Operation of a TCA cycle subnetwork in the mammalian nucleus

Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these required metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in the cell. Here we show that a substantial part of the mitochondrial tricarboxylic acid (TCA) cycle, the biosynthetic hub of epigenetic modification factors, is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins, supporting their nuclear location. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization and gene expression regulation. This dataset includes the data relating to the use of LOPIT to determine the subcellular localisation of succinylated proteins.核酸与组蛋白修饰（nucleic acid and histone modifications）的底物及辅酶，高度依赖中心代谢途径供给。尽管已有少量与这类必需代谢物合成相关的酶被报道定位于细胞核，但对应的代谢通路通常被认为仅在细胞其他区域发挥功能。本研究证实，作为表观遗传修饰因子（epigenetic modification factors）生物合成枢纽的线粒体三羧酸循环（tricarboxylic acid cycle, TCA），其相当一部分组分在细胞核中同样具备代谢活性。借助13C示踪分析技术，我们在海拉细胞（HeLa）的细胞核中检测到了谷氨酰胺→延胡索酸、柠檬酸→琥珀酸以及谷氨酰胺→天冬氨酸这三条代谢通路的活性。邻近标记质谱法（proximity labeling mass-spectrometry）分析显示，上述代谢通路相关酶与核心核蛋白存在空间邻近性，佐证了其细胞核定位特性。我们进一步在小鼠胚胎干细胞中证实了顺乌头酸酶2（aconitase 2）与2-氧代戊二酸脱氢酶（2-oxoglutarate dehydrogenase）的细胞核定位。综上，本研究结果证实细胞核中存在一条延伸的代谢通路，这一发现亟需学界修正关于代谢区室化与基因表达调控的经典认知。本数据集涵盖了利用同位素标记细胞器蛋白定位法（Localization of Organelle Proteins by Isotope Tagging, LOPIT）鉴定琥珀酰化蛋白（succinylated proteins）亚细胞定位的相关实验数据。