Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901-6509, USA.
Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA.
J Mol Evol. 2018 Jan;86(1):77-89. doi: 10.1007/s00239-018-9827-y. Epub 2018 Jan 18.
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to mU54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons. First, experimental evidence suggests that human Pus10 participates in apoptosis induced by the tumor necrosis factor-related apoptosis-inducing ligand. Whether the function of human Pus10 is in place or in addition to of Ψ synthesis in tRNA is unknown. Second, Pus10 is found in earlier evolutionary branches of fungi (such as chytrid Batrachochytrium) but is absent in all dikaryon fungi surveyed (Ascomycetes and Basidiomycetes). We did a comprehensive analysis of sequenced genomes and found that orthologs of Pus10, TrmA, and TruB were present in all the animals, plants, and protozoa surveyed. This indicates that the common eukaryotic ancestor possesses all the three genes. Next, we examined 116 archaeal and eukaryotic Pus10 protein sequences to find that Pus10 existed as a single copy gene in all the surveyed genomes despite ancestral whole genome duplications had occurred. This indicates a possible deleterious gene dosage effect. Our results suggest that functional redundancy result in gene loss or neofunctionalization in different evolutionary lineages.
在古菌中，假尿嘧啶核苷（Ψ）合酶 Pus10 将尿嘧啶（U）修饰为 tRNA 中 54 和 55 位的 Ψ。相比之下，细菌中不存在 Pus10，这两个位置的修饰由 TrmA（U54 到 mU54）和 TruB（U55 到 Ψ55）完成。许多真核生物存在明显的冗余性；它们的基因组包含古菌 Pus10 和细菌 TrmA 和 TruB 的同源物。尽管真核 Pus10 基因与古菌 Pus10 基因共享保守的催化结构域，但由于以下两个原因，其生物学功能尚不清楚。首先，实验证据表明，人类 Pus10 参与肿瘤坏死因子相关凋亡诱导配体诱导的细胞凋亡。人类 Pus10 的功能是替代 tRNA 中 Ψ 的合成，还是除此之外的其他功能尚不清楚。其次，Pus10 存在于真菌的早期进化分支（如真菌性蛙眼病 Batrachochytrium）中，但在所有调查的双核真菌（子囊菌和担子菌）中都不存在。我们对已测序的基因组进行了全面分析，发现 Pus10、TrmA 和 TruB 的同源物存在于所有调查的动物、植物和原生动物中。这表明，真核生物的共同祖先拥有这三个基因。接下来，我们检查了 116 个古菌和真核 Pus10 蛋白序列，发现尽管发生了祖先全基因组加倍，但 Pus10 在所有调查的基因组中都作为单拷贝基因存在。这表明可能存在有害的基因剂量效应。我们的研究结果表明，功能冗余导致不同进化谱系中的基因丢失或新功能化。
