Plant Endocytosis Requires the ER Membrane-Anchored Proteins VAP27-1 and VAP27-3

VAP27-1 interacts with KCS6 and CER2 to facilitate the biosynthesis of very- long-chain fatty acids

Cuticular wax is primarily composed of very-long-chain fatty acids (VLCFAs) and their derivatives. It forms a critical hydrophobic layer on plant surfaces, acting as a protective barrier against biotic and abiotic stress. The biosynthesis of VLCFAs and their derivative wax occurs in endoplasmic reticulum (ER) and is subsequently transported to the plant surface. While substantial research has focused on cuticular wax biosynthesis enzymes and their transcriptional regulation, the mechanisms by which these enzymes are modulated by proteins within cytosol organelles remain poorly understood. In this study, we identified that β-ketoacyl-CoA synthase 6 (KCS6), an ER-localized rate-limiting enzyme in VLCFAs biosynthesis, also localized at ER-plasma membrane contact sites (EPCS). We further demonstrated that KCS6 and its cofactor ECERIFERUM 2 (CER2) interact with vesicle-associated membrane protein-associated protein 27-1 (VAP27-1), a key regulator of EPCS formation and stabilization. Overexpression of VAP27-1 in Arabidopsis thaliana resulted in a significant increase in almost all cuticular wax components compared to WT. Additionally, firefly luciferase complementation imaging assays (LCI) and yeast heterologous expression analysis revealed that VAP27-1 strengthens the interaction between the KCS6-CER2 complex, resulting in increased accumulation of VLCFAs. In conclusion, this study emphasized the critical role of VAP27-1 in regulating the biosynthesis of cuticular wax mediated by KCS6-CER2, providing new insights into the fine-tuning mechanisms of cuticular wax biosynthesis within the ER. Furthermore, the identification of VAP27-1 as a novel modulator of VLCFA synthases offers a potential target for enhancing plant resilience to environmental stresses.

Studying ER-membrane contact sites in plants using the optogenetic approach: Taking the LiMETER as an example

The endoplasmic reticulum (ER) links to multiple organelles through membrane contact sites (MCS), which play critical roles in signal transduction, cell homeostasis and stress response. However, studying the behaviour and functions of MCS in plants is still challenging, partially due to the lack of site-specific markers. Here, we used an optogenetic reporter, LiMETER (Light-inducible Membrane-Tethered cortical ER), to study the structure and dynamics of ER-PM contact sites (EPCS) in plants. Upon blue light activation, LiMETER is recruited to the EPCS rapidly, while this process is reversible when blue light is turned off. Compared with other EPCS reporters, LiMETER specifically and reversibly labels the contact sites, causing little side-effects on the ER structure and plant development. With its help, we re-examined the formation of ER-PM connections induced by cell-intrinsic factors or extracellular stimuli. We found that EPCSs are preferably localised at ER tubules and the edge of ER cisternae, and their number increased significantly under abiotic stress conditions. The abundance of ER and PM interaction is also developmental dependent, suggesting a direct link between ER-PM interaction, ER function and cell homeostasis. Taken together, we showed that LiMETER is an improved marker for functional and microscopical studies of ER-PM interaction, demonstrating the effectiveness of optogenetic tools in future research.

XopM, An FFAT Motif-Containing Type III Effector Protein From Xanthomonas, Suppresses MTI Responses at the Plant Plasma Membrane

