Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States.
Research School of Chemistry, Australian National University, Canberra, Australia.
Elife. 2022 Sep 1;11:e79790. doi: 10.7554/eLife.79790.
Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study.
核糖核苷酸还原酶（RNRs）被所有自由生活的生物和许多病毒用来催化 DNA 前体从头生物合成中的一个必需步骤。RNRs 在一级序列和辅助因子需求上差异很大，同时具有保守的折叠和基于自由基的核苷酸还原机制。在这里，我们通过保守的催化桶对不同的 RNR 家族进行结构比对，以重建第一个由 6779 个序列组成的大规模系统发育，将所有现存的 RNR 家族类群统一起来，并进行进化速度分析，独立验证我们的进化模型。有了一个稳健的系统发育，我们发现了一个新的、在系统发育上截然不同的分支，它被置于 I 类和 II 类 RNRs 的祖先位置，我们称之为分支 Ø。我们采用小角 X 射线散射（SAXS）、低温电子显微镜（cryo-EM）和 AlphaFold2 来研究来自噬菌体 S-CBP4 的这个分支的一个成员，并报告迄今为止最简化的 RNR 结构。基于我们的分析，我们提出了 RNR 家族多样化的进化模型，并阐明了我们的系统发育如何可以作为未来有针对性研究的路线图。
