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RNA in evolution

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Abstract RNA has played a variety of roles in the evolutionary history of life on the Earth. While this molecule was once considered a poor cousin of the more influential polymers in the cell, namely DNA and proteins, a string of important discoveries over the last 50 years has revealed that RNA may in fact be the cornerstone of biological function. In particular, the finding that RNA can be catalytic, and thus possess both a genotype and a phenotype, has forced us to consider the possibility that life's origins began with RNA, and that the subsequent diversification of life is aptly described as a string of innovations by RNA to adapt to a changing environment. Some of these adaptations include riboswitches, ribonucleoproteins (RNPs), RNA editing, and RNA interference (RNAi). Although many of these functions may seem at first glance to be recent evolutionary developments, it may be the case that all of their catalytic activities trace their roots back to a primordial ‘RNA World’ some four billion years ago, and that RNA's diversity has a continuous thread that pervades life from its very origins. Copyright © 2010 John Wiley & Sons, Ltd. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions

The RNA Tie Club, 1955. This group of scientists was the first to consider seriously the important roles that RNA plays in both the evolution and the current operation of life on the Earth. In this picture, from left to right, are Francis Crick, Alexander Rich, Leslie E. Orgel, and James Watson (image credit: Alexander Rich).

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An RNA riboswitch. This type of RNA changes conformation upon binding of a small molecule. In the case shown here, the binding of adenine alters the conformation of the RNA in such a way to allow the expression of the gene downstream of the riboswitch, ydhL, which is involved in adenine metabolism in Bacillus subtilis.34.

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The self‐splicing of the two halves of a tRNA in bacteria by a group I intron ribozyme. The primary RNA transcript (top) contains an intron that folds into a ribozyme structure that catalyzes the subsequent splicing and recombining of the RNA pieces into the complete tRNA and the free intron (bottom). This reaction gives rise to speculation that the modern tRNA cloverleaf structure is evolutionarily derived from two pieces27–29 and that recombination among these pieces augmented the diversification of tRNA families.

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Examples of RNA fragments that play important roles in the metabolism of contemporary cells.

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A simplified phylogeny of all life, showing the RNA World giving rise ultimately to the three domains of life. Sample lineages are included, but only the branching order is meaningful, not the internode distances or branch lengths.

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Uridine and pseudouridine. The latter is an isomer of the standard RNA nucleotide (uridine) and is synthesized in vivo by the specialized protein enzyme pseudouridine synthase.7 Pseudouridine represents an evolutionary change of the chemical nature of RNA itself.

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RNA structure. (a) The primary (1°) structure, which is the nucleotide sequence of the RNA. (b) The secondary (2°) structure, which is the folded RNA that forms upon intra‐strand base pairing. (c) The tertiary (3°) structure, which is the three‐dimensional RNA that forms upon higher‐order interactions among the base‐paired regions (P1, P2, etc.). The RNA shown in all panels is that of the self‐splicing group I intron from the isoleucine tRNA in the purple bacterium Azoarcus. The intron sequence is denoted by upper‐case letters, while the ends of the tRNA are denoted in lower‐case letters, with the splice locations marked with arrows. Panel C (Reprinted with permission from Ref 43. Copyright 2004 Macmillan Publishers Ltd.).

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RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution

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