Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis

Abstract

Key messageExtensive modulation of numerous ARF transcripts in the embryogenic culture of Arabidopsis indicates a substantial role of auxin signaling in the mechanism of somatic embryogenesis induction.AbstractSomatic embryogenesis (SE) is induced by auxin in plants and auxin signaling is considered to play a key role in the molecular mechanism that controls the embryogenic transition of plant somatic cells. Accordingly, the expression of AUXIN RESPONSE FACTOR (ARF) genes in embryogenic culture of Arabidopsis was analyzed. The study revealed that 14 of the 22 ARFs were transcribed during SE in Arabidopsis. RT-qPCR analysis indicated that the expression of six ARFs (ARF5, ARF6, ARF8, ARF10, ARF16, and ARF17) was significantly up-regulated, whereas five other genes (ARF1, ARF2, ARF3, ARF11, and ARF18) were substantially down-regulated in the SE-induced explants. The activity of ARFs during SE was also monitored with GFP reporter lines and the ARFs that were expressed in areas of the explants engaged in SE induction were detected. A functional test of ARFs transcribed during SE was performed and the embryogenic potential of the arf mutants and overexpressor lines was evaluated. ARFs with a significantly modulated expression during SE coupled with an impaired embryogenic response of the relevant mutant and/or overexpressor line, including ARF1, ARF2, ARF3, ARF5, ARF6, ARF8, and ARF11 were indicated as possibly being involved in SE induction. The study provides evidence that embryogenic induction strongly depends on ARFs, which are key regulators of the auxin signaling. Some clues on the possible functions of the candidate ARFs, especially ARF5, in the mechanism of embryogenic transition are discussed. The results provide guidelines for further research on the auxin-related functional genomics of SE and the developmental plasticity of somatic cells.Electronic supplementary materialThe online version of this article (doi:10.1007/s00299-017-2114-3) contains supplementary material, which is available to authorized users.

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

“…A positive impact of auxin on the CMT3 expression has also been reported by others (Parizot et al 2010;Shemer et al 2015). In support of the auxin-controlled expression of CMT3 is the presence of the auxin-responsive motif, AuxRE, in the promoter of this gene (http://arabi dopsi s.med.ohio-state .edu/Atcis DB/), which implies that ARFs, the core elements of auxin signalling that are believed to play roles in SE induction in Arabidopsis (Weijers and Wagner 2016;Wójcikowska and Gaj 2017), might regulate CMT3 in response to auxin treatment. In contrast to CMT3, the impact of auxin on MET1 up-regulation in SE appears to be indirect due to the lack of auxin-responsive motifs in the gene promoter.…”

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

“…Thus, although TSA seems to target the auxin-responsive genes preferentially, the effects of TSA vs. 2,4-D on the gene expression level could differ to some extent. In support of this, the downregulation vs. the upregulation of ARF10 and ARF17 during TSA-vs. 2,4-D-induced SE, respectively, was reported in Arabidopsis [22,93]. The targets of histone acetylation also involve the MIRNA genes, including those encoding auxin-related miRNA [187][188][189][190].…”

“…The auxin-related miRNAs frequently target the fundamental components of the auxin signaling pathway, including the ARFs, which are involved in SE induction [27,93]. Accordingly, insights into embryogenic cultures of Arabidopsis and other plants indicated that miR160 could directly regulate the expression of ARF10, ARF16, and ARF17; miR167 seems to the control expression of ARF6 and ARF8, while miR390 possibly downregulates the ARF2, ARF3, ARF4 transcripts [55,63,64,68,81,85,86].…”

“…Accordingly, miR390-targeted ARF5/MONOPTEROS (MP) was recently found to bind auxin-responsive elements (AuxRE) in the promoter of the MIR390a gene to control the MIR390 expression in the root meristem [109]. Although both ARF5/MP and miR390 have been suggested to control SE induction in Arabidopsis, their regulatory interactions in this process require experimental validation [55,93].…”

Variation in the expression of a transmembrane protein influences cell growth inArabidopsis thalianapetals by altering auxin availability

“…BPEp is highly expressed during the later stages of petal development, while ARF8 is ubiquitously expressed, but more highly expressed during the later stages of petal development. The expression of both FRL1 and ARF8 is increased in response to auxin [23,24,35], and as auxin responses are reduced in KSK over-expressing lines ( Figure 6E), it is possible that KSK over-expression may reduce expression of these auxin-responsive negative regulators of petal cell size, leading to increased petal cell size and overall increases in petal area. The down-regulation of ANT expression in KSK over-expression lines ( Figure 4C) is consistent with reduced auxin responses, as auxin increases ANT gene expression [36].…”