Membrane nanodomains to shape plant cellular functions and signaling

Abstract

Plasma membrane (PM) nanodomains have emerged as pivotal elements in the regulation of plant cellular functions and signal transduction. These nanoscale membrane regions, enriched in specific lipids and proteins, behave as regulatory/signaling hubs spatially and temporally coordinating critical cellular functions. In this review, we first examine the mechanisms underlying the formation and maintenance of PM nanodomains in plant cells, highlighting the roles of PM lipid composition, protein oligomerization and interactions with cytoskeletal and cell wall components. Then, we discuss how nanodomains act as organizing centers by mediating protein-protein interactions that orchestrate essential processes such as symbiosis, defense against pathogens, ion transport or hormonal and reactive oxygen species (ROS) signaling. Finally, we introduce the concept of nanoenvironments, where localized physicochemical variations are generated in the very close proximity of PM nanodomains, in response to stimuli. After decoding by a dedicated machinery likely localized in the vicinity of nanodomains, this enrichment of secondary messengers, such as ROS or Ca²⁺, would allow specific downstream cellular responses. This review provides insights into the dynamic nature of nanodomains and proposes future research to better understand their contribution to the intricate signaling networks that govern plant development and stress responses.

Keywords: lipids; nanodomain; nanoenvironment; plant; plasma membrane; protein–protein interactions; signaling.

Fig. 1

Confinement in nanodomains influences biochemical reactions by increasing the local concentration of biomolecules, such as proteins, as well as reducing their diffusion. (a) Confining proteins in a thin layer at the membrane surface or within membrane nanodomains increases their concentration. (b) Association of proteins with membranes and even more so within nanodomains drastically reduces their diffusion. V and D correspond to volume and diffusion, respectively. cyto, cytoplasm; ND, nanodomain; PM, plasma membrane.

Fig. 2

Mechanisms insuring the formation and the maintenance of plasma membrane (PM) nanodomains in plant cells. (a) Schematic representation of plant cell PM heterogeneity. The PM is highly heterogeneous and made up of a wide range of lipids and proteins. These elements can arrange into nanodomains of varying complexity. The cell wall, mostly composed of cellulose and pectin, has an important effect on protein organization in nanodomains. On the cytoplasmic side, the cytoskeleton, made up mainly of microtubules and actin microfilaments, also contributes to the stability of nanodomains. (b) Upon auxin stimulation of Arabidopsis root cells, Rho of Plant6 (ROP6) organizes in PM nanodomains. These domains contain phosphatidylserine (PS) that helps ROP6 stabilization through electrostatic interactions. In the absence of PS, as in the pss1‐3 mutant, ROP6 nanodomains are still present, but ROP6 stability in the domains is decreased (as represented by an inverted double arrow). (c) In response to flagellin, actin polymerization proteins named type‐I formin oligomerize and arrange in PM nanoclusters. This local condensation and stabilization activate formins that in turn induce actin nucleation. (d) The receptor‐like kinase FERONIA (FER) interacts with both pectins and rapid alkalinization factor (RALF) and acts as a cell growth regulator. Interestingly, upon abiotic stimulation, RALF and pectin phase separate and recruit FER together with the co‐receptor Lorelei‐Like GPI‐anchored protein 1 (LLG1) into PM nanodomains. This complex stimulates global endocytosis ensuring plant resilience under stress. WT, wild‐type.

