Coexistence of Multiple Codes in Messenger RNA Molecules

Abstract The coexistence of multiple codes in messenger RNA molecules is investigated. A unique biological example of multiple coding is revealed by the rev responsive element (RRE) of lentiviruses. This element overlaps with the env gene and forms a specific, multibranched RNA conformation. An analysis of the similarity in the nucleotide sequences and the similarity in the secondary structures, as well as their relationship, is described. The data suggest a novel evolutionary pathway for the RRE structures: the shifting of base pairings in the secondary structure while preserving both a similar overall RNA conformation and, apparently, the activity of the protein encoded by the overlapping gene. This means that corresponding parts of the consensus secondary structure in different RRE species are formed by non-homologous nucleotides. This pattern has so far not been observed in comparative structural studies of other sets of functionally equivalent RNAs (like tRNAs and rRNAs). The multiple-coding problem is discussed with respect to the structure and function of the RRE and the high rate of viral evolution.

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