Despite over a billion years of evolutionary divergence, several thousand human genes possess clearly identifiable orthologs in yeast, and many have undergone lineage-specific duplications in one or both lineages. These duplicated genes may have been free to diverge in function since their expansion, and it is unclear how or at what rate ancestral functions are retained or partitioned among co-orthologs between species and within gene families. Thus, in order to investigate how ancestral functions are retained or lost post-duplication, we systematically replaced hundreds of essential yeast genes with their human orthologs from gene families that have undergone lineage-specific duplications, including those with single duplications (1 yeast gene to 2 human genes, 1:2) or higher-order expansions (1:>2) in the human lineage. We observe a variable pattern of replaceability across different ortholog classes, with an obvious trend toward differential replaceability inside gene families, and rarely observe replaceability by all members of a family. We quantify the ability of various properties of the orthologs to predict replaceability, showing that in the case of 1:2 orthologs, replaceability is predicted largely by the divergence and tissue-specific expression of the human co-orthologs, i.e., the human proteins that are less diverged from their yeast counterpart and more ubiquitously expressed across human tissues more often replace their single yeast ortholog. These trends were consistent with in silico simulations demonstrating that when only one ortholog can replace its corresponding yeast equivalent, it tends to be the least diverged of the pair. Replaceability of yeast genes having more than 2 human co-orthologs was marked by retention of orthologous interactions in functional or protein networks as well as by more ancestral subcellular localization. Overall, we performed >400 human gene replaceability assays, revealing 50 new human-yeast complementation pairs, thus opening up avenues to further functionally characterize these human genes in a simplified organismal context.

中文翻译：

---

具有多个人类直系同源物的酵母基因的人源化揭示了旁系同源物之间的功能差异。

尽管存在超过十亿年的进化分歧，数千个人类基因在酵母中拥有明显可识别的直向同源物，并且许多基因在一个或两个谱系中经历了谱系特异性重复。这些重复基因自扩展以来可能在功能上自由分化，目前尚不清楚祖先功能如何或以何种速率在物种之间和基因家族内的共直向同源物之间保留或分配。因此，为了研究复制后祖先功能如何保留或丢失，我们系统地用来自经历谱系特异性复制的基因家族的人类直系同源物替换了数百个必需酵母基因，包括那些具有单一复制的基因（1个酵母基因到1个酵母基因） 2 个人类基因，1:2) 或人类谱系中的高阶扩展 (1:>2)。我们观察到不同直系同源类别之间的可变模式可替换性，在基因家族内具有明显的差异可替换性趋势，并且很少观察到家族所有成员的可替换性。我们量化了直向同源物的各种特性预测可替换性的能力，表明在 1:2 直向同源物的情况下，可替换性很大程度上是通过人类共同直向同源物（即，与酵母对应物的差异较小，并且在人体组织中更普遍表达，更经常取代其单一酵母直系同源物。这些趋势与计算机模拟一致，表明当只有一个直系同源物可以取代其相应的酵母等同物时，它往往是这对中分歧最小的。具有超过 2 个人类共同直向同源物的酵母基因的可替换性以功能或蛋白质网络中直向同源相互作用的保留以及更多祖先的亚细胞定位为标志。总体而言，我们进行了超过 400 次人类基因可替换性测定，揭示了 50 个新的人类-酵母互补对，从而为在简化的有机体背景下进一步对这些人类基因进行功能表征开辟了途径。