Many gram-negative pathogenic bacteria use type III effector proteins (T3Es) as essential virulence factors to suppress host immunity and to cause disease. However, in many cases the molecular function of T3Es remains unknown. The plant pathogen Xanthomonas campestris pv. vesicatoria (Xcv) is the causal agent of bacterial spot disease on tomato and pepper plants and is known to translocate around 36 T3Es into its host cell, which collectively suppress plant defence and promote infection. XopM is an Xcv core T3E with unknown function that has no similarity to any other known protein. We found that XopM interacts with vesicle-associated membrane protein (VAMP)-associated proteins (VAPs) in an isoform-specific manner. The endoplasmic reticulum (ER) integral membrane protein VAP is a common component of membrane contact sites involved in both tethering and lipid transfer by binding directly to proteins containing an FFAT (two phenylalanines [FF] in an acidic tract [AT]) motif. Sequence analyses revealed that XopM displays two FFAT motifs that cooperatively mediated the interaction of XopM with VAP. When expressed in plants, XopM supported growth of a nonpathogenic bacterial strain and dampened the production of reactive oxygen species, indicating its ability to suppress plant immunity. Further analyses revealed that the interaction with VAP and the ability to suppress microbe-associated molecular pattern-triggered immunity (MTI) are structurally and functionally separable, although XopM requires localisation to the host membrane system for full MTI suppression activity. We discuss a working model in which XopM uses FFAT motifs to target the membrane to interfere with early MTI responses.

ER-associated VAP27-1 and VAP27-3 proteins functionally link the lipid-binding ORP2A at the ER-chloroplast contact sites

The plant endoplasmic reticulum (ER) contacts heterotypic membranes at membrane contact sites (MCSs) through largely undefined mechanisms. For instance, despite the well-established and essential role of the plant ER-chloroplast interactions for lipid biosynthesis, and the reported existence of physical contacts between these organelles, almost nothing is known about the ER-chloroplast MCS identity. Here we show that the Arabidopsis ER membrane-associated VAP27 proteins and the lipid-binding protein ORP2A define a functional complex at the ER-chloroplast MCSs. Specifically, through in vivo and in vitro association assays, we found that VAP27 proteins interact with the outer envelope membrane (OEM) of chloroplasts, where they bind to ORP2A. Through lipidomic analyses, we established that VAP27 proteins and ORP2A directly interact with the chloroplast OEM monogalactosyldiacylglycerol (MGDG), and we demonstrated that the loss of the VAP27-ORP2A complex is accompanied by subtle changes in the acyl composition of MGDG and PG. We also found that ORP2A interacts with phytosterols and established that the loss of the VAP27-ORP2A complex alters sterol levels in chloroplasts. We propose that, by interacting directly with OEM lipids, the VAP27-ORP2A complex defines plant-unique MCSs that bridge ER and chloroplasts and are involved in chloroplast lipid homeostasis.

Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis

Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana. Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.

The VAMP-associated protein VAP27-1 plays a crucial role in plant resistance to ER stress by modulating ER-PM contact architecture in Arabidopsis

The endoplasmic reticulum (ER) and the plasma membrane (PM) form ER-PM contact sites (EPCSs) that allow the ER and PM to exchange materials and information. Stress-induced disruption of protein folding triggers ER stress, and the cell initiates the unfolded protein response (UPR) to resist the stress. However, whether EPCSs play a role in ER stress in plants remains unclear. VESICLE-ASSOCIATED MEMBRANE PROTEIN (VAMP)-ASSOCIATED PROTEIN 27-1 (VAP27-1) functions in EPCS tethering and is encoded by a family of 10 genes (VAP27-1-10) in Arabidopsis thaliana. Here, we used CRISPR-Cas9-mediated genome editing to obtain a homozygous vap27-1 vap27-3 vap27-4 (vap27-1/3/4) triple mutant lacking three of the key VAP27 family members in Arabidopsis. The vap27-1/3/4 mutant exhibits defects in ER-PM connectivity and EPCS architecture, as well as excessive UPR signaling. We further showed that relocation of VAP27-1 to the PM mediates specific VAP27-1-related EPCS remodeling and expansion under ER stress. Moreover, the spatiotemporal dynamics of VAP27-1 at the PM increase ER-PM connectivity and enhance Arabidopsis resistance to ER stress. In addition, we revealed an important role for intracellular calcium homeostasis in the regulation of UPR signaling. Taken together, these results broaden our understanding of the molecular and cellular mechanisms of ER stress and UPR signaling in plants, providing additional clues for improving plant broad-spectrum resistance to different stresses.

