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J Mol Evol. 2018 Jan;86(1):77-89. doi: 10.1007/s00239-018-9827-y. Epub 2018 Jan 18.

Evolution of Eukaryal and Archaeal Pseudouridine Synthase Pus10.

Author information

1
Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901-6509, USA.
2
Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA.
3
Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL, 62901-4413, USA.
4
Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.
5
Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901-6509, USA. mgeisler@plant.siu.edu.

Abstract

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 m5U54) 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.

KEYWORDS:

Orthologs; Phylogeny; Protein evolution; Pseudogene; Subfunctionalization

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