Zhang Lichao, Winkler Sebastian, Schlottmann Fabian P, Kohlbacher Oliver, Elias Josh E, Skotheim Jan M, Ewald Jennifer C
Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States.
Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.
Front Cell Dev Biol. 2019 Dec 17;7:338. doi: 10.3389/fcell.2019.00338. eCollection 2019.
The coordination of metabolism and growth with cell division is crucial for proliferation. While it has long been known that cell metabolism regulates the cell division cycle, it is becoming increasingly clear that the cell division cycle also regulates metabolism. In budding yeast, we previously showed that over half of all measured metabolites change concentration through the cell cycle indicating that metabolic fluxes are extensively regulated during cell cycle progression. However, how this regulation is achieved still remains poorly understood. Since both the cell cycle and metabolism are regulated to a large extent by protein phosphorylation, we here decided to measure the phosphoproteome through the budding yeast cell cycle. Specifically, we chose a cell cycle synchronization strategy that avoids stress and nutrient-related perturbations of metabolism, and we grew the yeast on ethanol minimal medium to force cells to utilize their full biosynthetic repertoire. Using a tandem-mass-tagging approach, we found over 200 sites on metabolic enzymes and transporters to be phospho-regulated. These sites were distributed among many pathways including carbohydrate catabolism, lipid metabolism, and amino acid synthesis and therefore likely contribute to changing metabolic fluxes through the cell cycle. Among all one thousand sites whose phosphorylation increases through the cell cycle, the CDK consensus motif and an arginine-directed motif were highly enriched. This arginine-directed R-R-x-S motif is associated with protein-kinase A, which regulates metabolism and promotes growth. Finally, we also found over one thousand sites that are dephosphorylated through the G1/S transition. We speculate that the phosphatase Glc7/PP1, known to regulate both the cell cycle and carbon metabolism, may play an important role because its regulatory subunits are phospho-regulated in our data. In summary, our results identify extensive cell cycle dependent phosphorylation and dephosphorylation of metabolic enzymes and suggest multiple mechanisms through which the cell division cycle regulates metabolic signaling pathways to temporally coordinate biosynthesis with distinct phases of the cell division cycle.
新陈代谢与生长和细胞分裂的协调对于细胞增殖至关重要。虽然人们早就知道细胞代谢调节细胞分裂周期，但越来越清楚的是，细胞分裂周期也调节新陈代谢。在芽殖酵母中，我们之前表明，所有测量的代谢物中有超过一半在细胞周期中浓度发生变化，这表明在细胞周期进程中代谢通量受到广泛调节。然而，这种调节是如何实现的仍然知之甚少。由于细胞周期和新陈代谢在很大程度上都受蛋白质磷酸化调节，我们在此决定通过芽殖酵母细胞周期测量磷酸化蛋白质组。具体而言，我们选择了一种避免代谢受到应激和营养相关干扰的细胞周期同步策略，并在乙醇基本培养基上培养酵母，以迫使细胞利用其完整的生物合成能力。使用串联质量标签方法，我们发现代谢酶和转运蛋白上有超过200个位点受到磷酸化调节。这些位点分布在许多途径中，包括碳水化合物分解代谢、脂质代谢和氨基酸合成，因此可能有助于在细胞周期中改变代谢通量。在所有磷酸化在细胞周期中增加的一千个位点中，CDK共有基序和精氨酸导向基序高度富集。这种精氨酸导向的R-R-x-S基序与蛋白激酶A相关，蛋白激酶A调节新陈代谢并促进生长。最后，我们还发现有一千多个位点在G1/S转变过程中去磷酸化。我们推测，已知调节细胞周期和碳代谢的磷酸酶Glc7/PP1可能起重要作用，因为其调节亚基在我们的数据中受到磷酸化调节。总之，我们的结果确定了代谢酶广泛的细胞周期依赖性磷酸化和去磷酸化，并提出了多种机制，通过这些机制细胞分裂周期调节代谢信号通路，以在时间上协调生物合成与细胞分裂周期的不同阶段。