Fig. 3

Nanodomain organization of proteins to generate regulatory/signaling hubs involved in different biological processes. (a) Symbiosis is regulated by nanodomain‐recruited protein machinery. Flotillin 4 (FLOT4)/SYMREM1 proteins act as a hub to stabilize the symbiotic receptor Lysine Motif Kianse3 (LYK3) that is involved in the perception of NOD factors. This mechanism prevents LYK3 endocytosis, thus ensuring root hair infection and the establishment of symbiosis. (b) Role of nanodomain‐organized proteins in plant immunity. In plasma membrane (PM) nanodomains, Brassinosteroid insensitive 1‐Associated receptor Kinase 1 (BAK1), Brassinosteroid Signaling Kinase 1 (BSK1) and Botrytis‐Induced Kinase 1 (BIK1) proteins interact with the flagellin receptor Flagellin‐Sensing 2 (FLS2) to initiate a phosphorylation cascade resulting in immune signaling. FLS2 nanodomains also contain Remorins (REM). FERONIA (FER) and CAR proteins physically interact and the rapid alkalinization factor 1 (RALF1)‐FER pathway induces an accumulation of CAR proteins that are recruited to the PM to stabilize the PM liquid‐ordered phase, which in turn allows the formation of the FLS2–BAK1 complex. Myosin, that allows the transport of cargoes along actin filaments, interacts with REM to recruit and stabilize BIK1 in FLS2‐containing nanodomains, which facilitates FLS2–BIK1 complex formation. Formins oligomerize and arrange in PM nanoclusters in response to flagellin, which induces their activation and further actin polymerization. This mechanism depends on the oligomerization of REM proteins that physically interact with formins. Hypersensitive Induced Reaction (HIR) are scaffolding nanodomain‐organized proteins that interact with proteins linked to immunity, although the meaning of these interactions remains to be determined. Triangles with the letter P represent phosphorylation. (c) The formation and dissociation of protein complexes in PM nanodomains regulate ion transport. The anion channel Slow Anion channel 1 Homologue 3 (SLAH3) can interact with its activating kinase CPK21 in PM nanodomains containing REM1.3, in an abscisic acid (ABA) dependent manner. In this condition, SLAH3 is fully active. In absence of ABA, the phosphatase Protein Phosphatase 2C/Abscisic acid Insensitive 1 (PP2C/ABI1) inhibits the interaction between CPK21 and SLAH3 and also probably induces a displacement of SLAH3 outside of nanodomains. This results in a reduction in SLAH3‐mediated transport. (d) Nanodomains in hormonal signaling. In rice, ABA upregulates the expression of OsREM4.1 that interacts with OsSERK1, an orthologue of Arabidopsis BAK1, to inhibit its interaction with the receptor OsBRI1. This represses OsSERK1‐catalyzed transphosphorylation of OsBRI1, thus inhibiting brassinosteroid (BR) signaling. This mechanism likely occurs in PM nanodomains. In Arabidopsis, BRI1 arranges in PM nanodomains where it interacts with BAK1, BSK1 and BIK1 to regulate BR signaling. Salicylic acid (SA) induces an accumulation of REM as well as their higher‐order oligomerization in the PM in a 14‐3‐3 protein‐dependent manner. This likely increases the liquid‐ordered phase of the PM. The SA‐mediated reorganization of nanodomains also induces a hyper‐clusterization of PIN2 at the PM resulting in an impaired root gravitropic response. (e) Reactive oxygen species (ROS) signaling in response to an osmotic signal is initiated through the cooperation of nanodomain‐organized proteins. In response to an osmotic constraint, Rho of Plant6 (ROP6) accumulates in PM nanodomains where it physically interacts with and activates Respiratory Burst Oxidase Homologue D (RBOHD) that produces superoxide ions (O₂ ⁻) in the apoplast. O₂ ⁻ ions are dismutated to hydrogen peroxide (H₂O₂) that is then likely transported across the PM by aquaporins to ensure intracellular signaling. Osmotically induced ROS production is regulated by the receptor kinase FER that stimulates phosphatidylserine (PS) PM accumulation and nanoclustering, which in turn favors ROP6 nano‐partitioning. For clarity, not all the mechanisms presented in the corresponding section of this review were illustrated in this figure.

Fig. 4

Nanoenvironments to generate signaling pathways. (a) Model for signal‐induced reactive oxygen species (ROS) nanoenvironment at the plasma membrane (PM). Upon stimulus, nicotinamide adenine dinucleotide phosphate oxidases RBHOD and F are activated leading to the production of superoxide ions (O₂ ⁻) in the apoplast that are then dismutated to H₂O₂, which in turn is likely transported inside the cell by aquaporins. We propose that this mechanism leads to a highly localized oxidation in both the apoplast and the cytoplasm at the immediate vicinity of the PM that we call H₂O₂ nanoenvironment. This H₂O₂ accumulation in the cytoplasm may cause the oxidation of molecular actors of the ROS decoding machinery that would be, for some of them, organized in clusters at the cytosolic face of the PM. This activates the downstream signaling. (b) Model for signal‐induced calcium nano/microenvironment at the PM. Following the same principle than for H₂O₂ nanoenvironment, upon stimulus, calcium channels putatively present in PM nanodomains are activated leading to a localized accumulation of calcium ion in the cytosol close to nanodomains. Molecular actors of the calcium decoding machinery that may be, for some of them, organized in PM clusters would then be activated. (c) Model for nanometric organization of enzymatic complexes to generate channeling processes. Efficiency of enzymatic reaction relies on biochemical environment and substrate availability. Here, we propose that clustered enzymatic complexes could be a way to locally enrich substrates, especially in the case of multi‐step reactions involving several enzymes, to optimize the production of certain molecules. We can imagine that the relocalization of certain enzymes among enzymatic clusters upon signals could be a way to activate the pathway.