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Step-by-step explanation:
How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 1010–1012 different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056–14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence.
How new genes emerge and functionally diversify are very fundamental questions in biology, as new genes provide the raw material for evolutionary innovation that allows organisms to adapt, increase in complexity, and form new species. An organism can acquire new genes through at least three distinct, but potentially overlapping, mechanisms (Fig. 1). Thus, a pre-existing gene can be transferred ready made from another organism by lateral gene transfer (via transformation, transduction, and conjugation), or it can evolve by modification of an already existing gene (by duplication–divergence or gene fusion/fission) or it can be generated de novo from noncoding DNA. It is clear that these mechanisms have generated the diversity of genes and proteins that underlies the existence of all organisms, but their relative importance in new gene evolution and functional diversification is unclear. Thus, their importance will depend on several factors, including the organism and gene studied, the time scales involved (e.g., over recent time scales in the majority of eubacteria lateral gene transfer is a more dominant process than the others), and the methodological problems associated with an unambiguous identification of a gene emerging within an organism (a paralog) or being imported from another organism (a xenolog). In this article, we will focus on the roles of the two latter processes (gene duplication–divergence and de novo origination) as generators of new genes, mainly because they address the basic question of how new genes actually emerge (rather than how functional genes are transferred).
