Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase

Leene, Jelle Van; Han, Chao; Gadeyne, Astrid; Eeckhout, Dominique; Matthijs, Caroline; Cannoot, Bernard; Winne, Nancy De; Persiau, Geert; Slijke, Eveline Van De; Cotte, Brigitte van de; Stes, Elisabeth; Bel, Michiel Van; Storme, Véronique; Impens, Francis; Gevaert, Kris; Vandepoele, Klaas; Smet, Ive De; Jaeger, Geert De

doi:10.1038/s41477-019-0378-z

Cited by 221 publications

(270 citation statements)

References 49 publications

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“…This is also supported by the western blot analyses of STT7 and PSI core protein levels, both of which were reduced in TOR kinase inhibited cells (Figure e). This result is consistent with a recent phospho‐proteomic study in Arabidopsis showing STT7 and a handful of light‐harvesting proteins as interactors of TOR and, hence, potential phosphorylation targets of this kinase (Van Leene et al, ). Moreover, we also observe that TOR kinase inhibition triggered a gradual reduction in the PsaA protein leading to its near complete loss by 12 hr of inhibition, suggesting that PSI super‐complexes are adversely affected by TOR kinase inhibition.…”

Section: Discussionsupporting

confidence: 92%

“…Arabidopsis showing STT7 and a handful of light-harvesting proteins as interactors of TOR and, hence, potential phosphorylation targets of this kinase (Van Leene et al, 2019). Moreover, we also observe that TOR kinase inhibition triggered a gradual reduction in the PsaA protein leading to its near complete loss by 12 hr of inhibition, suggesting that PSI super-complexes are adversely affected by TOR kinase inhibition.…”

Section: This Results Is Consistent With a Recent Phospho-proteomic Stmentioning

confidence: 50%

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Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii

Upadhyaya

Rao

2019

Plant Direct

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While the role of TOR kinase in the chloroplast biogenesis and transcriptional regulation of photosynthesis is well documented in Arabidopsis, the functional relevance of this metabolic sensor kinase in chloroplast–mitochondria cross talk is unknown. Using Chlamydomonas reinhardtii as the model system, we demonstrate the role of TOR kinase in the regulation of chloroplast and mitochondrial functions: We show that TOR kinase inhibition impairs the maintenance of high ETR associated with PSII and low NPQ and inhibits efficient state transitions between PSII and PSI. While compromised photosynthetic functions are observed in TOR kinase inhibited cells, same conditions lead to augmentation in mitochondrial basal respiration rate by twofold and concomitantly a rise in ATP production. Interestingly, such upregulated mitochondrial functions in TOR‐inhibited cells are mediated by fragmented mitochondria via upregulating COXIIb and downregulating Hxk1 and AOX1 protein levels. We propose that TOR kinase may act as a sensor that counter‐regulates chloroplast versus mitochondrial functions in a normal C. reinhardtii cell.

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Section: Discussionsupporting

confidence: 92%

Section: This Results Is Consistent With a Recent Phospho-proteomic Stmentioning

confidence: 50%

Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii

Upadhyaya

Rao

2019

Plant Direct

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“…To further evaluate PDL, we compared the relative levels compared to the bait by which the different TPC subunits were detected using PDL using our stringent washing protocol with a one-step IgG-based pull-down (PD) protocol using the GS rhino tandem affinity purification (TAP) tag (Van Leene et al, 2019). To do this, we used the Maxquant iBAQ value, which is the result of the summed intensity values of the identified peptides, divided by the number of theoretical peptides.…”

Section: Resultsmentioning

confidence: 99%

“…TPLATE-CGSrhino pull-downs with home-made IgG beads were performed as described in (Van Leene et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

“…Protein lists significantly enriched with TPLATE can be found in Supplemental Table 5. For all TPC subunits, the values for Difference and −log(p-value) from the Perseus ttests were presented in Figure 4, in order to compare the different TPLATE PBLs.TPLATE-CGSrhino pull-downs were analyzed as described in Van Leene et al, 2019. Briefly, pull down triplicates were analyzed by LC-MSMS on Q Exactive (ThermoFisher Scientific), raw data were searched with the Mascot search engine (Matrix Science) and average Normalized Spectral Abundance Factors (NASF) for the identified proteins were compared in a t-test versus a large dataset of similar experiments consisting of non-related baits.…”

Section: Methodsmentioning

confidence: 99%

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Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems

Arora

Abel

Liu

et al. 2019

Preprint

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35Proximity-dependent biotin labelling (PDL) uses a promiscuous biotin ligase (PBL) or a 36 peroxidase fused to a protein of interest. This enables covalent biotin labelling of proteins and 37 allows subsequent capture and identification of interacting and neighbouring proteins without 38 the need for the protein complex to remain intact. To date, only few papers report on the use of 39 PDL in plants. Here we present the results of a systematic study applying a variety of PDL 40 approaches in several plant systems using various conditions and bait proteins. We show that 41TurboID is the most promiscuous variant in several plant model systems and establish protocols 42 which combine Mass Spectrometry-based analysis with harsh extraction and washing 43 conditions. We demonstrate the applicability of TurboID in capturing membrane-associated 44 protein interactomes using Lotus japonicus symbiotically active receptor kinases as test-case. 45We further benchmark the efficiency of various PBLs in comparison with one-step affinity 46 purification approaches. We identified both known as well as novel interactors of the endocytic 47Protein-protein interaction (PPI) studies often fail to capture low-affinity interactions as these 53 are usually not maintained following cell lysis, protein extraction and protein complex 54 purification. Particularly, this is the case for PPI's of integral membrane proteins because of 55 the harsh conditions during protein extraction and purification. Proximity-dependent biotin 56 labelling (PDL) on the contrary, uses covalent biotinylation of proteins that are interactors or 57 near-neighbours of a bait protein of interest in vivo (Varnaite and MacNeill, 2016). Hence, to 58 identify interactions, they do not need to remain intact during purification. Although biotin is 59 an essential cofactor for a small number of omnipresent biotin-dependent enzymes involved 60 mainly in the transfer of CO2 during HCO3 --dependent carboxylation reactions, biotinylation 61 is a relatively rare in vivo protein modification. Moreover, biotinylated proteins can be 62 selectively isolated with high affinity using streptavidin-biotin pairing. PDL, therefore, permits 63

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Shedding Light on the Role of Phosphorylation in Plant Autophagy

Liao

Zheng

et al. 2022

FEBS Letters

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Autophagy is a highly conserved quality control process that maintains cellular health by eliminating deleterious cargoes. Compared with the extensive studies in yeast and mammalian models, the molecular details and significance of post-translational modifications (PTMs) in the autophagy process in plants remain less well defined. In this review, we discuss recent progress in our understanding of phosphorylation, one of the most extensively studied PTMs, in the regulation of autophagosome biogenesis and autophagic degradation in plants. Based on the plant mass spectrometric database, we summarize the experimentally verified phosphorylation sites of the core autophagy machinery in plants. Furthermore, we put forward several approaches to test the roles of phosphorylation in the regulation of plant autophagy.

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Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase

Cited by 221 publications

References 49 publications

Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii

Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii

Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems

Shedding Light on the Role of Phosphorylation in Plant Autophagy

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