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The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Abascal F, Tress ML, Valencia A - Genome Biol Evol (2015)

Bottom Line: We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication.At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes.That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain fabascal@cnio.es mtress@cnio.es.

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Splice isoform separation of CALU in teleosts by differential retention of ancestral MEHEs (A) that code for the first EF-hand domain (B) is strongly supported by the position in the ML exon tree of two distinct teleost genes, CALUA and CALUB, each within the group of monophyly defined by each ancestral MEHE (C; with the best-fit evolutionary model LG+I+G). Numbers close to nodes indicate cases with more than 70% of bootstrap support based on 1,000 replicates. The multiple sequence alignment reveals some positions (blue arrows) with specific conservation patterns between MEHEs of human, spotted gar and coelacanth, and between duplicated genes in zebrafish and other teleosts (D).
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evv076-F2: Splice isoform separation of CALU in teleosts by differential retention of ancestral MEHEs (A) that code for the first EF-hand domain (B) is strongly supported by the position in the ML exon tree of two distinct teleost genes, CALUA and CALUB, each within the group of monophyly defined by each ancestral MEHE (C; with the best-fit evolutionary model LG+I+G). Numbers close to nodes indicate cases with more than 70% of bootstrap support based on 1,000 replicates. The multiple sequence alignment reveals some positions (blue arrows) with specific conservation patterns between MEHEs of human, spotted gar and coelacanth, and between duplicated genes in zebrafish and other teleosts (D).

Mentions: The CALU gene is ubiquitously expressed and encodes a protein (calumenin) distributed throughout the secretory pathway (Vorum et al. 1999), known to inhibit vitamin-K-dependent protein carboxylation (Wajih et al. 2004) and involved in protein sorting and folding (Tsukumo et al. 2009; Wang et al. 2012). CALU contains six calcium-binding EF-hand domains, the first of which is coded by one of two MEHEs (fig. 2A and B). Little is known about the functional role of the splicing of MEHEs exons in CALU. Calumenin MEHEs may be differentially expressed in human primary tumors (Dutertre et al. 2010). This, together with the observation that CALU is a phosphorylation substrate of v-Src (Shah and Shokat 2002), suggests that it may participate in signal transduction pathways related to transformation (Honoré 2009).Fig. 2.—


The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Abascal F, Tress ML, Valencia A - Genome Biol Evol (2015)

Splice isoform separation of CALU in teleosts by differential retention of ancestral MEHEs (A) that code for the first EF-hand domain (B) is strongly supported by the position in the ML exon tree of two distinct teleost genes, CALUA and CALUB, each within the group of monophyly defined by each ancestral MEHE (C; with the best-fit evolutionary model LG+I+G). Numbers close to nodes indicate cases with more than 70% of bootstrap support based on 1,000 replicates. The multiple sequence alignment reveals some positions (blue arrows) with specific conservation patterns between MEHEs of human, spotted gar and coelacanth, and between duplicated genes in zebrafish and other teleosts (D).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494069&req=5

evv076-F2: Splice isoform separation of CALU in teleosts by differential retention of ancestral MEHEs (A) that code for the first EF-hand domain (B) is strongly supported by the position in the ML exon tree of two distinct teleost genes, CALUA and CALUB, each within the group of monophyly defined by each ancestral MEHE (C; with the best-fit evolutionary model LG+I+G). Numbers close to nodes indicate cases with more than 70% of bootstrap support based on 1,000 replicates. The multiple sequence alignment reveals some positions (blue arrows) with specific conservation patterns between MEHEs of human, spotted gar and coelacanth, and between duplicated genes in zebrafish and other teleosts (D).
Mentions: The CALU gene is ubiquitously expressed and encodes a protein (calumenin) distributed throughout the secretory pathway (Vorum et al. 1999), known to inhibit vitamin-K-dependent protein carboxylation (Wajih et al. 2004) and involved in protein sorting and folding (Tsukumo et al. 2009; Wang et al. 2012). CALU contains six calcium-binding EF-hand domains, the first of which is coded by one of two MEHEs (fig. 2A and B). Little is known about the functional role of the splicing of MEHEs exons in CALU. Calumenin MEHEs may be differentially expressed in human primary tumors (Dutertre et al. 2010). This, together with the observation that CALU is a phosphorylation substrate of v-Src (Shah and Shokat 2002), suggests that it may participate in signal transduction pathways related to transformation (Honoré 2009).Fig. 2.—

Bottom Line: We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication.At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes.That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain fabascal@cnio.es mtress@cnio.es.

Show MeSH
Related in: MedlinePlus