Protein interactomes for plant lipid biosynthesis and their biotechnological applications

Plant lipids have essential biological roles in plant development and stress responses through their functions in cell membrane formation, energy storage and signalling. Vegetable oil, which is composed mainly of the storage lipid triacylglycerol, also has important applications in food, biofuel and oleochemical industries. Lipid biosynthesis occurs in multiple subcellular compartments and involves the coordinated action of various pathways. Although biochemical and molecular biology research over the last few decades has identified many proteins associated with lipid metabolism, our current understanding of the dynamic protein interactomes involved in lipid biosynthesis, modification and channelling is limited. This review examines advances in the identification and characterization of protein interactomes involved in plant lipid biosynthesis, with a focus on protein complexes consisting of different subunits for sequential reactions such as those in fatty acid biosynthesis and modification, as well as transient or dynamic interactomes formed from enzymes in cooperative pathways such as assemblies of membrane-bound enzymes for triacylglycerol biosynthesis. We also showcase a selection of representative protein interactome structures predicted using AlphaFold2, and discuss current and prospective strategies involving the use of interactome knowledge in plant lipid biotechnology. Finally, unresolved questions in this research area and possible approaches to address them are also discussed.

Endoplasmic reticulum membrane contact sites: cross-talk between membrane-bound organelles in plant cells

Eukaryotic cells contain organelles surrounded by monolayer or bilayer membranes. Organelles take part in highly dynamic and organized interactions at membrane contact sites, which play vital roles during development and response to stress. The endoplasmic reticulum extends throughout the cell and acts as an architectural scaffold to maintain the spatial distribution of other membrane-bound organelles. In this review, we highlight the structural organization, dynamics, and physiological functions of membrane contact sites between the endoplasmic reticulum and various membrane-bound organelles, especially recent advances in plants. We briefly introduce how the combined use of dynamic and static imaging techniques can enable monitoring of the cross-talk between organelles via membrane contact sites. Finally, we discuss future directions for research fields related to membrane contact.

Dynamic Regulation of Lipid Droplet Biogenesis in Plant Cells and Proteins Involved in the Process

Lipid droplets (LDs) are ubiquitous, dynamic organelles found in almost all organisms, including animals, protists, plants and prokaryotes. The cell biology of LDs, especially biogenesis, has attracted increasing attention in recent decades because of their important role in cellular lipid metabolism and other newly identified processes. Emerging evidence suggests that LD biogenesis is a highly coordinated and stepwise process in animals and yeasts, occurring at specific sites of the endoplasmic reticulum (ER) that are defined by both evolutionarily conserved and organism- and cell type-specific LD lipids and proteins. In plants, understanding of the mechanistic details of LD formation is elusive as many questions remain. In some ways LD biogenesis differs between plants and animals. Several homologous proteins involved in the regulation of animal LD formation in plants have been identified. We try to describe how these proteins are synthesized, transported to the ER and specifically targeted to LD, and how these proteins participate in the regulation of LD biogenesis. Here, we review current work on the molecular processes that control LD formation in plant cells and highlight the proteins that govern this process, hoping to provide useful clues for future research.

Keep in contact: multiple roles of endoplasmic reticulum-membrane contact sites and the organelle interaction network in plants

Functional regulation and structural maintenance of the different organelles in plants contribute directly to plant development, reproduction and stress responses. To ensure these activities take place effectively, cells have evolved an interconnected network amongst various subcellular compartments, regulating rapid signal transduction and the exchange of biomaterial. Many proteins that regulate membrane connections have recently been identified in plants, and this is the first step in elucidating both the mechanism and function of these connections. Amongst all organelles, the endoplasmic reticulum is the key structure, which likely links most of the different subcellular compartments through membrane contact sites (MCS) and the ER-PM contact sites (EPCS) have been the most intensely studied in plants. However, the molecular composition and function of plant MCS are being found to be different from other eukaryotic systems. In this article, we will summarise the most recent advances in this field and discuss the mechanism and biological relevance of these essential links in plants.

