Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways

Li et al. BMC Evolutionary Biology 2011, 11:122 http://www.biomedcentral.com/1471-2148/11/122 RESEARCH ARTICLE Open Access Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways Yang Li1,2, Chaoqun Li3, Guohui Ding4 and Youxin Jin1,2* Abstract Background: 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. 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. Results: We 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. Conclusions: Our 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. Background 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. Many biological processes including development, senescence, metabolism and stress responses are regulated by miRNAs [1,2]. In plants, miRNAs are distinguished from other small RNAs in that they are excised precisely from specific * Correspondence: 1 School of Life Sciences, Shanghai University, 200444, Shanghai, P.R.China Full list of author information is available at the end of the article positions on stem-loop precursors by DICER-LIKE 1 (DCL1) with the assistance of HYL1 and SERRATE [2,3]. The mature miRNAs are 2’-o-methylated at 3’ end by HEN1 and exported into cytoplasm. After being loaded into RNA Induced Silencing Complex (RISC) the miRNAs anneal to the complementary sites on target mRNAs to impose translational repression or/and cleavage of target mRNAs [2]. 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 © 2011 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Li et al. BMC Evolutionary Biology 2011, 11:122 http://www.biomedcentral.com/1471-2148/11/122 nucleotides. However, they have distinct target genes due to sequence specificity and different expression patterns [5]. MiR159 restricts the expression of some MYB transcription factors, while miR319 targets a subset of TCP transcription factor genes [5-8]. Expression of miR159 is abundant and widespread over the whole plant, while miR319 is expressed at much lower level and confined to specific tissues and developmental stages [9]. MiR159 can not induce mRNA cleavage of the miR319-targeted TCP transcription factors due to sequence specificity. Although the miR319 can also mediate the cleavage of MYB33 and MYB65 mRNAs, miR319 does not normally make significant contribution to the regulation of MYB because of its low and specialized expression [5]. The interplay of miR159 and its target MYB is involved in the regulation of vegetative growth, flowering time, anther development, seed shape and germination [8,10,11]. In contrast to miR159, miR319 and corresponding targets regulate embryonic patterning, jasmonate synthesis, leaf morphogenesis and senescence [6,12,13]. A recent study also showed the regulatory role of miR319 in the development of petal and stamen [14]. A distinguished feature of the MIR159 and MIR319 genes conserved from moss to flowering plant is that their stem-loop precursors usually have elongated stem structure. A loop-proximal segment on the MIR159/319 stem-loop precursor outside of the miRNA and miRNA* is also conserved, albeit to a much weaker extent [6,15,16]. Recent studies show that the MIR159 and MIR319 precursors are processed from loop to base to liberate three phased miRNA duplexes [15,17,18]. The miR319 or miR159 can not be efficiently excised without correct processing of the loop-proximal miRNA duplex [17]. According to this scenario, when miR159 or miR319 duplexes are produced the same amount of miRNAs derived from the other two duplexes must be generated. However, only the mature miR159 or miR319 are abundantly expressed while the alternative miRNAs are expressed at low levels, indicating that only miR159 or miR319 are incorporated into RISC and stabilized. Conservation of such an uncommon pattern in biogenesis during the long time evolution of land plants is inexplicable by the known function of miR159 and miR319. The underlying significance of such unusual style of maturation for the MIR159/319 genes remains unknown. With similarities in sequence, conservation pattern and biogenesis, miR159 and miR319 might originate from a common ancestor. Conversely, differences in expression patterns, target genes and functions indicate that miR159 and miR319 are evolutionarily distinct groups. Although clear evidences are absent to support the common origin of miR159 and miR319 [5], they are Page 2 of 18 categorized into one miRNA gene family in the miRbase and some other studies [7,19 (...truncated)