Castoe Todd A, Jiang Zhi J, Gu Wanjun, Wang Zhengyuan O, Pollock David D
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.
PLoS One. 2008 May 21;3(5):e2201. doi: 10.1371/journal.pone.0002201.
Adaptive evolutionary episodes in core metabolic proteins are uncommon, and are even more rarely linked to major macroevolutionary shifts.
METHODOLOGY/PRINCIPAL FINDINGS: We conducted extensive molecular evolutionary analyses on snake mitochondrial proteins and discovered multiple lines of evidence suggesting that the proteins at the core of aerobic metabolism in snakes have undergone remarkably large episodic bursts of adaptive change. We show that snake mitochondrial proteins experienced unprecedented levels of positive selection, coevolution, convergence, and reversion at functionally critical residues. We examined Cytochrome C oxidase subunit I (COI) in detail, and show that it experienced extensive modification of normally conserved residues involved in proton transport and delivery of electrons and oxygen. Thus, adaptive changes likely altered the flow of protons and other aspects of function in CO, thereby influencing fundamental characteristics of aerobic metabolism. We refer to these processes as "evolutionary redesign" because of the magnitude of the episodic bursts and the degree to which they affected core functional residues.
CONCLUSIONS/SIGNIFICANCE: The evolutionary redesign of snake COI coincided with adaptive bursts in other mitochondrial proteins and substantial changes in mitochondrial genome structure. It also generally coincided with or preceded major shifts in ecological niche and the evolution of extensive physiological adaptations related to lung reduction, large prey consumption, and venom evolution. The parallel timing of these major evolutionary events suggests that evolutionary redesign of metabolic and mitochondrial function may be related to, or underlie, the extreme changes in physiological and metabolic efficiency, flexibility, and innovation observed in snake evolution.
核心代谢蛋白中的适应性进化事件并不常见，与重大宏观进化转变的关联更为罕见。
方法/主要发现：我们对蛇的线粒体蛋白进行了广泛的分子进化分析，发现多条证据表明，蛇有氧代谢核心的蛋白经历了显著的适应性变化的 episodic 爆发。我们表明，蛇的线粒体蛋白在功能关键残基处经历了前所未有的正选择、协同进化、趋同和回复水平。我们详细研究了细胞色素 C 氧化酶亚基 I（COI），并表明它经历了参与质子运输以及电子和氧气传递的正常保守残基的广泛修饰。因此，适应性变化可能改变了 CO 中质子的流动和功能的其他方面，从而影响了有氧代谢的基本特征。由于 episodic 爆发的规模及其对核心功能残基的影响程度，我们将这些过程称为“进化重新设计”。
结论/意义：蛇 COI 的进化重新设计与其他线粒体蛋白的适应性爆发以及线粒体基因组结构的重大变化同时发生。它通常也与生态位的重大转变以及与肺缩小、大型猎物消耗和毒液进化相关的广泛生理适应的进化同时发生或先于这些转变。这些主要进化事件的平行时间表明，代谢和线粒体功能的进化重新设计可能与蛇进化中观察到的生理和代谢效率、灵活性和创新性的极端变化有关，或者是其基础。
