miR393 contributes to the embryogenic transition induced in vitro in Arabidopsis via the modification of the tissue sensitivity to auxin treatment

Abstract

Main conclusionmiR393 was found to control embryogenic transition in somatic cells in Arabidopsis via control of theTIR1andAFB2auxin receptors genes of the F-box family.miR393 molecules are believed to regulate the expression of the auxin receptors of the TAAR clade. Considering the central role of auxin in the induction of somatic embryogenesis (SE) in plant explants cultured in vitro, the involvement of miR393 in the embryogenic transition of somatic cells has been hypothesised. To verify this assumption, the reporter, overexpressor and mutant lines in genes encoded MIR393 and TIR1/AFB proteins of the F-box family were analysed during SE in Arabidopsis. Expression profiling of MIR393a and MIR393b, mature miR393 and the target genes (TIR1, AFB1, AFB2, AFB3) were investigated in explants undergoing SE. In addition, the embryogenic potential of various genotypes with a modified activity of the MIR393 and TIR1/AFB targets was evaluated. The distinct increase in the accumulation of miR393 that was coupled with a notable down-regulation of TIR1 and AFB2 targets was observed at the early phase of SE induction. Relevant to this observation, the GUS/GFP monitored expression of MIR393, TIR1 and AFB2 transcripts was localised in explant tissue undergoing SE induction. The results suggest the miR393-mediated regulation of TIR1 and AFB2 during embryogenic transition induced in Arabidopsis and a modification of the explant sensitivity to auxin treatment is proposed as underlying this regulatory pathway.Electronic supplementary materialThe online version of this article (doi:10.1007/s00425-016-2505-7) contains supplementary material, which is available to authorized users.

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

“…The expression of different MIRNA gene family members is strictly regulated during plant development in an organ-and tissue-specific manner [80,81], and thus reporter line analyses could be important in identifying the specific MIRNA genes that contribute to SE induction. Accordingly, the expression of MIR167c, MIR393a,b, and MIR396b have been found to colocalize with the SE-induction sites of the explants, which supports the contribution of these genes to miRNA-mediated regulation of SE [56,82,83]. However, most of the reporter lines monitor the gene promoter activity rather than localize the corresponding gene transcript.…”

“…Extensive modulation of the TF genes in an embryogenic culture of Arabidopsis is accompanied by differential expression of numerous miRNAs, suggesting the function of miRNA-regulation in the embryogenic transition of plant somatic cells [54,55]. In support, the dcl1 mutant, a defect in the DICERLIKE1 (DCL1) gene with a key role in miRNA biogenesis, was shown to be unable for SE induction [56]. In addition to Arabidopsis, numerous miRNAs with a differential expression have been identified in embryogenic cultures of different gymnosperm, mono-and dicot plants, including economically important species .…”

“…In addition, an analysis of the STTM (short target tandem mimic) and MIM (artificial miRNA target mimic) lines with a deregulated expression of MIRNA genes and miRNA targets [91,92] provided a powerful tool for identifying the miRNA function in plant development including SE induction. It was shown that a deregulated expression of MIR160, MIR165/166, MIR167, MIR393, and MIR396 significantly affected the auxin accumulation and sensitivity to auxin in cultured explants of Arabidopsis [56,82,83,85].…”

MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis

“…Among them, miR393 , which plays a key role in auxin signaling during plant development, was identified (Navarro et al, 2006; Si-Ammour et al, 2011). A recent report on SE in Arabidopsis confirmed that miR393 contributes to embryogenic transition by targeting the auxin receptors, TIR1 and AFB2 , and modulating tissue sensitivity to auxin treatment (Wójcik and Gaj, 2016). Another auxin signaling-related miRNA candidate, miR160 , was indicated as controlling the development of various organs in Arabidopsis, particularly zygotic embryos, by targeting ARF10, ARF16 , and ARF17 (Liu et al, 2007; Liu and Chen, 2010).…”

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

“…Thus, to fully understand the function of DNA methylation in the embryogenic transition the functional outcome of DNA methylation in the context of other epigenetic changes remains to be uncovered. Moreover, it is of importance to reveal the relation of DNA methylation with the recently identified miRNA that plays a regulatory role in the SE of Arabidopsis (Wójcik and Gaj 2016;Szyrajew et al 2017;Wójcik et al 2017). …”