16 Evolution of Functional Structures of RNA

Abstract

Evolution of new functions for RNA has been crucial to the history of life. New functions could have evolved before the DNA era in RNA molecules capable of replicating or, later, in RNA molecules specified by a DNA genome. Despite the importance of this process during molecular evolution, no one has undertaken a systematic analysis to elucidate the principles and mechanisms involved. Because appearance of a new function would have to be preceded by formation of a new structure, insight can be gained by studying relevant molecular architecture in contemporary RNA. In this chapter, I discuss ways in which certain underlying structures of RNA could evolve new functions.

Many RNA molecules are multifunctional. Any such molecule has probably evolved through sequential addition of domains that have favorable selective effects on the molecule or on the cell carrying it. Each gained function would represent one manifestation of the basic mechanism of evolution within an RNA species. This mechanism can be approached by analysis of multifunctional RNA molecules only, because one cannot imagine the precursors of a monofunctional molecule.

One of the best-studied examples of multifunctional RNA is the primer for DNA replication of plasmid ColE1 in Escherichia coli. This 555-nucleotide RNA must form a specific folded structure before it can serve as a primer; it consists of four functional domains, each composed of one, two, or three stem-loops. A number of other plasmid species replicate by means of primer RNAs with nucleotide sequences and structures similar to those in ColE1, so...