iDePP: a genetically encoded system for the inducible depletion of PI(4,5)P 2 in Arabidopsis thaliana

Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] is a low abundant lipid present at the plasma membrane of eukaryotic cells. Extensive studies in animal cells revealed the pleiotropic functions of PI(4,5)P 2 . In plant cells, PI(4,5)P 2 is involved in various cellular processes including the regulation of cell polarity and tip growth, clathrin-mediated endocytosis, polar auxin transport, actin dynamics or membrane-contact sites. To date, most studies investigating the role of PI(4,5)P 2 in plants have relied on mutants lacking enzymes responsible for PI(4,5)P 2 synthesis and degradation. However, such genetic perturbations only allow steady-state analysis of plants undergoing their life cycle in PI(4,5)P 2 deficient conditions and the corresponding mutants are likely to induce a range of non-causal (untargeted) effects driven by compensatory mechanisms. In addition, there are no small molecule inhibitors that are available in plants to specifically block the production of this lipid. Thus, there is currently no system to fine tune PI(4,5)P 2 content in plant cells. Here we report a genetically encoded and inducible synthetic system, iDePP (Inducible De pletion of P I(4,5)P 2 in P lants), that efficiently removes PI(4,5)P 2 from the plasma membrane in different organs of Arabidopsis thaliana , including root meristem, root hair and shoot apical meristem. We show that iDePP allows the inducible depletion of PI(4,5)P 2 in less than three hours. Using this strategy, we reveal that PI(4,5)P 2 is critical for cortical microtubule organization. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P 2 in given cellular or developmental responses but also to evaluate the importance of this lipid in protein localization.Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a low abundant lipid present at the plasma membrane of eukaryotic cells. Extensive studies in animal cells revealed the pleiotropic functions of PI(4,5)P2. In plant cells, PI(4,5)P2 is involved in various cellular processes including the regulation of cell polarity and tip growth, clathrin-mediated endocytosis, polar auxin transport, actin dynamics or membrane-contact sites. To date, most studies investigating the role of PI(4,5)P2 in plants have relied on mutants lacking enzymes responsible for PI(4,5)P2 synthesis and degradation. However, such genetic perturbations only allow steady-state analysis of plants undergoing their life cycle in PI(4,5)P2 deficient conditions and the corresponding mutants are likely to induce a range of non-causal (untargeted) effects driven by compensatory mechanisms. In addition, there are no small molecule inhibitors that are available in plants to specifically block the production of this lipid. Thus, there is currently no system to fine tune PI(4,5)P2 content in plant cells. Here we report a genetically encoded and inducible synthetic system, iDePP (Inducible Depletion of PI(4,5)P2 in Plants), that efficiently removes PI(4,5)P2 from the plasma membrane in different organs of Arabidopsis thaliana, including root meristem, root hair and shoot apical meristem. We show that iDePP allows the inducible depletion of PI(4,5)P2 in less than three hours. Using this strategy, we reveal that PI(4,5)P2 is critical for cortical microtubule organization. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P2 in given cellular or developmental responses but also to evaluate the importance of this lipid in protein localization

Inducible depletion of PI(4,5)P2 by the synthetic iDePP system in Arabidopsis

International audiencePI(4,5)P-2 is importantly involved in a broad array of cellular processes, including polar auxin transport, vesicle trafficking and anisotropic cell growth. An inducible system is developed in Arabidopsis to conduct tunable depletion of PI(4,5)P-2 and reveal new roles of this membrane lipid.Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P-2) is a low-abundance membrane lipid essential for plasma membrane function(1,2). In plants, mutations in phosphatidylinositol 4-phosphate (PI4P) 5-kinases (PIP5K) suggest that PI(4,5)P-2 production is involved in development, immunity and reproduction(3-5). However, phospholipid synthesis is highly intricate(6). It is thus likely that steady-state depletion of PI(4,5)P-2 triggers confounding indirect effects. Furthermore, inducible tools available in plants allow PI(4,5)P-2 to increase(7-9) but not decrease, and no PIP5K inhibitors are available. Here, we introduce iDePP (inducible depletion of PI(4,5)P-2 in plants), a system for the inducible and tunable depletion of PI(4,5)P-2 in plants in less than three hours. Using this strategy, we confirm that PI(4,5)P-2 is critical for various aspects of plant development, including root growth, root-hair elongation and organ initiation. We show that PI(4,5)P-2 is required to recruit various endocytic proteins, including AP2-mu, to the plasma membrane, and thus to regulate clathrin-mediated endocytosis. Finally, we find that inducible PI(4,5)P-2 perturbation impacts the dynamics of the actin cytoskeleton as well as microtubule anisotropy. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P-2 in given cellular or developmental responses, and also to evaluate the importance of this lipid in protein localization

Developmental control of plant Rho GTPase nano-organization by the lipid phosphatidylserine

