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Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.

Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM - PLoS Comput. Biol. (2014)

Bottom Line: We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes.We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation.Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.

ABSTRACT
Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

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Correlated evolution of short linear motifs.Top panel shows the procedure to obtain the number of lineage specific changes in constraints in a single protein. Red double arrow illustrates the duplication event. Stars represent significant changes in constraints along the lineage. Significant changes in constraints detected on short linear motifs are shown in dotted red boxes. Bottom panel shows the distribution of the total cumulated number of lineage specific changes in constraints from a non-parametric permutation test. Arrow shows the observed total difference for all 20 paralog pairs.
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pcbi-1003977-g003: Correlated evolution of short linear motifs.Top panel shows the procedure to obtain the number of lineage specific changes in constraints in a single protein. Red double arrow illustrates the duplication event. Stars represent significant changes in constraints along the lineage. Significant changes in constraints detected on short linear motifs are shown in dotted red boxes. Bottom panel shows the distribution of the total cumulated number of lineage specific changes in constraints from a non-parametric permutation test. Arrow shows the observed total difference for all 20 paralog pairs.

Mentions: Despite some evidence for complementarity, the majority of paralogs (13/20) with more than a single change in constraints appeared to have a lineage bias in their posttranslational regulatory changes. We tested this using the set of 20 paralog pairs described above and asked whether the motifs were more likely to have correlated evolution than expected by chance. To do so, we randomly permutated the changes in constraints across paralogous pairs to establish the expectation of random assortment and counted the lineage differences in changes in constraints (see Methods). We ensured that the lineage bias was not caused by technical issues, such as large-scale alignment errors or bipartite motifs being predicted as two motifs by the phylo-HMM, by grouping motifs when they were within 35 amino acids of each other for this test (see Methods). This analysis revealed a lineage bias in changes in constraints for regulatory sequences (p-value  = 0.01106, one-tailed non-parametric permutation test, Fig. 3). Therefore, proteins that change function after duplication may typically change multiple short linear motifs in concert, consistent with the idea that multiple regulatory mechanisms often work together to control protein function. For example, multisite phosphorylation from individual or multiple kinases can form intricate regulatory modules on single proteins (reviewed in [40]) and these clusters of phosphorylation sites have been found to be frequently conserved through evolution [41]–[43] and have been shown to turnover [44].


Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.

Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM - PLoS Comput. Biol. (2014)

Correlated evolution of short linear motifs.Top panel shows the procedure to obtain the number of lineage specific changes in constraints in a single protein. Red double arrow illustrates the duplication event. Stars represent significant changes in constraints along the lineage. Significant changes in constraints detected on short linear motifs are shown in dotted red boxes. Bottom panel shows the distribution of the total cumulated number of lineage specific changes in constraints from a non-parametric permutation test. Arrow shows the observed total difference for all 20 paralog pairs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4256066&req=5

pcbi-1003977-g003: Correlated evolution of short linear motifs.Top panel shows the procedure to obtain the number of lineage specific changes in constraints in a single protein. Red double arrow illustrates the duplication event. Stars represent significant changes in constraints along the lineage. Significant changes in constraints detected on short linear motifs are shown in dotted red boxes. Bottom panel shows the distribution of the total cumulated number of lineage specific changes in constraints from a non-parametric permutation test. Arrow shows the observed total difference for all 20 paralog pairs.
Mentions: Despite some evidence for complementarity, the majority of paralogs (13/20) with more than a single change in constraints appeared to have a lineage bias in their posttranslational regulatory changes. We tested this using the set of 20 paralog pairs described above and asked whether the motifs were more likely to have correlated evolution than expected by chance. To do so, we randomly permutated the changes in constraints across paralogous pairs to establish the expectation of random assortment and counted the lineage differences in changes in constraints (see Methods). We ensured that the lineage bias was not caused by technical issues, such as large-scale alignment errors or bipartite motifs being predicted as two motifs by the phylo-HMM, by grouping motifs when they were within 35 amino acids of each other for this test (see Methods). This analysis revealed a lineage bias in changes in constraints for regulatory sequences (p-value  = 0.01106, one-tailed non-parametric permutation test, Fig. 3). Therefore, proteins that change function after duplication may typically change multiple short linear motifs in concert, consistent with the idea that multiple regulatory mechanisms often work together to control protein function. For example, multisite phosphorylation from individual or multiple kinases can form intricate regulatory modules on single proteins (reviewed in [40]) and these clusters of phosphorylation sites have been found to be frequently conserved through evolution [41]–[43] and have been shown to turnover [44].

Bottom Line: We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes.We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation.Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.

ABSTRACT
Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

Show MeSH