Shaiwale Nayana S, Basu Bhakti, Deobagkar Deepti D, Deobagkar Dileep N, Apte Shree K
Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India; Department of Zoology, Centre for Advanced Studies, University of Pune, Pune 411007, India.
Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
J Proteomics. 2015 Aug 3;126:131-9. doi: 10.1016/j.jprot.2015.05.036. Epub 2015 Jun 3.
The protein encoded by DR_0643 gene from Deinococcus radiodurans was shown to be an active N-6 adenine-specific DNA methyltransferase (Dam). Deletion of corresponding protein reduced adenine methylation in the genome by 60% and resulted in slow-growth phenotype. Proteomic changes induced by DNA adenine hypomethylation were mapped by two-dimensional protein electrophoresis coupled with mass spectrometry. As compared to wild type D. radiodurans cells, at least 54 proteins were differentially expressed in Δdam mutant. Among these, 39 metabolic enzymes were differentially expressed in Δdam mutant. The most prominent change was DNA adenine hypomethylation induced de-repression of pyruvate dehydrogenase complex, E1 component (aceE) gene resulting in 10 fold increase in the abundance of corresponding protein. The observed differential expression profile of metabolic enzymes included increased abundance of enzymes involved in fatty acid and amino acid degradation to replenish acetyl Co-A and TCA cycle intermediates and diversion of phosphoenolpyruvate and pyruvate into amino acid biosynthesis, a metabolic rewiring attempt by Δdam mutant to restore energy generation via glycolysis-TCA cycle axis. This is the first report of DNA adenine hypomethylation mediated rewiring of metabolic pathways in prokaryotes.
研究表明，耐辐射球菌（Deinococcus radiodurans）的DR_0643基因编码的蛋白质是一种活性N-6腺嘌呤特异性DNA甲基转移酶（Dam）。相应蛋白质的缺失使基因组中的腺嘌呤甲基化减少了60%，并导致生长缓慢的表型。通过二维蛋白质电泳结合质谱法对DNA腺嘌呤低甲基化诱导的蛋白质组变化进行了图谱分析。与野生型耐辐射球菌细胞相比，Δdam突变体中至少有54种蛋白质差异表达。其中，39种代谢酶在Δdam突变体中差异表达。最显著的变化是DNA腺嘌呤低甲基化诱导丙酮酸脱氢酶复合体E1亚基（aceE）基因的去抑制，导致相应蛋白质的丰度增加了10倍。观察到的代谢酶差异表达谱包括参与脂肪酸和氨基酸降解以补充乙酰辅酶A和三羧酸循环中间体的酶的丰度增加，以及磷酸烯醇丙酮酸和丙酮酸转向氨基酸生物合成，这是Δdam突变体通过糖酵解-三羧酸循环轴恢复能量生成的代谢重布线尝试。这是关于DNA腺嘌呤低甲基化介导原核生物代谢途径重布线的首次报道。