Arabidopsis ORP2A mediates ER-autophagosomal membrane contact sites and regulates PI3P in plant autophagy

Autophagy is an intracellular degradation system for cytoplasmic constituents which is mediated by the formation of a double-membrane organelle termed the autophagosome and its subsequent fusion with the lysosome/vacuole. The formation of the autophagosome requires membrane from the endoplasmic reticulum (ER) and is tightly regulated by a series of autophagy-related (ATG) proteins and lipids. However, how the ER contacts autophagosomes and regulates autophagy remain elusive in plants. In this study, we identified and demonstrated the roles of Arabidopsis oxysterol-binding protein-related protein 2A (ORP2A) in mediating ER-autophagosomal membrane contacts and autophagosome biogenesis. We showed that ORP2A localizes to both ER-plasma membrane contact sites (EPCSs) and autophagosomes, and that ORP2A interacts with both the ER-localized VAMP-associated protein (VAP) 27-1 and ATG8e on the autophagosomes to mediate the membrane contact sites (MCSs). In ORP2A artificial microRNA knockdown (KD) plants, seedlings display retarded growth and impaired autophagy levels. Both ATG1a and ATG8e accumulated and associated with the ER membrane in ORP2A KD lines. Moreover, ORP2A binds multiple phospholipids and shows colocalization with phosphatidylinositol 3-phosphate (PI3P) in vivo. Taken together, ORP2A mediates ER-autophagosomal MCSs and regulates autophagy through PI3P redistribution.

TraB family proteins are components of ER-mitochondrial contact sites and regulate ER-mitochondrial interactions and mitophagy

ER-mitochondrial contact sites (EMCSs) are important for mitochondrial function. Here, we have identified a EMCS complex, comprising a family of uncharacterised mitochondrial outer membrane proteins, TRB1, TRB2, and the ER protein, VAP27-1. In Arabidopsis, there are three TraB family isoforms and the trb1/trb2 double mutant exhibits abnormal mitochondrial morphology, strong starch accumulation, and impaired energy metabolism, indicating that these proteins are essential for normal mitochondrial function. Moreover, TRB1 and TRB2 proteins also interact with ATG8 in order to regulate mitochondrial degradation (mitophagy). The turnover of depolarised mitochondria is significantly reduced in both trb1/trb2 and VAP27 mutants (vap27-1,3,4,6) under mitochondrial stress conditions, with an increased population of dysfunctional mitochondria present in the cytoplasm. Consequently, plant recovery after stress is significantly perturbed, suggesting that TRB1-regulated mitophagy and ER-mitochondrial interaction are two closely related processes. Taken together, we ascribe a dual role to TraB family proteins which are component of the EMCS complex in eukaryotes, regulating both interaction of the mitochondria to the ER and mitophagy.

Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants

Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.

Advances in structural, spatial, and temporal mechanics of plant endocytosis

Endocytic trafficking underlies processes essential for plant growth and development, including the perception of and response to abiotic and extracellular stimuli, post-Golgi and exocytic trafficking, and cytokinesis. Protein adaptors and regulatory factors of clathrin-mediated endocytosis that contribute to the formation of endocytic clathrin-coated vesicles are evolutionarily conserved. Yet, work of the last ten years has identified differences between the endocytic mechanisms of plants and Opisthokonts involving the endocytic adaptor TPLATE complex, the requirement of actin during CME, and the function of clathrin-independent endocytosis in the uptake of plant-specific plasma membrane proteins. Here, we review clathrin-mediated and -independent pathways in plants and describe recent advances enabled by new proteomic and imaging methods, and conditional perturbation of endocytosis. In addition, we summarize the formation and trafficking of clathrin-coated vesicles based on temporal and structural data garnered from high-resolution quantitative imaging studies. Finally, new information about the cross-talk between endocytosis and other endomembrane trafficking pathways and organelles will also be discussed.

Membrane contact sites and cytoskeleton-membrane interactions in autophagy

In Eukaryotes, organelle interactions occur at specialised contact sites between organelle membranes. Contact sites are regulated by specialised tethering proteins, which bring organelle membranes into close proximity, and facilitate functional crosstalk between compartments. While contact site proteins are well characterised in mammals and yeast, the regulators of plant contact site formation are only now beginning to emerge. Having unique subcellular structures, plants must also utilise unique mechanisms of organelle interaction to regulate plant‐specific functions. The recently characterised NETWORKED proteins are the first dedicated family of plant‐specific contact site proteins. Research into the NET proteins and their interacting partners continues to uncover plant‐specific mechanisms of organelle interaction and the importance of these organelle contacts to plant life. Moreover, it is becoming increasingly apparent that organelle interactions are fundamental to autophagy in plants. Here, we will present recent developments in our understanding of the mechanisms of plant organelle interactions, their functions, and emerging roles in autophagy.

