Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

Abstract

Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is therefore highly relevant in the context of circadian biology, but its characterization on the proteome-wide scale and its circadian clock dependence are still poorly described. Here, we provide a comprehensive and rhythmic acetylome map of the mouse liver. Rhythmic acetylated proteins showed subcellular localization-specific phases that correlated with the related metabolites in the regulated pathways. Mitochondrial proteins were over-represented among the rhythmically acetylated proteins and were highly correlated with SIRT3-dependent deacetylation. SIRT3 activity being nicotinamide adenine dinucleotide (NAD)⁺ level-dependent, we show that NAD⁺ is orchestrated by both feeding rhythms and the circadian clock through the NAD⁺ salvage pathway but also via the nicotinamide riboside pathway. Hence, the diurnal acetylome relies on a functional circadian clock and affects important diurnal metabolic pathways in the mouse liver.

Keywords: NAD(+); SILAC proteomics; SIRT3; acetylation; circadian clock; liver metabolism.

Graphical abstract

Figure 1

Characterization of the Liver Acetylome (A) Distribution of sample number for the quantified acetylation sites in TE (red bars plotted on the left y axis) and NE (green bars plotted on the right y axis). (B) Venn diagram showing the number of acetylated proteins quantified in TE (red circle, 309 acetylated proteins identified) and NE (green circle, 162 acetylated proteins identified). (C) Distribution of cellular localization of proteins with quantified acetylation sites in TE (left), TE and NE (center), and NE (right). Data are expressed in percent. (D) Venn diagram comparing the TE dataset of acetylated proteins with the previous circadian liver acetylome (Masri et al., 2013) (176 unique acetylated proteins identified). (E) Matrix layout for all intersections (vertical bars), sorted by size, of our TE dataset, with the data from studies performed using liver mitochondrial protein extract: Schwer et al. (2009) (356 acetylated proteins), Rardin et al. (2013b) (483 acetylated proteins), Still et al. (2013) (729 acetylated proteins), and Hebert et al. (2013) (834 acetylated proteins). Color-coded circles in the matrix indicate sets that are part of the intersection and, the top horizontal bar graph displays the protein number for each study.

Figure 2

Rhythmicity Analysis of the Liver Acetylome (A–C) Heatmaps showing rhythmic acetylation sites normalized by their corresponding total protein amount in TE (A) and NE (B) under light/dark and night-restricted feeding conditions. Data were standardized by rows, and gray blocks indicate missing protein data. The polar plots on the right of each heatmap display peak phase distribution of the rhythmic acetylation (Ac) sites, and (C) shows amplitude. The colors of the polar plots (A and B) and histograms (C) indicate Ac sites that have a corresponding total protein with a defined mitochondrial (n = 80 Ac sites, red) or cytoplasmic (n = 40 Ac sites, blue) localization or Ac sites that are identified in NE (n = 27 Ac sites, green). (D) Western blot (WB) analysis of total protein extracts using acetyl-K68 SOD2 (top blot) or total SOD2 (bottom blot). MS data in red, mean ± SEM, are from Table S2. WB data in black, mean ± SEM, are from three independent biological samples and represent the ratio of the acetyl-K68 SOD2 signal on the total SOD2 signal. Data (MS and WB) are normalized to the temporal mean. Naphtol blue black staining of the membranes was used as a loading control (LC) and served as a reference for normalization of the quantified values.

Figure 3

Rhythmic Behavior of Non-SIRT3 and SIRT3 Targets (A–C) Peak phase (A), amplitude (B), and cellular localization (C) of rhythmic acetylation sites non-targeted (left) or targeted (right) by the SIRT3 deacetylase. Acetylation sites were defined as targeted by SIRT3 when their levels were significantly upregulated in Sirt3 KO mice in Rardin et al., 2013b, Hebert et al., 2013, or Dittenhafer-Reed et al. (2015) (Table S3).

Figure 4

Regulation of Global Acetylation and NAD⁺ Metabolism by the Circadian Clock (A) Western blot analysis of global lysine acetylation performed on total protein extract from Cry1/2 DKO, Bmal1 KO, and their corresponding WT control mice (left). Naphtol blue black staining of the membrane was used as a loading control (center) and served as a reference for normalization of the quantified values displayed at the right. The average acetylation level was compared between clock-disrupted mice and their controls using Student’s t test (n = 12/genotype). Error bars represent min to max. (B) NAD⁺ liver concentrations in Bmal1 KO (n = 2/time point) and Cry1/2 DKO mice (n = 2/time point) and their corresponding WT controls (mean ± SEM). (C) Top: mRNA expression levels of Nampt, Nmrk1, Nmnat1, and Nmnat3 in Bmal1 KO mice (green) and their WT littermates (black) under night-restricted feeding conditions. Bottom: the same results in Cry1/2 DKO (red) mice and their WT controls (black). The data are from Atger et al. (2015); n = 2 for each time point and each genotype). Error bars represent ±SEM. (D) WB analysis in TE extracts of NRK1 in Bmal1 KO and Cry1/2 DKO mice. Quantifications of the blots are displayed below. Naphtol blue black staining of the membranes was used as a loading control and served as a reference for normalization of the quantified values. Error bars represent ±SEM. (E) Temporal binding of circadian clock core regulators on the Nampt, Nmrk1, and Nmnat3 gene promoters. At each time point, for each factor, the averages of all rhythmic bindings are presented. The data are from Koike et al. (2012).

Figure 5

Metabolic Pathways Affected by Rhythmic Acetylation Rhythmic protein acetylations and their regulation by the circadian clock for fatty acid oxydation, urea cycle, ketogenesis, and ethanol metabolism. Each dot represents a unique acetylation site within the protein of interest. Grey and black dots represent non-rhythmic identified and quantified acetylation sites, respectively, whereas phases of maximum acetylation levels for rhythmic acetylation sites are color-coded. Superscripted red dots and green asterisks indicate protein acetylation levels significantly different in Cry1/2 DKO and Bmal1 KO mice, respectively.

Figure 6

Impact of Rhythmic Acetylation on Metabolite Levels Liver temporal profiles of metabolites in Bmal1 KO (green lines) and WT littermates (black lines). Data (mean ± SEM) are expressed relative to the temporal mean of WT values. The analysis is related to key metabolites of the urea cycle, ketogenesis, and ethanol metabolism. Student’s t test was performed to compare the average level of metabolite at every time point between different genotypes (n = 4). ^∗p < 0.05 between Bmal1 KO and WT mice.

Figure 7

Interconnection between Feeding and Circadian Rhythms in Regulating NAD⁺ Synthesis and Circadian Clock Disruption Effects on Lysine Succinylation and Malonylation (A) Rhythmic feeding effect (blue) versus the circadian clock (red) on key components implicated in acetyl-CoA-dependent acetylation and the regulation NAD⁺ synthesis during the day (fasting phase) and night (feeding phase). (B and C) Western blot analysis of global lysine succinylation (B) and malonylation (C) performed on total protein extract from Cry1/2 DKO, Bmal1 KO, and their corresponding WT control mice (left). Naphtol blue black staining of the membrane was used as a loading control (center) and served as a reference for normalization of the quantified values displayed at the right. Average acetylation levels were compared between clock-disrupted mice and their controls using Student’s t test (n = 4). Error bars represent min to max.