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Bioinformatics Advance Access published online on August 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth475
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received March 4, 2004
Revised July 22, 2004
Accepted August 8, 2004

Article

Origins of introns based on the definition of exon modules and their conserved interfaces

Albert D. G. de Roos 1*

1 The Beagle Armada, Postbus 964, 4600 AZ Bergen op Zoom, The Netherlands

* To whom correspondence should be addressed. E-mail: albert.de.roos{at}thebeaglearmada.nl.


  Abstract

Central in the unraveling of the early evolution of the genome is the origin and role of introns. The evolution of the genome can be characterized by a continuous expansion of functional modules that occurs without interruption of existing processes. The design-by-contract methodology of software development offers a modular approach to design that seeks to increase flexibility by focusing on the design of constant interfaces between functional modules. Here, it is shown that design-by-contract can offer a framework for genome evolution. The definition of an ancient exon module with identical splice sites leads to a relatively simple sequence of events that explains the role of introns, intron phase differences and the evolution of multi-exon proteins in an RNA world. An interaction of the experimentally-defined six-nucleotide splicing consensus sequence together with a limited number of primitive ribozymes can account for a rapid creation of protein diversity.


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