MicroRNA Genes in Plants Organization Conservation and Origin

As of June 2007, the miRBase (http://microrna.sanger.ac.uk/sequences/index.shtml) version 9.2 contains a total of 959 MIR genes from 10 plant species including moss, dicots, and monocots. Several features of plant MIR genes can be readily discerned from the current sets of miRNAs. First, plant MIR genes often have paralogs such that the 184 Arabidopsis miRNAs in miRBase version 9.2 represent approximately 100 families of related miRNAs. MIR gene families arose from the process of gene duplication and diversification that also drives the evolution of protein-coding gene families (Maher et al. 2006). Second, each species has an evolutionarily fluid set of miRNAs. Some miRNA families, such as miR156, miR160, miR319, and miR390, appear to be of ancient origin such that they are conserved from mosses to flowering plants (Arazi et al. 2005; Axtell and Bartel 2005). Since the complete genome of a nonflowering land plant is not currently available, it is not possible to determine how many miRNA families are conserved among land plants through homol-ogy searches. Some miRNA families evolved after mosses and flowering plants diverged but before the divergence of monocots and dicots. Intriguingly, a large set of miRNA families is not shared among two of the three sequenced angiosperm genomes (Arabidopsis, poplar, and rice), suggesting that these miRNAs are evolutionarily "young" miRNAs. Among the known families of miRNAs in Arabidopsis, 4 are conserved down to mosses, 20 are shared between Arabidopsis and rice, while 22 are conserved between Arabidopsis and poplar. The remaining families are so far unique to Arabidopsis, but as the genomes of species closely related to Arabidopsis become available, some of these families may be found to be common to these related species. Consistent with the notion that the nonconserved miRNAs represent evolutionarily "young" miRNAs, these miRNAs are predominantly found at single loci in the genome. Third, the great majority of plant miRNA genes are located in intergenic regions, which is in contrast to animal miRNA genes that tend to be localized in introns or exons of protein-coding genes (reviewed in Kim 2005). Finally, unlike animal miRNA genes that are often found in clusters and that are transcribed into a polycistronic RNA (reviewed in Kim 2005), plant miRNA genes are usually not arranged in tandem in the genome or co-expressed. In the current set of Arabidopsis miRNAs, only three pairs of MIR genes (MIR169i and MIR169j; MIR169k and MIR1691; MIR169m and MIR169n) are arranged such that the two miRNAs are in the same orientation and are within 500 bp of each other. It is possible that each gene pair is co-transcribed.

The fact that Arabidopsis has many MIR gene families that are not found in poplar or rice suggests that MIR genes continue to be generated during the evolution of land plants. Some of these "young" Arabidopsis miRNAs (such as miR161, miR163, miR826, miR841, miR842, and miR846) revealed one potential mechanism by which miRNA genes originate in evolution (Allen et al. 2004; Rajagopalan et al. 2006; Fahlgren et al. 2007). The precursors to these miRNAs show extensive sequence similarity to their target genes, which led to the model that de novo generation of miRNA genes results from an inverted duplication event of the target genes. Transcription through the inverted repeats, which are likely to diverge in sequence after the initial duplication event, would result in an RNA with an imperfect hairpin structure reminiscent of miRNA precursors.

Plants and animals were thought to have evolved miRNAs independently since they do not share common miRNAs. However, a recent study identified an Arabidopsis miRNA, miR854, that has potential homologs in four examined animal (including human) genomes, and these homologs only differ from miR854 by one nucleotide (Arteaga-Vazquez et al. 2006). Human and mice miR854 were detectable by RNA filter hybridization. Arabidopsis miR854 has multiple binding sites in the 3' untranslated region (UTR) of the UBP1 gene that encodes an hnRNP protein and causes translation inhibition of UBP1 expression. The animal miR854 is also complementary to a site in the 3' UTR of the UBP1 homologs. If the animal miR854 is to be confirmed as a regulator of its predicted target in animals in the future, miR854 and its target gene will be the first example of a conserved miRNA/ target pair between plant and animal kingdoms.

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