Published June 23, 2022 | Version v1
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Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: the showcase of polypyrimidine tract binding proteins

Description

Dataset and scripts for the article "Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: the showcase of polypyrimidine tract binding proteins "

Abstract

Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When the two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel gene functions. Here we focused on the evolutionary history of the three polypyrimidine tract binding protein (PTBP) paralogs and their concurrent evolution of differential codon usage preferences in vertebrate species.

PTBP1-3 show high identity at the amino acid level (up to 80%), but display strongly different nucleotide composition, divergent CUPrefs and distinct tissue-specific expression levels. Phylogenetic inference suggests that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates. We identify a distinct substitution pattern towards GC3-enriching mutations in PTBP1, concurrent with a trend for the use of common codons and for a tissue-wide expression. Genomic context analysis shows that GC3-rich nucleotide composition for PTBP1s is driven by local mutational processes. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. Nucleotide composition and CUPrefs of PTBP2 are only partly driven by local mutational forces, and could have been shaped by selective forces. Interestingly, trends for use of UUG-Leu codon match those of AT-ending codons.

Our interpretation is that a combination of directional mutation–selection has differentially shaped CUPrefs of PTBPs in Vertebrates: GC-enrichment of PTBP1 is linked to the strong and broad tissue expression, while AT-enrichment of PTBP2 and PTBP3 are linked to rare CUPrefs and specialized spatio-temporal expression. This scenario is compatible with a gene subfunctionalisation process by differential expression regulation associated to the evolution of specific CUPrefs.

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PTBP_dataset_and_scripts.zip

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Funding

CODOVIREVOL – Evolution of viral codon usage preferences:manipulation of translation accuracy and evasion of immune response 647916
European Commission