Phosphorus absorbed in the form of phosphate (H 2 PO 4 À) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding of how plants respond to phosphate starvation is essential for the development of more phosphate-efficient crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses to 48 h of phosphate versus phosphite (H 2 PO 3 À) resupply to phosphate-deprived Arabidopsis thaliana suspension cells. Phosphite is similarly sensed, taken up and transported by plant cells as phosphate, but cannot be metabolized or used as a nutrient. Phosphite is thus a useful tool for differentiating between non-specific processes related to phosphate sensing and transport and specific responses to phosphorus nutrition. We found that responses to phosphate versus phosphite resupply occurred mainly at the level of protein phosphorylation, complemented by limited changes in protein abundance, primarily in protein translation, phosphate transport and scavenging, and central metabolism proteins. Altered phosphorylation of proteins involved in core processes such as translation, RNA splicing and kinase signaling was especially important. We also found differential phosphorylation in response to phosphate and phosphite in 69 proteins, including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 histone acetyltransferasepotential phosphoswitches signaling changes in phosphorus nutrition. Our study illuminates several new aspects of the phosphate starvation response and identifies important targets for further investigation and potential crop improvement.
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter, but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h - days) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM Mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while PTMs do not. Further, we find significant changes in PTMs and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulphur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
22Phosphorus absorbed in the form of phosphate (H2PO4 -) is an essential but limiting macronutrient 23for plant growth and agricultural productivity. A comprehensive understanding of how plants 24respond to phosphate starvation is essential to develop more phosphate-efficient crops. Here we 25 employed label-free proteomics and phosphoproteomics to quantify protein-level responses to 48 26 h of phosphate versus phosphite (H2PO3 -) resupply to phosphate-deprived Arabidopsis thaliana 27 suspension cells. Phosphite is similarly sensed, taken up, and transported by plant cells as 28phosphate, but cannot be metabolized or used as a nutrient. Phosphite is thus a useful tool to 29 delineate between non-specific processes related to phosphate sensing and transport, and specific 30 responses to phosphorus nutrition. We found that responses to phosphate versus phosphite 31 resupply occurred mainly at the level of protein phosphorylation, complemented by limited 32 changes in protein abundance, primarily in protein translation, phosphate transport and 33 scavenging, and central metabolism proteins. Altered phosphorylation of proteins involved in core 34 processes such as translation, RNA splicing, and kinase signalling were especially important. We 35 also found differential phosphorylation in response to phosphate and phosphite in 69 proteins, 36including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 37 histone acetyltransferase-potential phospho-switches signalling changes in phosphorus nutrition. 38Our study illuminates several new aspects of the phosphate-starvation response and identifies 39 important targets for further investigation and potential crop improvement. 40
The plant circadian clock governs growth and development by syncing biological processes to periodic environmental changes. Decades of research has shown how the clock enables plants to respond to two environmental variables that change at different latitudes and over different seasons: photoperiod and temperature. However, a third variable, twilight length, has so far gone unstudied. The duration of twilight changes across the planet, lengthening with latitude and changing across seasons, and yet most circadian experiments are performed in lab environments with no twilight. Here, using controlled growth setups, we show that twilight length optimizes plant growth and changes flowering time through the LHY/CCA1 morning module of the Arabidopsis circadian clock. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiod. Further, transcriptome and proteome analyses showed that twilight length alters plant biology via protein-level regulation of proteins involved in reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Overall, our findings call for more nuanced models of daylength perception in plants and posit that twilight length is an important determinant of plant growth, development, and circadian function.
Environmental conditions contributing to abiotic stress such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter, but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h - days), less well understood. In addition to protein abundance and phosphorylation changes, evidence suggests reversible protein acetylation may also be important for abiotic stress responses. Therefore, to characterize protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM Mannitol and 150 mM NaCl for 24 hours. We assessed protein phosphorylation, acetylation and changes in abundance, detecting significant changes in the status of 106, 66 and 447 proteins, respectively. Comparison with available transcriptome data from analogous treatments, indicate that transcriptome- and proteome-level changes occur in parallel. Furthermore, significant changes in abundance, phosphorylation and acetylation involve different proteins from the same networks, indicating a concerted, multifaceted regulatory approach to prolonged osmotic and/or salt stress. Lastly, our quantitative proteomic approach uncovered a new root elongation protein, Armadillo repeat protein 2 (ARO2), which exhibits a salt stress dependent phenotype. Collectively, our findings indicate dynamic protein-level changes continue to occur in plant roots 24 hours from the onset of osmotic and salt stress and that these changes differ across multiple levels of the proteome.
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