Abstract
BackgroundPL10 homologs exist in a wide range of eukaryotes from yeast, plants to animals. They share a DEAD motif and belong to the DEAD-box polypeptide 3 (DDX3) subfamily with a major role in RNA metabolism. The lineage-specific expression patterns and various genomic structures and locations of PL10 homologs indicate these homologs have an interesting evolutionary history.ResultsPhylogenetic analyses revealed that, in addition to the sex chromosome-linked PL10 homologs, DDX3X and DDX3Y, a single autosomal PL10 putative homologous sequence is present in each genome of the studied non-rodent eutheria. These autosomal homologous sequences originated from the retroposition of DDX3X but were pseudogenized during the evolution. In rodents, besides Ddx3x and Ddx3y, we found not only Pl10 but another autosomal homologous region, both of which also originated from the Ddx3x retroposition. These retropositions occurred after the divergence of eutheria and opossum. In contrast, an additional X putative homologous sequence was detected in primates and originated from the transposition of DDX3Y. The evolution of PL10 homologs was under positive selection and the elevated Ka/Ks ratios were observed in the eutherian lineages for DDX3Y but not PL10 and DDX3X, suggesting relaxed selective constraints on DDX3Y. Contrary to the highly conserved domains, several sites with relaxed selective constraints flanking the domains in the mammalian PL10 homologs may play roles in enhancing the gene function in a lineage-specific manner.ConclusionThe eutherian DDX3X/DDX3Y in the X/Y-added region originated from the translocation of the ancient PL10 ortholog on the ancestral autosome, whereas the eutherian PL10 was retroposed from DDX3X. In addition to the functional PL10/DDX3X/DDX3Y, conserved homologous regions on the autosomes and X chromosome are present. The autosomal homologs were also derived from DDX3X, whereas the additional X-homologs were derived from DDX3Y. These homologs were apparently pseudogenized but may still be active transcriptionally. The evolution of PL10 homologs was positively selected.
Highlights
PL10 homologs exist in a wide range of eukaryotes from yeast, plants to animals
In addition to the 22 annotated sequences for PL10, DDX3X and DDX3Y, we identified 15 PL10 putative homologous regions in the genomes of mammals (Table 1)
In the non-eutherian lineages, PL10 is the sole member of the DEAD-box polypeptide 3 (DDX3) subfamily, whereas in eutheria, the ancient PL10 gene is located on the ancestral sex Chrs, resulting in the sex Chr-linked orthologs, DDX3X and DDX3Y (Fig. 1)
Summary
PL10 homologs exist in a wide range of eukaryotes from yeast, plants to animals. They share a DEAD motif and belong to the DEAD-box polypeptide 3 (DDX3) subfamily with a major role in RNA metabolism. PL10 was first identified in mouse by using a human Y chromosome (Chr) derived probe [1] and is present in a wide range of eukaryotes from yeast, plants, and animals, including humans [2]. PL10 has two closely-related paralogs, DDX3X (DEAD box polypeptide 3, X-linked) and DDX3Y (DEAD box polypeptide 3, Y-linked), located on the sex Chrs. PL10, DDX3X and DDX3Y share the DEAD motif and constitute the DDX3/ DED1 (ATP-dependent DEAD-box RNA helicase) sub-. DDX3X plays a role in HIV infection and becomes an impor-
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