Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

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Abstract
Modern organisms contain many protein-devoid RNA elements which have important roles in various cellular processes. The collection of cleaving and splicing ribozymes has been recently supplemented by several eukaryotic and prokaryotic genome-encoded ribozymes that are present in pre-mRNA and mRNA molecules. These ribozymes seem to be involved in gene expression control and possibly in other basic cellular functions. Other RNA-based elements and molecules, such as thermosensors, sRNAs, riboswitches and other RNA switches, can sense or react to changes in the environment and regulate gene expression through various mechanisms, including transcriptional, translational and splicing control. The three-dimensional structures of ribozymes and riboswitches share several architectural principals. Given this commonality, some of these RNA molecules show striking similarities in molecular recognition and mechanistic aspects of their function. RNA-based elements are probably more versatile than previously thought: they show some features that are typical of proteins and, in some situations, they might have functional advantages over proteins. For example, riboswitches can directly sense the concentration of cellular metabolites and control gene expression without a requirement for proteins, conserving cellular resources and providing fine control of gene expression. Although the origins and evolution of RNA-based elements are not clear, some of these RNAs might have descended from a hypothetical primordial 'RNA world'.

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