Mutator-like transposable elements (MULEs) are a superfamily of DNA elements found in many eukaryotes and are especially common in plants (reviewed in Bennetzen, 2005). Plant genomes carry large numbers of chimeric MULEs called Pack-MULES, which contain fragments of genes, suggesting that these elements might constitute an important mechanism of gene evolution in plants (Jiang et al., 2004). There is also evidence that gene fragments inside Pack-MULEs are transcribed, and it is possible that these encode functional proteins and/or functional transcripts, for example, antisense transcripts that could influence the expression of their parental genes in the genome. However, evidence for such functionality has been lacking or inconclusive. Now, Hanada et al. (pages 25–38) present a detailed inventory and analysis of Pack-MULEs and their parental genes in the rice genome and show that Pack-MULEs are frequently expressed and many are subject to significant functional constraints indicative of purifying selection.
Overall, the expression level of Pack-MULEs was found to be lower than that of the cognate parental genes, but a significant number of them were transcribed at a higher level than their parental genes.
The nature of selective constraints that may be acting on coding sequences inside Pack-MULEs was examined by calculating ratios of nonsynonymous (mutations that alter amino acid sequence) and synonymous (mutations that do not alter amino acid sequence) substitution rates in Pack-MULEs and their parental genes and comparing this to calculations obtained from a set of human pseudogenes and their paralogous genes. This analysis indicated that Pack-MULEs and their parental genes have been subject to purifying selection, although the pressure on Pack-MULEs is relatively relaxed (see figure), and more Pack-MULEs than human pseudogenes are subject to strong purifying selection. The selection for coding capacity and high frequency of expression among Pack-MULEs suggest that the formation and retention of some Pack-MULEs has contributed to the generation of novel functional components in plant genomes.
Figure 1.
Relationships between nonsynonymous (Ka) and synonymous (Ks) values corresponding to pack-MULE and parental gene lineages indicates that purifying selection is acting on these elements.
The authors also provide evidence that Pack-MULEs may influence the expression of their parental genes through the action of small RNAs. For example, the small RNAs shared with Pack-MULEs made up the largest source of small RNAs corresponding to parental genes, and parental genes with shared small RNAs showed lower expression levels relative to genes without associated small RNAs. The generation of Pack-MULEs is an evolutionary process that produces new combinations of both coding and regulatory sequences. Although the majority of Pack-MULEs are likely to be nonfunctional, this study provides evidence that a subset of Pack-MULEs plays important roles in plants.
References
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