Evolution of Vault RNAs


Vault ribonucleic acids (RNAs) are small, about 100 nt long, polymerase transcripts contained in the vault particles of eukaryotic cells. Although vaults are present in many but by no means all eukaryotes, an RNA component has been described in metazoa only. The RNAs exhibit conserved regions at the 3′ and 5′ ends containing also internal promoter elements. They form a panhandle‐like well‐conserved secondary structure. Most genomes contain only one or a small number of closely related vault RNA sequences. Only eutheria exhibit two clearly distinguished paralogues at syntenically conserved genomic locations. Their phylogenetic distribution is characterised by losses in major clades, whereas lophotrochozoa have vault particles and vault RNAs, and the entire system has been deleted in all ecdysozoa.

Key Concepts:

  • Vault RNA can be traced evolutionarily along with the vault particle and its key protein components, most notably MVP.

  • Vault RNA exhibits a concserved pan‐handle secondary structure and expression patterns that are often mistaken as a microRNA.

Keywords: RNA secondary structure; animal genomes; polymerase III transcripts

Figure 1.

The distribution of the MVP protein through the major eukaryotic clades shows that vaults are most likely ancient but have been lost many times. A black circle indicates clades in which MVP is found in most complete genomes or the available EST data. In green plants, MVP is present in many of the EST databases but so far is not contained in one of the assembled genomes.

Figure 2.

Genomic locations of the two vault RNA loci. Triangle show the orientation in the genomic context, circles the presence of clear orthologues in the absence of clear linkage information.

Figure 3.

Conserved elements associated with mammalian vtRNAs. The diagram, adapted from Stadler et al., shows patterns discovered by meme and indicates well‐known pol‐III upstream elements: distal sequence element, DSE; cyclic AMP response element CRE, which is a part of the larger proximal sequence element, PSE and the TATA box. The vtRNA genes themselves are delimited by conserved sequence patterns (5′‐side: motif 2 [blue] containing a Box A motif; 3′‐side: motifs 1 and 3 [cyan, red] containing the Box B motif and the pol‐III terminator signal). Primate vtRNA‐1 genes have a second copy of the Box B and terminator downstream of the experimentally determined end of the transcript. Mouse and rat vtRNA have an extended structure (Kickhoefer et al., ).

Figure 4.

Expression of the computationally predicted vault RNAs is supported by short read sequencing data for both loci in Ciona intestinalis (Shi et al., ) and Schmidtea mediterranea (Friedländer et al., ; Lu et al., ).

Figure 5.

Sequence and structure conservation in vtRNA (adapted from Stadler et al., and extended by lophotrochozoa vtRNA). (A) Lophotrochozoa (Schmidtea mediterrana, Helobdella robusta, Lottia gigantea, Echinococcus multilocularis, Capitella teleta, Aplysia californica, Hydra magnipapillata, Schicstosoma japonicum and Schistosoma mansoni). (B) basal deuterstomes, (C) teleosts, (D) shark (Callorhinchus milli) and sarcopterygii except eutheria, (E) eutherian vtRNA2 locus and (F) eutherian vtRNA1 (PCDH) locus. The upper panel shows the consensus secondary structures derived from (Stadler et al., ) extended by the newly discovered vtRNA sequences in lophotrochozoa described here. Although the essential hairpin in the secondary structure (circles in the secondary structure drawings indicating compensatory substitutions) and the box A motif (highlighted in blue) is well conserved in the lophotrochozoa vtRNA, the box B motif (highlighted in purple) appears lost in lophotrochozoa compared to all other known vtRNA genes.



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Further Reading

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Mosig, Axel, and Stadler, Peter F(Feb 2011) Evolution of Vault RNAs. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022883]