Succinyl-CoA synthetase deficiency in mouse forebrain results in hyper-succinylation with perturbed neuronal transcriptional regulation and metabolism (RNA-Seq)

Lysine-succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the TCA cycle. Deficiency of succinyl-CoA synthetase (SCS), the TCA-cycle enzyme catalyzing the reversible conversion of succinyl-CoA to succinate, leads to mitochondrial encephalomyopathy in humans and embryonic lethality in mice. This report presents a conditional forebrain-specific knock-out (KO0 mouse model of Sucla2, the gene encoding the ATP-specific beta isoform of SCS, resulting in postnatal deficiency of the entire SCS complex. Results demonstrate that the accumulation of succinyl-CoA in the absence of SCS leads to hyper-succinylation within the cerebral cortex of adult mice. With previous research identifying succinylation marks on histones, and with proteomic evidence of histone lysine-succinylation within the presented model, global chromatin accessibility was surveyed in Sucla2 mutant and control mice via ATAC-sequencing. Data show wide-scale alterations in chromatin landscape and global gene expression. Computational analysis of combined chromatin-accessibility and gene expression data reveal perturbation of neuronal transcriptional regulatory networks in the mutant forebrain, suggesting SCS-related changes in the protein succinylome and chromatin accessibility play a significant role in the neuronal pathogenesis of SCS-deficiency. Assessment of global chromatin accessibiliy and bulk mRNA-sequencing in murine cortex with enriched protein succinylation resulting from loss of Kreb's Cycle enzyme succinyl-CoA synthetase赖氨酸琥珀酰化（lysine succinylation）是蛋白质酰化的一个亚型，与三羧酸循环（TCA cycle）中琥珀酰辅酶A的代谢调控密切相关。琥珀酰辅酶A合成酶（succinyl-CoA synthetase, SCS）是催化琥珀酰辅酶A与琥珀酸发生可逆互变的三羧酸循环核心酶，该酶的缺失会导致人类罹患线粒体脑肌病，并导致小鼠胚胎致死。本研究构建了Sucla2基因的条件性前脑特异性敲除（conditional forebrain-specific knock-out, KO）小鼠模型：Sucla2编码SCS的ATP特异性β亚型，该模型可使整个SCS复合物在小鼠出生后完全缺失。实验结果显示，SCS缺失引发的琥珀酰辅酶A积累，会使成年小鼠大脑皮层内出现过度琥珀酰化修饰。既往研究已鉴定出组蛋白上的琥珀酰化修饰位点，且本模型中存在组蛋白赖氨酸琥珀酰化的蛋白质组学证据，因此本研究通过ATAC测序（ATAC-sequencing）对Sucla2突变小鼠与对照小鼠的全基因组染色质开放程度进行了检测。数据分析结果表明，突变小鼠的染色质景观与全局基因表达均发生广泛改变。对染色质开放程度与基因表达的联合数据集开展计算分析后发现，突变小鼠前脑内的神经元转录调控网络受到扰动，这提示SCS缺失所引发的蛋白质琥珀酰化组与染色质开放程度改变，在SCS缺乏症的神经元发病机制中发挥了重要作用。本研究还针对因三羧酸循环酶琥珀酰辅酶A合成酶缺失而出现蛋白质高度琥珀酰化的小鼠大脑皮层，完成了全基因组染色质开放程度与批量mRNA测序（bulk mRNA-sequencing）的评估分析。