Abstract
BackgroundMicroRNAs (miRNAs) are prevalent and important endogenous gene regulators in eukaryotes. MiR159 and miR319 are highly conserved miRNAs essential for plant development and fertility. Despite high similarity in conservation pattern and mature miRNA sequences, miR159 and miR319 have distinct expression patterns, targets and functions. In addition, both MIR319 and MIR159 precursors produce multiple miRNAs in a phased loop-to-base manner. Thus, MIR159 and MIR319 appear to be related in origin and considerably diverged. However the phylogeny of MIR159 and MIR319 genes and why such unusual style of miRNA production has been conserved during evolution is not well understood.ResultsWe reconstructed the phylogeny of MIR159/319 genes and analyzed their mature miRNA expression. The inferred phylogeny suggests that the MIR159/319 genes may have formed at least ten extant early-branching clades through gene duplication and loss. A series of duplications occurred in the common ancestor of seed plants leading to the original split of flowering plant MIR159 and MIR319. The results also indicate that the expression of MIR159/319 is regulated at post-transcriptional level to switch on the expression of alternative miRNAs during development in a highly spatio-temporal specific manner, and to selectively respond to the disruption of defensive siRNA pathways. Such intra-stem-loop regulation appears diverged across the early-branching clades of MIR159/319 genes.ConclusionsOur results support that the MIR159 and MIR319 genes evolve from a common ancestor, which is likely to be a phased stem-loop small RNA. Through duplication and loss of genes this miRNA gene family formed clades specific to moss, lycopods, gymnosperms and angiosperms including the two major clades of flowering plants containing the founding members of MIR319 and MIR159 genes in A.thaliana. Our analyses also suggest that some MIR159/319 have evolved into unusual miRNA genes that are regulated at post-transcriptional level to express multiple mature products with variable proportions under different circumstances. Moreover, our analyses reveal conserved regulatory link of MIR159/319 genes to siRNA pathway through post-transcriptional regulation.
Highlights
IntroductionMicroRNAs (miRNAs) are prevalent and important endogenous gene regulators in eukaryotes
MicroRNAs are prevalent and important endogenous gene regulators in eukaryotes
Our analysis suggests that post-transcriptional regulations of MIR159/319 expression have evolved during plant evolution, through which MIR159/319 miRNAs respond to defensive siRNA deficiency
Summary
MicroRNAs (miRNAs) are prevalent and important endogenous gene regulators in eukaryotes. MiR159 and miR319 are highly conserved miRNAs essential for plant development and fertility. Despite high similarity in conservation pattern and mature miRNA sequences, miR159 and miR319 have distinct expression patterns, targets and functions. Both MIR319 and MIR159 precursors produce multiple miRNAs in a phased loop-to-base manner. MicroRNA is a class of approximately 21-nucleotide (nt) small RNA that regulate endogenous gene expression in eukaryotes ranging from single cellular green alga to mammals and flowering plants. MiR159 and miR319 are highly conserved miRNAs that play important roles in plant growth, morphogenesis and reproduction [4]. In Arabidopsis, the 21-nt mature miR159 and miR319 share 17 identical nucleotides They have distinct target genes due to sequence specificity and different expression patterns [5]. A recent study showed the regulatory role of miR319 in the development of petal and stamen [14]
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