Abstract
BackgroundMicroRNAs (miRNAs) are important regulatory elements of gene expression. Similarly to coding genes, miRNA genes follow a birth and death pattern of evolution likely reflecting functional relevance and divergence. For instance, miRNA529 is evolutionarily related to miRNA156 (a highly conserved miRNA in land plants), but it is lost in Arabidopsis thaliana. Interestingly, both miRNAs target sequences overlap in some members of the SQUAMOSA promoter-binding protein like (SPL) family, raising important questions regarding the diversification of the miR156/miR529-associated regulatory network in land plants.ResultsIn this study, through phylogenic reconstruction of miR156/529 target sequences from several taxonomic groups, we have found that specific eudicot SPLs, despite miRNA529 loss, retained the corresponding target site. Detailed molecular evolutionary analyses of miR156/miR529-target sequence showed that loss of miR529 in core eudicots, such as Arabidopsis, is correlated with a more relaxed selection of the miRNA529 specific target element, while miRNA156-specific target sequence is under stronger selection, indicating that these two target sites might be under distinct evolutionary constraints. Importantly, over-expression in Arabidopsis of MIR529 precursor from a monocot, but not from a basal eudicot, demonstrates specific miR529 regulation of AtSPL9 and AtSPL15 genes, which contain conserved responsive elements for both miR156 and miR529.ConclusionsOur results suggest loss of functionality of MIR529 genes in the evolutionary history of eudicots and show that the miR529-responsive element present in some eudicot SPLs is still functional. Our data support the notion that particular miRNA156 family members might have compensated for the loss of miR529 regulation in eudicot species, which concomitantly may have favored diversification of eudicot SPLs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0716-5) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs are important regulatory elements of gene expression
To get a better view of the extent to which a miR529-responsive element is conserved in land plants, we searched for miR529-responsive elements in SQUAMOSA promoter-binding protein like (SPL) genes from species with publicly available genome sequences, including those species in which miRNA529 is absent in their genomes or in transcribed sequences identified far
The miR156/529-responsive element in eudicot SPLs resides only in coding regions, to what is observed in monocots and bryophytes (Additional file 1; [24])
Summary
MicroRNAs (miRNAs) are important regulatory elements of gene expression. to coding genes, miRNA genes follow a birth and death pattern of evolution likely reflecting functional relevance and divergence. MiRNA529 is evolutionarily related to miRNA156 (a highly conserved miRNA in land plants), but it is lost in Arabidopsis thaliana Both miRNAs target sequences overlap in some members of the SQUAMOSA promoter-binding protein like (SPL) family, raising important questions regarding the diversification of the miR156/miR529-associated regulatory network in land plants. Both miRNAs have a common ancestor in embryophytes, miR529 seems to have been lost in some taxonomic groups, including core eudicots such as Arabidopsis thaliana [12,13,14] Both miRNAs share target genes, which are members of the SQUAMOSA promoter-binding protein like (SPL) family [15]. Sites for miR156 reside in coding as well as untranslated regions of target sequences, whereas miR529 binding sites are located in coding regions and overlap with miR156 sites [24, 25]
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