Abstract
Key messageHere we report the existence of six putative Dicer-likegenes in theMedicago truncatulagenome. They are ubiquitously expressed throughout the plant and significantly induced in root nodules.Over the past decade, small noncoding RNAs (sncRNA) have emerged as widespread and important regulatory molecules influencing both the structure and expression of plant genomes. One of the key factors involved in sncRNA biogenesis in plants is a group of RNase III-type nucleases known as Dicer-like (DCL) proteins. Based on functional analysis of DCL proteins identified in Arabidopsis thaliana, four types of DCLs were distinguished (DCL1-4). DCL1 mainly produces 21 nt miRNAs. The products generated by DCL2, DCL3, and DCL4 belong to various classes of siRNAs that are 22, 24 and 21 nt in length, respectively. M. truncatula is a model legume plant closely related to many economically important cultivable species. By screening the recent M. truncatula genome assembly, we were able to identify three new DCL genes in addition to the MtDCL1-3 genes that had been earlier characterized. The newly found genes include MtDCL4 and two MtDCL2 homologs. We showed that all six M. truncatula DCL genes are expressed in plant cells. The first of the identified MtDCL2 paralogs encodes a truncated version of the DCL2 protein, while the second undergoes substantial and specific upregulation in the root nodules. Additionally, we identified an alternative splicing variant of MtDCL1 mRNA, similar to the one found in Arabidopsis. Our results indicate that DCL genes are differently activated during Medicago symbiosis with nitrogen fixing bacteria and upon pathogen infection. In addition, we hypothesize that the alternative splicing variant of MtDCL1 mRNA may be involved in tissue-specific regulation of the DCL1 level.Electronic supplementary materialThe online version of this article (doi:10.1007/s00299-016-1936-8) contains supplementary material, which is available to authorized users.
Highlights
IntroductionSncRNAs are involved in the regulation of numerous biological processes, such as development, stress response and pathogen defense (Kurzynska-Kokorniak et al 2009; Jackowiak et al 2011; Castel and Martienssen 2013; Martınez de Alba et al 2013)
We report the existence of six putative DCL genes in the M. truncatula genome
We showed that MtDCL4 undergoes significant upregulation in nodules of plants treated with S. meliloti Rm1021 and in roots of plants treated with flg22 implying that this gene may be involved in both symbiotic interactions and antibacterial defense
Summary
SncRNAs are involved in the regulation of numerous biological processes, such as development, stress response and pathogen defense (Kurzynska-Kokorniak et al 2009; Jackowiak et al 2011; Castel and Martienssen 2013; Martınez de Alba et al 2013) Biogenesis of both miRNAs and siRNAs depends on a group of endonucleolytic enzymes that are members of the RNase III family, known as Dicer proteins in animals (Kurzynska-Kokorniak et al 2015) and Dicer-. In the miRNA biogenesis pathway, DCL1 produces duplexes formed by two 21 nt RNA strands: miRNA and a complementary passenger strand referred to as miRNA* Both PAZ and the helicase domains are known for their role in proper positioning of the sncRNA precursor within the enzyme (Macrae et al 2006; Gu et al 2012), while the helicase allows processive cleavage of longer substrates (Cenik et al 2011; Welker et al 2011). It may be involved in a negative feedback regulation mechanism controlling the level of the DCL1 protein as it has been earlier shown for Arabidopsis
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