median half-lives of 17.2 d and 4.26 d. Mitochondria in the heart and those in the liver exhibited distinct turnover kinetics, with limited synchronization within functional clusters. We observed considerable interprotein differences in turnover rates in both organs, with half-lives spanning from hours to months (ϳ60 d). Our proteomics platform demonstrates the first large-scale analysis of mitochondrial protein turnover rates in vivo, with potential applications in translational research. Molecular & Cellular

Section: Rates Of Protein Turnover In Cardiac and Hepatic Mitochondrisupporting

confidence: 91%

Metabolic Labeling Reveals Proteome Dynamics of Mouse Mitochondria

Wang

Molecular & Cellular Proteomics

et al. 2012

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161

187

“…Mitochondrial dynamics, in particular biogenesis, fusion-fission, and autophagy, play critical roles in cardiac functions (33)(34)(35). Our previous observations of diverse and asynchronous mitochondrial protein turnover in the normal mouse heart led us to conclude that the turnover of individual proteins can influence the homeostasis and dynamics of mitochondria (16,36). Consistent with this notion, we found complex and bidirectional kinetic responses among individual mitochondrial proteins in the remodeling heart.…”

Section: Figuresupporting

confidence: 81%

Protein kinetic signatures of the remodeling heart following isoproterenol stimulation

et al. 2014

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Protein temporal dynamics play a critical role in time-dimensional pathophysiological processes, including the gradual cardiac remodeling that occurs in early-stage heart failure. Methods for quantitative assessments of protein kinetics are lacking, and despite knowledge gained from single-protein studies, integrative views of the coordinated behavior of multiple proteins in cardiac remodeling are scarce. Here, we developed a workflow that integrates deuterium oxide ( 2 H 2 O) labeling, high-resolution mass spectrometry (MS), and custom computational methods to systematically interrogate in vivo protein turnover. Using this workflow, we characterized the in vivo turnover kinetics of 2,964 proteins in a mouse model of β-adrenergic-induced cardiac remodeling. The data provided a quantitative and longitudinal view of cardiac remodeling at the molecular level, revealing widespread kinetic regulations in calcium signaling, metabolism, proteostasis, and mitochondrial dynamics. We translated the workflow to human studies, creating a reference dataset of 496 plasma protein turnover rates from 4 healthy adults. The approach is applicable to short, minimal label enrichment and can be performed on as little as a single biopsy, thereby overcoming critical obstacles to clinical investigations. The protein turnover quantitation experiments and computational workflow described here should be widely applicable to largescale biomolecular investigations of human disease mechanisms with a temporal perspective.

“…As discussed previously deletion of Pim1 in yeast led directly to accelerated ageing and proteasome inhibition, measured by a decline in proteasome peptidase activity (Erjavec et al, 2013). Conversely, an additional link between these systems has been found in ischemic mouse cardiac mitochondria and proteasomes where mitochondrial oxidative damage following reperfusion injury caused an increase in proteasome substrate specificity for damaged mitochondrial proteins (Lau et al, 2012). The mechanisms behind these differing effects of oxidised protein aggregates on proteolytic systems and the overall importance of these responses are still not understood and whether these effects are purely pathological or serve a cellular function have not yet been clarified.…”

Section: Damage To Proteolytic Pathways In Ageing and Diseasementioning

confidence: 78%

Oxidised protein metabolism: recent insights

Samardzic

Rodgers

2017

Biological Chemistry

Abstract:The 'oxygen paradox' arises from the fact that oxygen, the molecule that aerobic life depends on, threatens its very existence. An oxygen-rich environment provided life on Earth with more efficient bioenergetics and, with it, the challenge of having to deal with a host of oxygen-derived reactive species capable of damaging proteins and other crucial cellular components. In this minireview, we explore recent insights into the metabolism of proteins that have been reversibly or irreversibly damaged by oxygen-derived species. We discuss recent data on the important roles played by the proteasomal and lysosomal systems in the proteolytic degradation of oxidatively damaged proteins and the effects of oxidative damage on the function of the proteolytic pathways themselves. Mitochondria are central to oxygen utilisation in the cell, and their ability to handle oxygen-derived radicals is an important and still emerging area of research. Current knowledge of the proteolytic machinery in the mitochondria, including the ATPdependent AAA+ proteases and mitochondrial-derived vesicles, is also highlighted in the review. Significant progress is still being made in regard to understanding the mechanisms underlying the detection and degradation of oxidised proteins and how proteolytic pathways interact with each other. Finally, we highlight a few unanswered questions such as the possibility of oxidised amino acids released from oxidised proteins by proteolysis being re-utilised in protein synthesis thus establishing a vicious cycle of oxidation in cells.