Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome

Abstract

Summary Calorie restriction (CR) extends lifespan in diverse species. Mitochondria play a key role in CR adaptation, however, the molecular details remain elusive. We developed and applied a quantitative mass spectrometry method to probe the liver mitochondrial acetyl-proteome during CR vs. control diet in mice that were wild-type or lacked the protein deacetylase SIRT3. Quantification of 3,285 acetylation sites −2,193 from mitochondrial proteins rendered a comprehensive atlas of the acetyl-proteome and enabled global site-specific, relative acetyl occupancy measurements between all four experimental conditions. Bioinformatic and biochemical analyses provided additional support for the effects of specific acetylation on mitochondrial protein function. Our results (1) reveal widespread reprogramming of mitochondrial protein acetylation in response to CR and SIRT3, (2) identify three biochemically distinct classes of acetylation sites, and (3) provide evidence that SIRT3 is a prominent regulator in CR adaptation by coordinately deacetylating proteins involved in diverse pathways of metabolism and mitochondrial maintenance.

An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms

“…These results cannot identify the acetylation site affected, but they confirm that Sirt3 can deacetylate native MDH protein. Sirt3-dependent MDH deacetylation in vivo was indeed confirmed during the revision of this manuscript 37 . The site identified in this proteomics study, Lys239, corresponds to the MDH microarray peptide most efficiently deacetylated by Sirt3, demonstrating the suitability of our system for identifying promising sirtuin substrates and substrate sites.…”

NAD + and SIRT3 control microtubule dynamics and reduce susceptibility to antimicrotubule agents

“…Recent studies suggest that these sirtuins remove acyl modifications in proteins or deacetylate only a small subset of proteins in mitochondria (46)(47)(48). This finding contrasts with SIRT3, which is the major protein deacetylase in mitochondria (49), affecting the acetylation status of ∼100 proteins in mitochondria (40). Among the nonmitochondrial sirtuins, overexpression of SIRT1 showed a detectable, although statistically nonsignificant, inhibition of vinblastine-induced microtubule depolymerization.…”

“…39). The physiological targets of SIRT3 include over 100 mitochondrial proteins, including diverse proteins that suppress ROS generation (40). Acetylation of these proteins typically leads to increased ROS production, whereas SIRT3-mediated deacetylation leads to decreased ROS levels (41)(42)(43).…”

Mitochondrial Biogenesis through Activation of Nuclear Signaling Proteins

“…In addition, sirtuins deacetylate numerous metabolic enzymes to govern their specific activity. Changes in SIRT3 activity have been shown to be an important determinant in the acetylation state of mitochondrial in response to nutrient availability (Hirschey et al 2011;Hebert et al 2013). The acetylation of many mitochondrial proteins, such as isocitrate dehydrogenase 2 (Yu et al 2012), can alter their catalytic/biological function.…”