Department of Life Sciences and the Nation Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
J Mol Biol. 2010 Nov 19;404(1):158-71. doi: 10.1016/j.jmb.2010.09.029. Epub 2010 Sep 22.
Despite years of research, the structure of the largest mammalian oxidative phosphorylation (OXPHOS) complex, NADH-ubiquinone oxidoreductase (complex I), and the interactions among its 45 subunits are not fully understood. Since complex I harbors subunits encoded by mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) genomes, with the former evolving ∼10 times faster than the latter, tight cytonuclear coevolution is expected and observed. Recently, we identified three nDNA-encoded complex I subunits that underwent accelerated amino acid replacement, suggesting their adjustment to the elevated mtDNA rate of change. Hence, they constitute excellent candidates for binding mtDNA-encoded subunits. Here, we further disentangle the network of physical cytonuclear interactions within complex I by analyzing subunits coevolution. Firstly, relying on the bioinformatic analysis of 10 protein complexes possessing solved structures, we show that signals of coevolution identified physically interacting subunits with nearly 90% accuracy, thus lending support to our approach. When applying this approach to cytonuclear interaction within complex I, we predict that the 'rate-accelerated' nDNA-encoded subunits of complex I, NDUFC2 and NDUFA1, likely interact with the mtDNA-encoded subunits ND5/ND4 and ND5/ND4/ND1, respectively. Furthermore, we predicted interactions among mtDNA-encoded complex I subunits. Using the yeast two-hybrid system, we experimentally confirmed the predicted interactions of human NDUFC2 with ND4, the interactions of human NDUFA1 with ND1 and ND4, and the lack of interaction of NDUFC2 with ND3 and NDUFA1, thus providing a proof of concept for our approach. Our study shows, for the first time, evidence for direct interactions between nDNA-encoded and mtDNA-encoded subunits of human OXPHOS complex I and paves the path towards deciphering subunit interactions within complexes lacking three-dimensional structures. Our subunit-interactions-predicting method, ComplexCorr, is available at http://webclu.bio.wzw.tum.de/complexcorr.
尽管经过多年的研究，最大的哺乳动物氧化磷酸化（OXPHOS）复合物 NADH-泛醌氧化还原酶（复合物 I）的结构及其 45 个亚基之间的相互作用仍未完全了解。由于复合物 I 包含线粒体 DNA（mtDNA）和核 DNA（nDNA）基因组编码的亚基，前者的进化速度比后者快约 10 倍，因此预计并观察到紧密的核质协同进化。最近，我们鉴定了三个经历氨基酸替换加速的 nDNA 编码复合物 I 亚基，这表明它们适应了 mtDNA 变化率的升高。因此，它们是结合 mtDNA 编码亚基的优秀候选者。在这里，我们通过分析亚基协同进化进一步解开复合物 I 中核质相互作用的网络。首先，依靠对具有已解决结构的 10 种蛋白质复合物的生物信息学分析，我们表明，协同进化识别的信号可以以近 90%的准确率确定物理相互作用的亚基，从而为我们的方法提供支持。当将这种方法应用于复合物 I 中的核质相互作用时，我们预测复合物 I 的“速率加速”nDNA 编码亚基 NDUFC2 和 NDUFA1 可能分别与 mtDNA 编码的亚基 ND5/ND4 和 ND5/ND4/ND1 相互作用。此外，我们预测了 mtDNA 编码的复合物 I 亚基之间的相互作用。通过酵母双杂交系统，我们实验证实了人 NDUFC2 与 ND4、人 NDUFA1 与 ND1 和 ND4 以及 NDUFC2 与 ND3 和 NDUFA1 之间缺乏相互作用的预测相互作用，从而为我们的方法提供了概念验证。我们的研究首次为人类 OXPHOS 复合物 I 的 nDNA 编码和 mtDNA 编码亚基之间的直接相互作用提供了证据，并为解析缺乏三维结构的复合物中亚基相互作用铺平了道路。我们的亚基相互作用预测方法 ComplexCorr 可在 http://webclu.bio.wzw.tum.de/complexcorr 上获得。
