The evolutionary history of the HUP domain

Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP’s most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well-packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.

在确证于最后通用共同祖先之前便已出现的酶超家族中，存在所谓的HUP超家族，其涵盖I类氨酰-tRNA合成酶（AARSs）以及介导烟酰胺腺嘌呤二核苷酸（NAD）、黄素腺嘌呤二核苷酸（FAD）与辅酶A（CoA）生物合成的各类酶类。本研究针对HUP超家族从起源到结构与功能分化的演化过程展开了详尽分析。HUP属于一类核苷酸结合结构域，其独特之处在于通过释放焦磷酸来催化腺苷酸化反应。与其他具有αβα三明治结构的古老核苷酸结合结构域（如P环核苷三磷酸酶（P-loop NTPases））不同，HUP最保守的特征并非结合磷酸基团，而是通过与β1链和/或β4链末端形成骨架相互作用来结合核糖。事实上，HUP展现出非同寻常的演化可塑性：尽管核糖结合位点保持保守，但该结构域与核苷酸碱基、磷酸基团以及反应底物的结合位置与结合模式均随时间推移发生了分化，其中尤以伴随I类氨酰-tRNA合成酶起源所发生的分化最为显著。HUP还直观展现了组装紧密的支架结构与可演化的表面元件相结合，如何推动演化创新的发生。最后，本研究提出了HUP从βαβ核心片段种子演化起源的假说，并指出尽管二者结构一致，HUP与罗斯曼折叠实为独立起源的结构。