Arabidopsis synaptotagmin 1 mediates lipid transport in a lipid composition-dependent manner

The endoplasmic reticulum (ER) - plasma membrane (PM) contact sites (EPCSs) are structurally conserved in eukaryotes. The Arabidopsis ER-anchored synaptotagmin 1 (SYT1), enriched in EPCSs, plays a critical role in plant abiotic stress tolerance. It has become clear that SYT1 interacts with PM to mediate ER-PM connectivity. However, whether SYT1 performs additional functions at EPCSs remains unknown. Here, we reported that SYT1 efficiently transfers phospholipids between membranes. The lipid transfer activity of SYT1 is highly dependent on PI(4,5)P₂ , a signal lipid accumulated at the PM under abiotic stress. Mechanically, while SYT1 transfers lipids fundamentally through the synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain, the efficient lipid transport requires the C2A domain-mediated membrane tethering. Interestingly, we observed that Ca²⁺ could stimulate SYT1-mediated lipid transport. In addition to PI(4,5)P₂ , the Ca²⁺ activation requires the phosphatidylserine, another negatively charged lipid on the opposed membrane. Together, our studies identified Arabidopsis SYT1 as a lipid transfer protein at EPCSs and demonstrated it takes conserved as well as divergent mechanisms with other extend-synaptotagmins. The critical role of lipid composition and Ca²⁺ reveals SYT1-mediated lipid transport is highly regulated by signals in response to abiotic stresses.

Low-Density Lipoprotein Internalization, Degradation and Receptor Recycling Along Membrane Contact Sites

Low-density lipoprotein (LDL) internalization, degradation, and receptor recycling is a fundamental process underlying hypercholesterolemia, a high blood cholesterol concentration, affecting more than 40% of the western population. Membrane contact sites influence endosomal dynamics, plasma membrane lipid composition, and cellular cholesterol distribution. However, if we focus on LDL-related trafficking events we mostly discuss them in an isolated fashion, without cellular context. It is our goal to change this perspective and to highlight that all steps from LDL internalization to receptor recycling are likely associated with dynamic membrane contact sites in which endosomes engage with the endoplasmic reticulum and other organelles.

A glossary of plant cell structures: Current insights and future questions

In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

NbSOBIR1 Partitions Into Plasma Membrane Microdomains and Binds ER-Localized NbRLP1

The receptor-like kinase Suppressor of BIR1 (SOBIR1) binds various receptor-like proteins (RLPs) that perceive microbe-associated molecular patterns (MAMPs) at the plasma membrane, which is thought to activate plant pattern-triggered immunity (PTI) against pathogen invasion. Despite its potentially crucial role, how SOBIR1 transmits immune signaling to ultimately elicit PTI remains largely unresolved. Herein, we report that a Nicotiana benthamiana gene NbRLP1, like NbSOBIR1, was highly induced upon Phytophthora parasitica infection. Intriguingly, NbRLP1 is characterized as a receptor-like protein localizing to the endoplasmic reticulum (ER) membrane rather than the plasma membrane. Using bimolecular fluorescence complementation and affinity purification assays, we established that NbRLP1 is likely to associate with NbSOBIR1 through the contact between the ER and plasma membrane. We further found that NbSOBIR1 at the plasma membrane partitions into mobile microdomains that undergo frequent lateral movement and internalization. Remarkably, the dynamics of NbSOBIR1 microdomain is coupled to the remodeling of the cortical ER network. When NbSOBIR1 microdomains were induced by the P. parasitica MAMP ParA1, tobacco cells overexpressing NbRLP1 accelerated NbSOBIR1 internalization. Overexpressing NbRLP1 in tobacco further exaggerated the ParA1-induced necrosis. Together, these findings have prompted us to propose that ER and the ER-localized NbRLP1 may play a role in transmitting plant immune signals by regulating NbSOBIR1 internalization.

