Limits...
The molecular evolution of PL10 homologs.

Chang TC, Liu WS - BMC Evol. Biol. (2010)

Bottom Line: 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 homologs were apparently pseudogenized but may still be active transcriptionally.The evolution of PL10 homologs was positively selected.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Dairy and Animal Science, The Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.

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.

Show MeSH

Related in: MedlinePlus

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2874800&req=5

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.

Mentions: Since some lineages were positively selected, especially in the case of DDX3Y, we further used a small dataset containing only the mammalian homologous coding sequences to examine the positively selected sites. The test statistic of likelihood ratio test (LRT) between the one-ratio model (M0) and the discrete model (M3) was 128.182 that is greater than the critical value = 13.28 when df = 4 [Additional File 1 and File 2]. This suggested that the selective pressure is diverse among the codons. Three site classes calculated under model M3 have prior probability of p0 = 0.887, p1 = 0.108, and p3 = 0.005 with the Ka/Ks ratios of w0 = 0.025, w1 = 0.316 and w2 = 2.549 [Additional File 1]. The posterior probabilities of site classes calculated in model M3 are shown in Fig. 3. However, the LRT of the other two pairs of models, M1a (Nearly Neutral)/M2a (Selection) and M7 (beta)/M8 (beta & w), generated an incongruent result. The test statistic of the M1a/M2a is insignificant (p > 1), whereas the M7/M8 generated a significant result with a LRT value of 16.97 greater than the critical value at df = 2, = 9.1 (p < 0.01) [Additional File 1 and File 2], which together gave rise to the marginal prediction of the codon sites with relaxed selective constraints. Four (9A, 10L, 24S, 425S) and six (9A, 10L, 24S, 425S, 608A, 609S) sites were inferred to contain increased w ratios under models M2a and M8, respectively. Four of the six inferred sites in model M8 coincided with the result of model M2a, including Ala9, Leu10, Ser24, Ser425, in which the Ser24 and Ser425 have posterior probability higher than 0.9 under model M8 [Additional File 1]. All of the inferred sites are located in the non-domain regions.


The molecular evolution of PL10 homologs.

Chang TC, Liu WS - BMC Evol. Biol. (2010)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874800&req=5

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.
Mentions: Since some lineages were positively selected, especially in the case of DDX3Y, we further used a small dataset containing only the mammalian homologous coding sequences to examine the positively selected sites. The test statistic of likelihood ratio test (LRT) between the one-ratio model (M0) and the discrete model (M3) was 128.182 that is greater than the critical value = 13.28 when df = 4 [Additional File 1 and File 2]. This suggested that the selective pressure is diverse among the codons. Three site classes calculated under model M3 have prior probability of p0 = 0.887, p1 = 0.108, and p3 = 0.005 with the Ka/Ks ratios of w0 = 0.025, w1 = 0.316 and w2 = 2.549 [Additional File 1]. The posterior probabilities of site classes calculated in model M3 are shown in Fig. 3. However, the LRT of the other two pairs of models, M1a (Nearly Neutral)/M2a (Selection) and M7 (beta)/M8 (beta & w), generated an incongruent result. The test statistic of the M1a/M2a is insignificant (p > 1), whereas the M7/M8 generated a significant result with a LRT value of 16.97 greater than the critical value at df = 2, = 9.1 (p < 0.01) [Additional File 1 and File 2], which together gave rise to the marginal prediction of the codon sites with relaxed selective constraints. Four (9A, 10L, 24S, 425S) and six (9A, 10L, 24S, 425S, 608A, 609S) sites were inferred to contain increased w ratios under models M2a and M8, respectively. Four of the six inferred sites in model M8 coincided with the result of model M2a, including Ala9, Leu10, Ser24, Ser425, in which the Ser24 and Ser425 have posterior probability higher than 0.9 under model M8 [Additional File 1]. All of the inferred sites are located in the non-domain regions.

Bottom Line: 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 homologs were apparently pseudogenized but may still be active transcriptionally.The evolution of PL10 homologs was positively selected.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Dairy and Animal Science, The Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.

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.

Show MeSH
Related in: MedlinePlus