TOR coordinates nucleotide availability with ribosome biogenesis in plants

Abstract

TARGET OF RAPAMYCIN (TOR) is a conserved eukaryotic Ser/Thr protein kinase that coordinates growth and metabolism with nutrient availability. We conducted a medium-throughput functional genetic screen to discover essential genes that promote TOR activity in plants, and identified a critical regulatory enzyme, cytosolic phosphoribosyl pyrophosphate (PRPP) synthetase (PRS4). PRS4 synthesizes cytosolic PRPP, a key upstream metabolite in nucleotide synthesis and salvage pathways. We found that prs4 knockouts are embryo-lethal in Arabidopsis thaliana, and that silencing PRS4 expression in Nicotiana benthamiana causes pleiotropic developmental phenotypes, including dwarfism, aberrant leaf shape, and delayed flowering. Transcriptomic analysis revealed that ribosome biogenesis is among the most strongly repressed processes in prs4 knockdowns. Building on these results, we discovered that TOR activity is inhibited by chemical or genetic disruption of nucleotide biosynthesis, but that this effect can be reversed by supplying plants with nucleobases. Finally, we show that TOR transcriptionally promotes nucleotide biosynthesis to support the demands of ribosomal RNA synthesis. We propose that TOR coordinates ribosome biogenesis with nucleotide availability in plants to maintain metabolic homeostasis and support growth.

Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana

“…When purine levels are reduced, TOR activity is decreased into Arabidopsis T2 family endoribonuclease RNS2 ( rns2-2 ) mutant, which in turn activates autophagy, suggesting that TOR mediates this catabolic process by responding to the levels of nucleotides to restore homeostasis ( Kazibwe et al, 2020 ). As a consequence, the autophagy-induced recycling of nutrients can reactivate the TOR pathway, while nucleotides promote TOR activity ( Busche et al, 2021 ).…”

Amino Acid Signaling for TOR in Eukaryotes: Sensors, Transducers, and a Sustainable Agricultural fuTORe

“…Therefore, the effects of ipms1 on amino acid metabolism are somehow transduced to TOR, and this is likely the primary cause of ipms1 cellular and developmental phenotypes. A functional genetic screen for Nicotiana benthamiana genes that regulate TOR activity identified phosphoribosyl pyrophosphate synthetase 4 (PRS4), which encodes an enzyme required for nucleotide biosynthesis in plant cells [13]. Plant TOR senses purine and pyrimidine availability, analogous to how mammalian TOR monitors nucleotide levels [13,20].…”

“…A functional genetic screen for Nicotiana benthamiana genes that regulate TOR activity identified phosphoribosyl pyrophosphate synthetase 4 (PRS4), which encodes an enzyme required for nucleotide biosynthesis in plant cells [13]. Plant TOR senses purine and pyrimidine availability, analogous to how mammalian TOR monitors nucleotide levels [13,20]. Thus, plant TOR reacts to disruptions in organic nutrient levels and biosynthetic pathways, but the sensors and transducers involved remain enigmatic (Figure 3).…”

“…N. benthamiana were grown on calcined clay and supplied with standard nutrients except for nitrogen, which was supplied as potassium nitrate at the indicated concentrations. Nitrate strongly stimulated plant growth and activated TOR, as measured by Western blots using phosphospecific antibodies against the canonical TOR substrate, S6K-pT449 (methods as in [13]).…”

“…Target of rapamycin (TOR) is a serine/threonine kinase that senses environmental cues, especially nutrient availability, to coordinate eukaryotic cellular metabolism [1][2][3][4][5]. TOR supports growth by activating anabolic processes, such as mRNA translation [6][7][8][9], nucleotide biosynthesis [10][11][12][13], and lipid biosynthesis [14][15][16], while inhibiting catabolic processes, such as autophagy [17][18][19][20][21]. TOR is especially responsive to amino acid signals.…”