A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication
| Autor: | Silvio C. E. Tosatto, Lisanna Paladin, Damiano Piovesan, Pablo Mier, Marco Necci, Miguel A. Andrade-Navarro |
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| Rok vydání: | 2020 |
| Předmět: |
Protein family
Structural alignment Biological data visualization Exon Computational biology Biology Evolution Molecular 03 medical and health sciences Protein structure Tandem repeat Structural Biology Gene duplication Animals Humans 030304 developmental biology 0303 health sciences 030302 biochemistry & molecular biology Intron Proteins Exons Protein superfamily Classification Introns Protein evolution Repeat protein Tandem Repeat Sequences |
| Zdroj: | Journal of Structural Biology |
| ISSN: | 1095-8657 |
| Popis: | Tandem Repeat Proteins (TRPs) are ubiquitous in cells and are enriched in eukaryotes. They contributed to the evolution of organism complexity, specializing for functions that require quick adaptability such as immunity-related functions. To investigate the hypothesis of repeat protein evolution through exon duplication and rearrangement, we designed a tool to analyze the relationships between exon/intron patterns and structural symmetries. The tool allows comparison of the structure fragments as defined by exon/intron boundaries from Ensembl against the structural element repetitions from RepeatsDB. The all-against-all pairwise structural alignment between fragments and comparison of the two definitions (structural units and exons) are visualized in a single matrix, the "repeat/exon plot". An analysis of different repeat protein families, including the solenoids Leucine-Rich, Ankyrin, Pumilio, HEAT repeats and the β propellers Kelch-like, WD40 and RCC1, shows different behaviors, illustrated here through examples. For each example, the analysis of the exon mapping in homologous proteins supports the conservation of their exon patterns. We propose that when a clear-cut relationship between exon and structural boundaries can be identified, it is possible to infer a specific "evolutionary pattern" which may improve TRPs detection and classification. |
| Databáze: | OpenAIRE |
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