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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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Posttranslational change in regulation after gene duplication in Swi5 and Ace2.A) Schematic of the gene tree relating the Ace2/Swi5 paralog pair with diagram of protein features found in proteins from different yeast species. Bolded species name indicate cloned genes assayed for localization in S. cerevisiae. The nuclear localization signal characterized in Swi5 is putatively altered and may not be functionally homologous in Candida and Ace2, but this difference was not predicted in our analysis (see Discussion and S3 Figure). B) Green-fluorescent protein tagged genes cloned from the labeled species were assayed for their localization in unsynchronized S. cerevisiae cells. Two representatives of each pre-/post-WGD genes were assayed. Orange and blue arrows indicate representative bud and mother nucleus pairs. C) The fluorescence intensity of the nucleus in cells expressing the labeled proteins was quantified, and mean difference of the intensity (bud-mother) is used as the measure of asymmetry (unfilled bars). Error bars show 95% confidence interval of the mean. Stars indicate 5% statistical significance. Red double arrow illustrates the duplication event. Scer: S. cerevisiae, Cgla: C. glabrata, Zrou: Z. rouxii, Lwal: L. waltii, Lklu: L. kluyveri, Calb: C. albicans.
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pcbi-1003977-g005: Posttranslational change in regulation after gene duplication in Swi5 and Ace2.A) Schematic of the gene tree relating the Ace2/Swi5 paralog pair with diagram of protein features found in proteins from different yeast species. Bolded species name indicate cloned genes assayed for localization in S. cerevisiae. The nuclear localization signal characterized in Swi5 is putatively altered and may not be functionally homologous in Candida and Ace2, but this difference was not predicted in our analysis (see Discussion and S3 Figure). B) Green-fluorescent protein tagged genes cloned from the labeled species were assayed for their localization in unsynchronized S. cerevisiae cells. Two representatives of each pre-/post-WGD genes were assayed. Orange and blue arrows indicate representative bud and mother nucleus pairs. C) The fluorescence intensity of the nucleus in cells expressing the labeled proteins was quantified, and mean difference of the intensity (bud-mother) is used as the measure of asymmetry (unfilled bars). Error bars show 95% confidence interval of the mean. Stars indicate 5% statistical significance. Red double arrow illustrates the duplication event. Scer: S. cerevisiae, Cgla: C. glabrata, Zrou: Z. rouxii, Lwal: L. waltii, Lklu: L. kluyveri, Calb: C. albicans.

Mentions: To confirm our sequence-based predictions about evolutionary divergence, we focused on the Swi5/Ace2 paralog pair. It has previously been shown that these motifs in the extant S. cerevisiae proteins control the differential localization pattern of the paralogs [52]. Because the ancestral protein likely contained critical regulatory motifs, we hypothesized that it was also regulated by Cbk1, and localized asymmetrically in the daughter cell (Fig. 4C). We therefore wanted to assess whether the localization before and after the gene duplication was consistent with our sequence analysis. To test this, we cloned and replaced the S. cerevisiae endogenous SWI5 gene with GFP-tagged Swi5/Ace2 homologs from multiple species that diverged before and after the whole-genome duplication and quantitatively assayed their localization pattern using fluorescence microscopy (Fig. 5A, see Methods and Text S1).


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)

Posttranslational change in regulation after gene duplication in Swi5 and Ace2.A) Schematic of the gene tree relating the Ace2/Swi5 paralog pair with diagram of protein features found in proteins from different yeast species. Bolded species name indicate cloned genes assayed for localization in S. cerevisiae. The nuclear localization signal characterized in Swi5 is putatively altered and may not be functionally homologous in Candida and Ace2, but this difference was not predicted in our analysis (see Discussion and S3 Figure). B) Green-fluorescent protein tagged genes cloned from the labeled species were assayed for their localization in unsynchronized S. cerevisiae cells. Two representatives of each pre-/post-WGD genes were assayed. Orange and blue arrows indicate representative bud and mother nucleus pairs. C) The fluorescence intensity of the nucleus in cells expressing the labeled proteins was quantified, and mean difference of the intensity (bud-mother) is used as the measure of asymmetry (unfilled bars). Error bars show 95% confidence interval of the mean. Stars indicate 5% statistical significance. Red double arrow illustrates the duplication event. Scer: S. cerevisiae, Cgla: C. glabrata, Zrou: Z. rouxii, Lwal: L. waltii, Lklu: L. kluyveri, Calb: C. albicans.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1003977-g005: Posttranslational change in regulation after gene duplication in Swi5 and Ace2.A) Schematic of the gene tree relating the Ace2/Swi5 paralog pair with diagram of protein features found in proteins from different yeast species. Bolded species name indicate cloned genes assayed for localization in S. cerevisiae. The nuclear localization signal characterized in Swi5 is putatively altered and may not be functionally homologous in Candida and Ace2, but this difference was not predicted in our analysis (see Discussion and S3 Figure). B) Green-fluorescent protein tagged genes cloned from the labeled species were assayed for their localization in unsynchronized S. cerevisiae cells. Two representatives of each pre-/post-WGD genes were assayed. Orange and blue arrows indicate representative bud and mother nucleus pairs. C) The fluorescence intensity of the nucleus in cells expressing the labeled proteins was quantified, and mean difference of the intensity (bud-mother) is used as the measure of asymmetry (unfilled bars). Error bars show 95% confidence interval of the mean. Stars indicate 5% statistical significance. Red double arrow illustrates the duplication event. Scer: S. cerevisiae, Cgla: C. glabrata, Zrou: Z. rouxii, Lwal: L. waltii, Lklu: L. kluyveri, Calb: C. albicans.
Mentions: To confirm our sequence-based predictions about evolutionary divergence, we focused on the Swi5/Ace2 paralog pair. It has previously been shown that these motifs in the extant S. cerevisiae proteins control the differential localization pattern of the paralogs [52]. Because the ancestral protein likely contained critical regulatory motifs, we hypothesized that it was also regulated by Cbk1, and localized asymmetrically in the daughter cell (Fig. 4C). We therefore wanted to assess whether the localization before and after the gene duplication was consistent with our sequence analysis. To test this, we cloned and replaced the S. cerevisiae endogenous SWI5 gene with GFP-tagged Swi5/Ace2 homologs from multiple species that diverged before and after the whole-genome duplication and quantitatively assayed their localization pattern using fluorescence microscopy (Fig. 5A, see Methods and Text S1).

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
Related in: MedlinePlus