Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Science.
Department of Biochemistry and Microbiology, and.
Proc Natl Acad Sci U S A. 2014 May 13;111(19):7042-7. doi: 10.1073/pnas.1403676111. Epub 2014 Apr 28.
Oxidoreductases mediate electron transfer (i.e., redox) reactions across the tree of life and ultimately facilitate the biologically driven fluxes of hydrogen, carbon, nitrogen, oxygen, and sulfur on Earth. The core enzymes responsible for these reactions are ancient, often small in size, and highly diverse in amino acid sequence, and many require specific transition metals in their active sites. Here we reconstruct the evolution of metal-binding domains in extant oxidoreductases using a flexible network approach and permissive profile alignments based on available microbial genome data. Our results suggest there were at least 10 independent origins of redox domain families. However, we also identified multiple ancient connections between Fe2S2- (adrenodoxin-like) and heme- (cytochrome c) binding domains. Our results suggest that these two iron-containing redox families had a single common ancestor that underwent duplication and divergence. The iron-containing protein family constitutes ∼50% of all metal-containing oxidoreductases and potentially catalyzed redox reactions in the Archean oceans. Heme-binding domains seem to be derived via modular evolutionary processes that ultimately form the backbone of redox reactions in both anaerobic and aerobic respiration and photosynthesis. The empirically discovered network allows us to peer into the ancient history of microbial metabolism on our planet.
氧化还原酶介导跨越生命之树的电子转移（即氧化还原）反应，并最终促进地球上氢、碳、氮、氧和硫的生物驱动通量。负责这些反应的核心酶非常古老，通常体积较小，氨基酸序列高度多样化，许多酶在其活性位点需要特定的过渡金属。在这里，我们使用灵活的网络方法和基于可用微生物基因组数据的宽松轮廓比对，重建了现存氧化还原酶中金属结合结构域的进化。我们的结果表明，至少有 10 种独立的氧化还原结构域家族起源。然而，我们还在 Fe2S2-（肾上腺皮质酮样）和血红素（细胞色素 c）结合结构域之间发现了多个古老的联系。我们的结果表明，这两个含铁的氧化还原家族有一个共同的祖先，经历了复制和分化。含铁蛋白家族构成了所有含金属氧化还原酶的约 50%，并可能在太古宙海洋中催化氧化还原反应。血红素结合结构域似乎是通过模块化进化过程产生的，最终形成了无氧呼吸、有氧呼吸和光合作用中氧化还原反应的骨干。经验发现的网络使我们能够深入了解我们星球上微生物代谢的古老历史。
