Abstract
TOR (Target of Rapamycin) kinase is an evolutionarily conserved protein kinase, which integrates stress-related cues with growth and metabolic outputs. Long non-coding RNAs (lncRNAs) play a vital role in the regulation of eukaryotic genes. However, little is known about TOR's function in regulating the expression of lncRNAs in plants. In this study, four putative homologous genes encoding the TOR protein were identified by utilizing the recently completed cotton genome. Pharmacological experiments with TOR inhibitor AZD8055 and on silencing GhTOR genes resulted in obvious cotton growth retardation, indicating the conserved role of TOR in plant growth. The expression pattern analyses in different tissues reveal that TOR may play a role in root development, and the transcript levels of TOR genes were changed under different stress conditions. Importantly, we found TOR may be a key player in regulating the expression of long non-coding RNAs (lncRNAs). A total of 10,315 lncRNAs were discovered in cotton seedlings, 90.7% of which were long intergenic ncRNAs. Moreover, we identified the differentially expressed lncRNAs, of which 296 were significantly upregulated and 105 were downregulated in TOR inactivated plants. GO and KEGG analyses of differentially expressed lncRNA neighboring genes reveal that these differentially expressed lncRNA-targeted genes are involved in many life processes, including stress response, glutathione, and ribosomes in cotton. A series of differentially expressed lncRNAs potentially involved in plant stress response was identified under TOR inhibition. Collectively, these results suggest that cotton TOR proteins may directly modulate the expression of putative stress-related lncRNAs and eventually play a potential role in the cotton stress response.
Highlights
TOR (Target of Rapamycin) is a highly evolutionarily conserved Ser/Thr protein kinase among eukaryotic species and modulates a broad spectrum of physiological and developmental processes (Rexin et al, 2015; Dobrenel et al, 2016)
We found that GhTOR1-At and GhTOR1-Dt had highly similar exon patterns, TABLE 1 | Gene loci information pertaining to cotton TOR genes
Little is known about the molecular mechanism of how the TOR signaling pathway regulates plant stress in the tetraploid cotton
Summary
TOR (Target of Rapamycin) is a highly evolutionarily conserved Ser/Thr protein kinase among eukaryotic species and modulates a broad spectrum of physiological and developmental processes (Rexin et al, 2015; Dobrenel et al, 2016). A new generation of ATP-competitive chemical inhibitors specific to TOR kinase such as Torin, Torin, KU0063794, and AZD8055 (AZD) have been applied for TOR studies in yeasts, plants, animals, and humans (Feldman et al, 2009; GarcíaMartínez et al, 2009; Chresta et al, 2010; Liu et al, 2011; Xiong et al, 2017). Among these inhibitors, AZD was the strongest inhibitor and has been widely used in plant TOR research (Dong et al, 2015; Li et al, 2015b; Deng et al, 2016; Song et al, 2017; Xiong et al, 2017)
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