Plant cytoskeletons and the endoplasmic reticulum network organization

Plant endoplasmic reticulum (ER) remodelling is likely to be important for its function in targeted protein secretion, organelle interaction and signal exchange. It has been known for decades that the structure and movement of the ER network is mainly regulated by the actin cytoskeleton through actin motor proteins and membrane-cytoskeleton adaptors. Recent discoveries also revealed alternative pathways that influence ER movement, through a microtubule-based machinery. Therefore, plants utilize both cytoskeletal components to drive ER dynamics, a process that is likely to be dependent on the cell type and the developmental stages. On the other hand, the ER membrane also has a direct effect towards the organization of the cytoskeletal network and disrupting the tethering factors at the ER-PM interface also rearranges the cytoskeletal structure. However, the influence of the ER network on the cytoskeleton organization has not been studied. In this review, we will provide an overview of the ER-cytoskeleton network in plants, and discuss the most recent discoveries in the field.

Geometry and cellular function of organelle membrane interfaces

A vast majority of cellular processes take root at the surface of biological membranes. By providing a two-dimensional platform with limited diffusion, membranes are, by nature, perfect devices to concentrate signaling and metabolic components. As such, membranes often act as "key processors" of cellular information. Biological membranes are highly dynamic and deformable and can be shaped into curved, tubular, or flat conformations, resulting in differentiated biophysical properties. At membrane contact sites, membranes from adjacent organelles come together into a unique 3D configuration, forming functionally distinct microdomains, which facilitate spatially regulated functions, such as organelle communication. Here, we describe the diversity of geometries of contact site-forming membranes in different eukaryotic organisms and explore the emerging notion that their shape, 3D architecture, and remodeling jointly define their cellular activity. The review also provides selected examples highlighting changes in membrane contact site architecture acting as rapid and local responses to cellular perturbations, and summarizes our current understanding of how those structural changes confer functional specificity to those cellular territories.

Anionic phospholipid gradients: an uncharacterized frontier of the plant endomembrane network

Anionic phospholipids include phosphatidic acid (PA), phosphatidylserine (PS), phosphatidylinositol (PI), and its phosphorylated derivatives the phosphoinositides (e.g. phosphatidylinositol-4-phosphate [PI4P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]). Although anionic phospholipids are low-abundant lipids, they are particularly important for membrane functions. In particular, anionic lipids act as biochemical and biophysical landmarks that contribute to the establishment of membrane identity, signaling activities, and compartment morphodynamics. Each anionic lipid accumulates in different endomembranes according to a unique subcellular pattern, where they locally provide docking platforms for proteins. As such, they are mostly believed to act in the compartments in which they accumulate. However, mounting evidence throughout eukaryotes suggests that anionic lipids are not as compartment-specific as initially thought and that they are instead organized as concentration gradients across different organelles. In this update, we review the evidence for the existence of anionic lipid gradients in plants. We then discuss the possible implication of these gradients in lipid dynamics and homeostasis, and also in coordinating subcellular activities. Finally, we introduce the notion that anionic lipid gradients at the cellular scale may translate into gradients at the tissue level, which could have implications for plant development.

Maintaining the structural and functional homeostasis of the plant endoplasmic reticulum

The endoplasmic reticulum (ER) is a ubiquitous organelle that is vital to the life of eukaryotic cells. It synthesizes essential lipids and proteins and initiates the glycosylation of intracellular and surface proteins. As such, the ER is necessary for cell growth and communication with the external environment. The ER is also a highly dynamic organelle, whose structure is continuously remodeled through an interaction with the cytoskeleton and the action of specialized ER shapers. Recent and significant advances in ER studies have brought to light conserved and unique features underlying the structure and function of this organelle in plant cells. In this review, exciting developments in the understanding of the mechanisms for plant ER structural and functional homeostasis, particularly those that underpin ER network architecture and ER degradation, are presented and discussed.

