Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
Structure. 2012 Jan 11;20(1):67-76. doi: 10.1016/j.str.2011.11.003.
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.
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演化仍然是一个谜。在这里，我们使用近 1000 个基因组的结构普查和折叠的分子钟来定义与单结构域酶相关的蛋白质家族出现的时间线。该时间线梳理了酶的募集，验证了代谢历史中的模式，并揭示了有氧代谢最古老的反应涉及吡哆醛 5'-磷酸或吡哆醛的合成，并且出现在 29 亿年前。这个原始反应的氧源可能是 Mn 过氧化氢酶，它同时出现，并可能将氧气作为过氧化氢解毒的副产物产生。最后，对转移组和代谢物片段的进化分析表明，氧化硫直到氧气出现后才参与代谢。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。
