Arf family GTPases are present in Asgard archaea

The evolution of eukaryotes is a fundamental event in the history of life. The closest prokaryotic lineage to eukaryotes, the Asgardarchaeota, encode proteins previously found only in eukaryotes, providing insight into their archaeal ancestor. Eukaryotic cells are characterized by endomembrane organelles, and the Arf family GTPases regulate organelle dynamics by recruiting effector proteins to membranes upon activation. The Arf family is ubiquitous among eukaryotes, but its origins remain elusive. We report a group of prokaryotic GTPases, the ArfRs, which are widely present in Asgardarchaeota. Phylogenetic analyses reveal that eukaryotic Arf family proteins arose from the ArfR group. Expression of representative Asgardarchaeota ArfR proteins in yeast and X-ray crystallographic studies demonstrate that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results indicate that Arf family GTPases originated in the archaeal ancestor of eukaryotes, consistent with an endomembrane system evolving early in eukaryogenesis.Here we provided source data for phylogenetic analyses. For each analysis, four files are provided:*_unaligned.fasta - unaligned protein sequences, in some cases trimmed to the GTPase domain*_alignment.fasta - multiple sequence alignment (details about programs are provided in Supplementary information and Supplementary Table 5)*_trimmed_alignment.fasta - trimmed multiple sequence alignment, input for phylogenetic analysis (details about programs and settings are provided in Supplementary information and Supplementary Table 5)*_newick tree.treefile - phylogenetic tree in the Newick formatPreprint is available at bioRxiv: https://doi.org/10.1101/2024.02.28.582541真核生物的演化是生命演化史上的根本性事件。与真核生物亲缘关系最近的原核类群——阿斯加德古菌（Asgardarchaeota），可编码此前仅在真核生物中发现的蛋白质，为解析其古菌祖先提供了关键线索。 真核细胞以内膜细胞器为典型特征，Arf家族GTP酶（Arf family GTPases）可在激活后将效应蛋白招募至膜上，从而调控细胞器的动态过程。Arf家族在真核生物中广泛分布，但其起源始终成谜。 本研究报道了一类原核GTP酶——ArfR蛋白（ArfRs），该类蛋白广泛存在于阿斯加德古菌中。系统发育分析结果显示，真核生物的Arf家族蛋白起源于ArfR类群。 将代表性阿斯加德古菌ArfR蛋白在酵母中进行异源表达，并结合X射线晶体学（X-ray crystallographic）研究，结果证实ArfR GTP酶具备Arf家族蛋白特有的膜结合机制与结构特征。 本研究结果表明，Arf家族GTP酶起源于真核生物的古菌祖先，这与内膜系统在真核生物演化早期即已形成的推论相符。 本研究提供了系统发育分析的原始数据。每项分析均包含四类文件： *_unaligned.fasta：未比对的蛋白质序列，部分序列已裁剪至GTP酶结构域区域； *_alignment.fasta：多序列比对结果（比对程序的详细信息见补充材料与补充表5）； *_trimmed_alignment.fasta：经裁剪的多序列比对结果，可直接作为系统发育分析的输入文件（程序与参数详情见补充材料与补充表5）； *_newick tree.treefile：Newick格式（Newick format）的系统发育树文件。 本研究的预印本已发布于bioRxiv平台：https://doi.org/10.1101/2024.02.28.582541