Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
Nat Ecol Evol. 2018 Apr;2(4):697-704. doi: 10.1038/s41559-018-0477-7. Epub 2018 Feb 19.
With the current explosion of genomic data, there is a greater need to draw inference on phenotypic information based on DNA sequence alone. We considered complete genomes from 35 diverse eukaryotic lineages, and discovered sets of proteins predictive of trophic mode, including a set of 485 proteins that are enriched among phagocytotic eukaryotes (organisms that internalize large particles). Our model is also predictive of other aspects of trophic mode, including photosynthesis and the ability to synthesize a set of organic compounds needed for growth (prototrophy for those molecules). We applied our model to the Asgard archaea, a group of uncultured microorganisms that show close affinities to eukaryotes, to test whether the organisms are capable of phagocytosis, a phenotypic trait often considered a prerequisite for mitochondrial acquisition. Our analyses suggest that members of the Asgard archaea-despite having some eukaryote-specific protein families not found in other prokaryotes-do not use phagocytosis. Moreover, our data suggest that the process of phagocytosis arose from a combination of both archaeal and bacterial components, but also required additional eukaryote-specific innovations.
随着基因组数据的爆炸式增长，人们越来越需要仅根据 DNA 序列推断表型信息。我们研究了来自 35 个不同真核生物谱系的完整基因组，发现了一些可预测营养方式的蛋白质组，其中包括一组在吞噬性真核生物（能够内化大颗粒的生物体）中富集的 485 种蛋白质。我们的模型还可预测营养方式的其他方面，包括光合作用和合成生长所需的一组有机化合物的能力（对于这些分子来说是原生质营养）。我们将该模型应用于 Asgard 古菌，这是一组未培养的微生物，与真核生物密切相关，以测试这些生物体是否能够吞噬，这是一种通常被认为是获得线粒体的先决条件的表型特征。我们的分析表明，尽管 Asgard 古菌具有一些在其他原核生物中未发现的真核生物特有的蛋白质家族，但它们并不进行吞噬作用。此外，我们的数据表明，吞噬作用的发生是由古菌和细菌成分的组合引起的，但也需要额外的真核生物特有的创新。
