Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen
Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen
复制标题
蛋白质结构域结构揭示了有氧代谢的起源和行星氧气的增加
DOI：
10.1016/j.str.2011.11.003
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发表时间：
2012-01-11
期刊：
影响因子：
5.7
通讯作者：
Caetano-Anolles, Gustavo
中科院分区：
文献类型：
--
作者：
Kim, Kyung Mo;Qin, Tao;Caetano-Anolles, Gustavo
尽管进化生物信息学取得了进展，但现代生物化学的起源和进化仍然是一个谜。在这里，我们使用近1,000个基因组的结构普查和分子时钟的折叠，以确定一个时间轴的蛋白质家族的外观连接到单域酶。时间轴整理了酶的募集，验证了代谢史中的模式，并揭示了最古老的有氧代谢反应涉及吡哆醛5 '-磷酸或吡哆醛的合成，并出现在2.9 Gyr前。这种原始反应的氧源可能是Mn过氧化氢酶，它同时出现，并可能产生氧气作为过氧化氢解毒的副产物。最后，转移基团和代谢产物片段的进化分析表明，氧化硫不参与代谢，直到氧气的上升。我们在分子和化学中发现的进化模式为生物化学和地球化学的共同进化提供了强有力的支持。
The origin and evolution of modern biochemistry remain a mystery despite advances in evolutionary bioinformatics. Here, we use a structural census in nearly 1,000 genomes and a molecular clock of folds to define a timeline of appearance of protein families linked to single-domain enzymes. The timeline sorts out enzymatic recruitment, validates patterns in metabolic history, and reveals that the most ancient reaction of aerobic metabolism involved the synthesis of pyridoxal 5'-phosphate or pyridoxal and appeared 2.9 Gyr ago. The oxygen source for this primordial reaction was probably Mn catalase, which appeared at the same time and could have generated oxygen as a side product of hydrogen peroxide detoxification. Finally, evolutionary analysis of transferred groups and metabolite fragments revealed that oxidized sulfur did not participate in metabolism until the rise of oxygen. The evolutionary patterns we uncover in molecules and chemistries provide strong support for the coevolution of biochemistry and geochemistry.