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Evolution of secondary structure in the family of 7SL-like RNAs

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Abstract

Primate and rodent genomes are populated with hundreds of thousands copies of Alu and B1 elements dispersed by retroposition, i.e., by genomic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the terminal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the signal recognition particle) is conserved from prokaryotes to distant eukaryotic species. Yet only in primates and rodents did this molecule give rise to retroposing Alu and B1 RNAs and to apparently functional BC200 and 4.5S RNAs. To understand this transition and the underlying molecular events, we examined, by comparative analysis, the evolution of RNA structure in this family of molecules derived from 7SL RNA.

RNA sequences of different simian (mostly human) and prosimian Alu subfamilies as well as rodent B1 repeats were derived from their genomic consensus sequences taken from the literature and our unpublished results (prosimian and New World Monkey). RNA secondary structures were determined by enzymatic studies (new data on 4.5S RNA are presented) and/or energy minimization analyses followed by phylogenetic comparison. Although, with the exception of 4.5S RNA, all 7SL-derived RNA species maintain the cruciform structure of their progenitor, the details of 7SL RNA folding domains are modified to a different extent in various RNA groups. Novel motifs found in retropositionally active RNAs are conserved among Alu and B1 subfamilies in different genomes. In RNAs that do not proliferate by retroposition these motifs are modified further. This indicates structural adaptation of 7SL-like RNA molecules to novel functions, presumably mediated by specific interactions with proteins; these functions were either useful for the host or served the selfish propagation of RNA templates within the host genome.

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Abbreviations

FAM:

fossil Alu element

FLAM:

free left Alu monomer

FRAM:

free right Alu monomer

L-Alu:

left Alu subunit

R-Alu:

right Alu subunit

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Authors and Affiliations

  1. Génétique Médicale, Centre de Recherche, Hôpital Sainte-Justine, Département de Pédiatrie, Université de Montréal, 3175 Chemin Côte Sainte-Catherine, H3T 1C5, Montréal, Québec, Canada

    Damian Labuda & Ewa Zitkiewicz

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  1. Damian Labuda
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  2. Ewa Zitkiewicz
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Dedicated to Dr. Robert Cedergren on the occasion of his 25th anniversary at the University of Montreal

Correspondence to: D. Labuda

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Labuda, D., Zitkiewicz, E. Evolution of secondary structure in the family of 7SL-like RNAs. J Mol Evol 39, 506–518 (1994). https://doi.org/10.1007/BF00173420

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