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'Why genes in pieces?'-revisited.

Ben Smithers¹, Matt Oates¹, Julian Gough^1,2

¹Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK.

Nucleic Acids Research

|April 19, 2019

Summary

Protein domain and exon boundary alignment is widespread across eukaryotes, suggesting domain shuffling in protein evolution. This alignment is more prevalent in newer protein sequences than older ones.

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Area of Science:

Molecular Biology
Evolutionary Biology
Bioinformatics

Background:

The evolutionary history of proteins is often linked to the modular nature of their sequences.
Domain shuffling, a proposed mechanism for protein evolution, suggests that protein domains may be rearranged like building blocks.
Evidence for domain shuffling has been sought by examining the relationship between protein domain boundaries and exon boundaries in genomic sequences.

Purpose of the Study:

To investigate the widespread occurrence of protein domain-exon boundary alignment across the eukaryotic tree.
To determine if intrinsically disordered protein regions exhibit similar alignment patterns with exons.
To explore the correlation between the evolutionary age of protein sequences and the prevalence of domain-exon alignment.

Main Methods:

Analysis of large-scale genomic and proteomic datasets from diverse eukaryotic species.
Computational methods to identify protein domains, exon boundaries, and intrinsically disordered regions.
Statistical analysis to assess the significance of alignment between these genomic and proteomic features.

Main Results:

Conclusive evidence demonstrating the widespread presence of protein domain-exon boundary alignment across eukaryotes.
Intrinsically disordered protein regions do not show a general alignment with exon boundaries in eukaryotes.
Domain-exon alignment is significantly more common in recently evolved protein sequences compared to ancient ones.

Conclusions:

The study provides robust evidence for domain shuffling as a significant evolutionary mechanism in eukaryotes.
The findings highlight a distinct relationship between protein structure, gene structure, and evolutionary age.
The prevalence of domain-exon alignment in newer proteins suggests ongoing evolutionary innovation through domain rearrangement.

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