Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis

Abstract

DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.

Shedding Light on the Dynamic Role of the “Target of Rapamycin” Kinase in the Fast-Growing C4 Species Setaria viridis, a Suitable Model for Biomass Crops

“…The temporal dynamics of TORC inhibition mediated by the chemical AZD8055, extensively employed to investigate the TOR pathway in plants (Montané and Menand, 2013;Dong et al, 2015;Ouibrahim et al, 2015;Dobrenel et al, 2016b;Prioretti et al, 2017;Schepetilnikov et al, 2017;Soprano et al, 2017;Inaba and Nagy, 2018;Mohammed et al, 2018;Riegler et al, 2018;Barrada et al, 2019;Forzani et al, 2019;Song et al, 2019;Van Leene et al, 2019;Méndez-Gómez et al, 2020;Zhu et al, 2020), was followed in seedlings of S. viridis and A. thaliana at specific and compatible developmental stages. Dose-dependent experiments, using the root GI 50 as a parameter (Figure 2), revealed that growth arrest is a phenotypic consequence of TORC repression in both species.…”

Molecular Mechanisms of Autophagy Regulation in Plants and Their Applications in Agriculture

“…Moreover, the methylation profiling of the DNA methyltransferase mutant drm2 showed that the levels of methylated CG in ATG6 and ATG7 were lower than those in wild-type Arabidopsis ( Zhong et al, 2015 ). Furthermore, the ATG8f promoter region was hypomethylated when evaluating global DNA methylation, and ATG8f expression was induced under TOR inhibition in Arabidopsis ( Zhu et al, 2020 ). These studies allowed us to propose that DNA methylation plays a critical role in the regulation of autophagy in plants.…”

Identifying Molecular Chechkpoints for Adventitious Root Induction: Are We Ready to Fill the Gaps?

“…TOR has been reported to regulate AR induction in Arabidopsis and potato ( Deng et al, 2017 ) and participate in meristem size regulation by controlling cell proliferation ( McCready et al, 2020 ). In addition, TOR inhibition has been reported to produce a decrease of DNA methylation affecting genes involved in hormone signaling, suggesting a role in chromatin remodeling ( Zhu et al, 2020 ). Overall, experimental evidence signals TOR as a candidate for adventitious rooting competence.…”