Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton

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.

Friend or Enemy: A Dual Role of Autophagy in Plant Virus Infection

“…Rapamycin acts as an allosteric inhibitor of mTOR upon association with the FK506-binding protein 12 (FKBP12) (Yang et al, 2013); however, many plants are insensitive to it (Xiong and Sheen, 2015). Another TOR inhibitor, AZD8055, an efficient autophagy inducer that works by suppressing TOR signaling, is widely used in plants (Dong et al, 2015;Pu et al, 2017;Song et al, 2019). Several inhibitors of autophagy in plant cells have been reported to impact on different stages of the process.…”

Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

“…In cotton, previous studies have shown that lncRNAs XLOC_063105-CotAD_37096 and XLOC_115463-CotAD_12502 probably function in cis-regulating responses to drought stress [32]. One lncRNA, TCONS_00061835-Gh_D06G1439 (GhMYB-like), regulates cotton fiber development [36] by complementary base pairing with the protein-coding gene, lncRNA, and the circRNA complex network, demonstrating that some lncRNAs are involved in biotic and abiotic stresses [31,33,34].…”

“…With the development of modern technology, the de novo assembly of Gossypium hirsutum and Gossypium barbadense genomes in high quality has improved contiguity and completeness in the available genome information [29,30]. In cotton, lncRNAs participate in resistance to Verticillium dahliae [31], drought stress [32], salt stress [33], and other abiotic stresses [34]. LncRNAs also participate in regulating fiber development [5,35] and in lint initiation [36].…”

TOR represses stress responses through global regulation of H3K27 trimethylation in plants

“…Since H3K27me 3 occupies the intergenic regions, we speculate that TOR impacts transcriptome through intergenic non-coding RNAs. In plants, AZD8055-mediated TOR inhibition can induce long non-coding RNA expression which is often marked by H3K27me 3 (Song et al, 2018). This suggests that global decrease of H3K27me 3 level in conditions of TOR inactivation could also affect transcription or translation through long non-coding RNAs.…”