International audienceRho GTPases are master regulators of cell signaling, but how they are regulated depending on the cellular context is unclear. Here, we show that the phospholipid phosphatidylserine acts as a 25 developmentally-controlled lipid rheostat that tunes Rho GTPase signaling in Arabidopsis. Live super-resolution single molecule imaging revealed that RHO-OF-PLANT6 (ROP6) is stabilized by phosphatidylserine into plasma membrane nanodomains, which is required for auxin signaling. Furthermore, we uncovered that the plasma membrane phosphatidylserine content varies during plant root development and that the level of phosphatidylserine modulates the quantity of ROP6 30 nanoclusters induced by auxin and hence downstream signaling, including regulation of endocytosis and gravitropism. Our work reveals that variations in phosphatidylserine levels are a physiological process that may be leveraged to regulate small GTPase signaling during development. One Sentence Summary: 35 Phosphatidylserine acts as a developmentally-controlled lipid rheostat that regulates auxin sensitivity and plant development

RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

<div><p>During biogenesis of the 40S and 60S ribosomal subunits, the pre-40S particles are exported to the cytoplasm prior to final cleavage of the 20S pre-rRNA to mature 18S rRNA. Amongst the factors involved in this maturation step, Fap7 is unusual, as it both interacts with ribosomal protein Rps14 and harbors adenylate kinase activity, a function not usually associated with ribonucleoprotein assembly. Human hFap7 also regulates Cajal body assembly and cell cycle progression via the p53–MDM2 pathway. This work presents the functional and structural characterization of the Fap7–Rps14 complex. We report that Fap7 association blocks the RNA binding surface of Rps14 and, conversely, Rps14 binding inhibits adenylate kinase activity of Fap7. In addition, the affinity of Fap7 for Rps14 is higher with bound ADP, whereas ATP hydrolysis dissociates the complex. These results suggest that Fap7 chaperones Rps14 assembly into pre-40S particles via RNA mimicry in an ATP-dependent manner. Incorporation of Rps14 by Fap7 leads to a structural rearrangement of the platform domain necessary for the pre-rRNA to acquire a cleavage competent conformation.</p></div

Fap7 ATPase activity regulates its association with Rsp14.

<p>Interaction between yFap7 and GST-Rps14 was tested by pulldown experiments. (A) Interaction of yFap7 with GST-Rps14 was tested by addition of 800 pmoles of yFap7 on GST-yRps14 beads resuspended in 1 ml of IP buffer. Effect of addition of ATP, ADP, or AMP-PNP at 1 mM final concentration in the presence of MgCl2 (5 mM) was tested. Protein associated with the beads was analyzed by Coomassie staining. For input controls, 10% of Fap7 (80 pmoles) and the same quantity of Rps14 beads used for the IP were loaded. (B) Effects of magnesium and nucleotide concentration were tested by using the same strategy in the presence of RNA (cf., D). Two quantities of nucleotides were used: 1 µmole (1 mM) or 10 nmole (10 µM). Experiments were done in the presence or in the absence of 5 mM MgCl₂. (C) Association of GST-yRps14 to RNA was assessed by a competition experiment using a different ratio between RNA and yFap7: 800 pmole Fap7 with 800 pmole RNA (1∶1), 400 pmole Fap7 with 800 pmole RNA (1∶2), and 200 pmole Fap7 with 800 pmole RNA (1∶4). Nucleotides were added at 1 mM final. Protein associated with the beads was analyzed by Coomassie staining. For input controls, 10% of Fap7 (80 pmoles) and the same quantity of Rps14 beads used for the IP were loaded. (D) Same as in C, but this time the RNA counterpart was followed on Urea-acrylamide gel after SYBR Safe staining. For input control, 80 pmole of RNA was loaded. (E) ATPase activity of yFap7 (black points) was followed by a coupled enzyme assay. Effect of addition after 10 min of MBP-yRps14 (black line), buffer (dotted dark line), or Prp43 (dotted dark grey line) was also monitored. In parallel, ATPase activity of MBP-yRps14 (light grey line) alone and the preformed complex yFap7–yRps14 (dark grey line) was also tested.</p

SAXS structure of the yeast and archaeal complexes.

<p>SAXS scattering profiles of (A) the aFap7–aRps14 complexes and (B) yeast yFap7–yRps14 complexes and (C) free yFap7. (Left) The experimental scattering profile is depicted in dashed red lines and the calculated profile from the best fit in blue lines. The residual is depicted below the scattering curve. The initial scattering profile of the initial yFap7 model is represented in green. (Right) Representation of the calculated envelope with the best fit model. Rps14 is represented in yellow and Fap7 in blue, except in (C) where yFap7 is colored blue (N terminus) to red (C terminus).</p

Structure of the aFap7–aRps14 complex.

<p>(A) Cartoon representation of the aFap7–aRps14 complex in complex with ADP. aFap7 is represented in blue/purple shades and Rps14 in orange for the CORE domain and red for the C-terminal extension. (B) Superposition of the ADP (light blue) and ATP (dark blue) aFap7 structure with the hFap7 in complex with ADP-Pi (magenta, PDB 3iil). (C) Superposition of aRps14 in complex with aFap7 (orange of the core domain, red for the Rps14-CE, and brown for the β4–α2 loop), with yRps14 in complex with the ribosome (green)</p