The existence of a nonclassical TCA cycle in the nucleus that wires the metabolic-epigenetic circuitry

Huajing Yu,Yue Wang,Jing Liang,Wenzhe Si,Yongfeng Shang,Haixia Li,Yu Zhang,Luyang Sun,Jie Ren,Lin He,Tong Jin,Xiaoping Li ,Jianguo Yang,Lu Xia,Xujun Liu,Yuan Peng ,Zihan Zhang,Wenting Zhang,Yunchao Huang,Xiaohan Yang,Shuo Lin ,Xiaoliang Cheng ,Shumeng Liu

doi:10.1038/s41392-021-00774-2

Abstract

The scope and variety of the metabolic intermediates from the mitochondrial tricarboxylic acid (TCA) cycle that are engaged in epigenetic regulation of the chromatin function in the nucleus raise an outstanding question about how timely and precise supply/consumption of these metabolites is achieved in the nucleus. We report here the identification of a nonclassical TCA cycle in the nucleus (nTCA cycle). We found that all the TCA cycle-associated enzymes including citrate synthase (CS), aconitase 2 (ACO2), isocitrate dehydrogenase 3 (IDH3), oxoglutarate dehydrogenase (OGDH), succinyl-CoA synthetase (SCS), fumarate hydratase (FH), and malate dehydrogenase 2 (MDH2), except for succinate dehydrogenase (SDH), a component of electron transport chain for generating ATP, exist in the nucleus. We showed that these nuclear enzymes catalyze an incomplete TCA cycle similar to that found in cyanobacteria. We propose that the nTCA cycle is implemented mainly to generate/consume metabolic intermediates, not for energy production. We demonstrated that the nTCA cycle is intrinsically linked to chromatin dynamics and transcription regulation. Together, our study uncovers the existence of a nonclassical TCA cycle in the nucleus that links the metabolic pathway to epigenetic regulation.

Highlights

The tricarboxylic acid (TCA) cycle, discovered by Hans Krebs in 1937 called Krebs cycle or citric acid cycle, is a central hub for metabolism and energy production
To further support the functional connection between the nTCA cycle and epigenetic regulation to extend the above observations to chromatin context, we investigated the effect of depletion of citrate synthase (CS) or IDH3A on chromatin dynamics in HepG2 cells using Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq).[29]
In nearly the last 2 decades, great progress has been made in understanding the inheritable changes in phenotype or gene expression governed by rules other than changes in underlying DNA sequence, the epigenetics

Summary

RESULTS

Of the mitochondrial TCA cycle-associated enzymes in the nucleus, The catalytic enzymes of the TCA cycle are found in the intact and pure nuclei were isolated from HepG2 cells using the nucleus nuclei-specific, high-sucrose gradient centrifugation protocol, and. Measurement by qRT-PCR and western blotting showed that the expression of EGFR decreased upon IDH3A depletion, an effect that could be rescued by reconstituting the expression of nuclear IDH3A through ectopic expression of IDH3AΔMLS (Fig. 7d) To further support this notion and to test the hypothesis that the modulation of EGFR expression by IDH3A is derived from the function of the nTCA cycle, not direct binding of IDH3A to the regulatory region of EGFR, qChIP assays were performed and possible recruitment of IDH3A on the promoter region of EGFR was examined. These experiments support a role for nuclear IDH3A in regulating cell proliferation through influencing EGFR expression

DISCUSSION

Findings

MATERIALS AND METHODS