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. 2010 May 3:10:127.
doi: 10.1186/1471-2148-10-127.

The molecular evolution of PL10 homologs

Ti-Cheng Chang  1 , Wan-Sheng Liu
Affiliations

The molecular evolution of PL10 homologs

Ti-Cheng Chang et al. BMC Evol Biol. .

Abstract

Background: 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. The lineage-specific expression patterns and various genomic structures and locations of PL10 homologs indicate these homologs have an interesting evolutionary history.

Results: Phylogenetic 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.

Conclusion: The 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.

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Figures

Figure 1
Figure 1
The bootstrap consensus tree of PL10 homologous sequences. The evolutionary tree was built based on the Neighbor-Joining method implemented in MEGA4 [55,62]. The bootstrap consensus tree is inferred from 1000 replicates and the branches corresponding to partitions reproduced in less than 65% bootstrap replicates are collapsed. The bootstrap values are shown as percentages next to the branches. The evolutionary distances were computed using the Maximum Composite Likelihood method [63] and in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 0.91). All positions containing alignment gaps and missing data were eliminated by pairwise deletion. A total of 3944 positions were in the final dataset [Additional File 6]. The branches leading to the non-annotated autosomal homologous clusters of PL10 are highlighted in blue; the branches leading to the rodent Pl10 are highlighted in green; the branches leading to the non-annotated X-homologs are highlighted in red. The PL10/DDX3X cluster and the DDX3Y cluster are marked by vertical lines on the right.
Figure 2
Figure 2
The tree of the DDX3 family established for the positive selection test based on Maximum Likelihood approach. The branch length was estimated in the unit of the number of nucleotide substitutions per nucleotide. Values larger than 0.1 are denoted in bold. The numbers in the parenthesis represent the estimated numbers of nonsynonymous substitutions against synonymous substitutions of the specific branch. Scale bar = 0.05 unit.
Figure 3
Figure 3
Posterior probabilities of three site classes with different selective pressures (measured by the w ratio) for codon sites along the mammalian PL10 homologs under the site model M3. The X-axis represents the codon positions which were labeled based on the human DDX3X amino acids. The probabilities of the site classes are indicated in the Y-axis. The DEAD/DEAH-box helicase domain and helicase conserved C-terminal domain are underlined.
Figure 4
Figure 4
The conserved domain and ATP binding site of the human DDX3X. A. The conservation score distribution on the human DDX3X (PDB: 2I4I) was assigned based on the empirical Bayesian method by ConSurf [21]. The domain regions are highlighted in dot-yellow halos. B. The ATP binding cleft depicted in PDBsum [64] corresponds to the conserved region in A.
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