title: Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments.
abstract: The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [(2)H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman's ρ = 0.57; P < 10(-4)), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Pabalu P
authors.initials: PP
authors.lastname: Karunadharma
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Basisty
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Ying Ann
authors.initials: YA
authors.lastname: Chiao
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Dao-Fu
authors.initials: DF
authors.lastname: Dai
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Drake
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Nick
authors.initials: N
authors.lastname: Levy
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Koh
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Mary J
authors.initials: MJ
authors.lastname: Emond
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Shane
authors.initials: S
authors.lastname: Kruse
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: David
authors.initials: D
authors.lastname: Marcinek
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Maccoss
authors.affiliation: *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA petersr@u.washington.edu.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Rabinovitch
mesh_terms: D000818:Animals; D005075:Biological Evolution; D031204:Caloric Restriction / Q000379:methods; D004579:Electron Transport / Q000502:physiology*; D005260:Female; D007553:Isotope Labeling / Q000379:methods; D007930:Leucine / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods; D051379:Mice; D008810:Mice, Inbred C57BL; D008928:Mitochondria / Q000502:physiology*; D021122:Protein Subunits / Q000378:metabolism; D011506:Proteins / Q000378:metabolism*; D059748:Proteolysis; D054875:Ubiquitination / Q000502:physiology
chemical_list: D021122:Protein Subunits; D011506:Proteins; D007930:Leucine
keywords: aging; caloric restriction; mitochondria; proteostasis; rapamycin