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Signs of Ancient and Modern Exon-Shuffling Are Correlated to the Distribution of Ancient and Modern Domains Along Proteins

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Abstract

Exon-shuffling is an important mechanism accounting for the origin of many new proteins in eukaryotes. However, its role in the creation of proteins in the ancestor of prokaryotes and eukaryotes is still debatable. Excess of symmetric exons is thought to represent evidence for exon-shuffling since the exchange of exons flanked by introns of the same phase does not disrupt the reading frame of the host gene. In this report, we found that there is a significant correlation between symmetric units of shuffling and the age of protein domains. Ancient domains, present in both prokaryotes and eukaryotes, are more frequently bounded by phase 0 introns and their distribution is biased towards the central part of proteins. Modern domains are more frequently bounded by phase 1 introns and are present predominantly at the ends of proteins. We propose a model in which shuffling of ancient domains mainly flanked by phase 0 introns was important in the ancestor of eukaryotes and prokaryotes, during the creation of the central part of proteins. Shuffling of modern domains, predominantly flanked by phase 1 introns, accounted for the origin of the extremities of proteins during eukaryotic evolution.

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Acknowledgments

The authors thank Walter Gilbert, Ricardo Brentani, and Natanja Kirschbaum-Slager for the critical reading of the manuscript. M.D.V. and N.T.S. are supported by fellowships from FAPESP.

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Authors and Affiliations

  1. Ludwig Institute for Cancer Research, Sao Paulo Branch, Rua Prof. Antonio Prudente 109 4° andar, CEP, São Paulo, SP, 01509-010, Brazil

    Maria Dulcetti Vibranovski, Noboru Jo Sakabe, Rodrigo Soares de Oliveira & Sandro José de Souza

  2. Ph.D Program, Departmento de Bioquímica, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Bloco 03 superior, sala 351, CEP, 05508-900, Cidade Universitária, São Paulo, SP, Brazil

    Maria Dulcetti Vibranovski & Noboru Jo Sakabe

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  1. Maria Dulcetti Vibranovski
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  2. Noboru Jo Sakabe
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  3. Rodrigo Soares de Oliveira
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  4. Sandro José de Souza
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Correspondence to Sandro José de Souza.

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Vibranovski, M.D., Sakabe, N.J., de Oliveira, R.S. et al. Signs of Ancient and Modern Exon-Shuffling Are Correlated to the Distribution of Ancient and Modern Domains Along Proteins. J Mol Evol 61, 341–350 (2005). https://doi.org/10.1007/s00239-004-0318-y

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  • DOI: https://doi.org/10.1007/s00239-004-0318-y

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