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees

BACKGROUND

Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.

RESULTS

In this study, we report on transgenic hybrid aspen (Populus tremula × tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20-44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26-50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.

CONCLUSIONS

The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.

Endoplasmic Reticulum-Plasma Membrane Contact Sites: Regulators, Mechanisms, and Physiological Functions

The endoplasmic reticulum (ER) forms direct membrane contact sites with the plasma membrane (PM) in eukaryotic cells. These ER-PM contact sites play essential roles in lipid homeostasis, ion dynamics, and cell signaling, which are carried out by protein-protein or protein-lipid interactions. Distinct tethering factors dynamically control the architecture of ER-PM junctions in response to intracellular signals or external stimuli. The physiological roles of ER-PM contact sites are dependent on a variety of regulators that individually or cooperatively perform functions in diverse cellular processes. This review focuses on proteins functioning at ER-PM contact sites and highlights the recent progress in their mechanisms and physiological roles.

The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor

Stems of bioenergy sorghum (Sorghum bicolor L. Moench.), a drought-tolerant C4 grass, contain up to 50 nodes and internodes of varying length that span 4-5 m and account for approximately 84% of harvested biomass. Stem internode growth impacts plant height and biomass accumulation and is regulated by brassinosteroid signaling, auxin transport, and gibberellin biosynthesis. In addition, an AGCVIII kinase (Dw2) regulates sorghum stem internode growth, but the underlying mechanism and signaling network are unknown. Here we provide evidence that mutation of Dw2 reduces cell proliferation in internode intercalary meristems, inhibits endocytosis, and alters the distribution of heteroxylan and mixed linkage glucan in cell walls. Phosphoproteomic analysis showed that Dw2 signaling influences the phosphorylation of proteins involved in lipid signaling (PLDδ), endomembrane trafficking, hormone, light, and receptor signaling, and photosynthesis. Together, our results show that Dw2 modulates endomembrane function and cell division during sorghum internode growth, providing insight into the regulation of monocot stem development.

Plant endomembranes and cytoskeleton: moving targets in immunity

Pathogens attack plant cells to divert resources toward pathogen proliferation. To resist pathogens, plant cells rely on multilayered signaling pathways that hinge upon the secretory pathway for the synthesis and trafficking of pathogen sensors and defense molecules. In recent years, significant strides have been made in the understanding of the functional relationship between pathogen response and membrane traffic. Here we discuss how the plant cytoskeleton and endomembranes are targeted by pathogen effectors and highlight an emerging role of membrane contact sites in biotic stress responses.

Plasma membrane aquaporins interact with the endoplasmic reticulum resident VAP27 proteins at ER-PM contact sites and endocytic structures

Plasma membrane (PM) intrinsic proteins (PIPs) are aquaporins facilitating the diffusion of water and small solutes. The functional importance of the PM organisation of PIPs in the interaction with other cellular structures is not completely understood. We performed a pull-down assay using maize (Zea mays) suspension cells expressing YFP-ZmPIP2;5 and validated the protein interactions by yeast split-ubiquitin and bimolecular fluorescence complementation assays. We expressed interacting proteins tagged with fluorescent proteins in Nicotiana benthamiana leaves and performed water transport assays in oocytes. Finally, a phylogenetic analysis was conducted. The PM-located ZmPIP2;5 physically interacts with the endoplasmic reticulum (ER) resident ZmVAP27-1. This interaction requires the ZmVAP27-1 cytoplasmic major sperm domain. ZmPIP2;5 and ZmVAP27-1 localise in close vicinity in ER-PM contact sites (EPCSs) and endocytic structures upon exposure to salt stress conditions. This interaction enhances PM water permeability in oocytes. Similarly, the Arabidopsis ZmVAP27-1 paralogue, AtVAP27-1, interacts with the AtPIP2;7 aquaporin. Together, these data indicate that the PIP2-VAP27 interaction in EPCSs is evolutionarily conserved, and suggest that VAP27 might stabilise the aquaporins and guide their endocytosis in response to salt stress.

The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions

The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.

Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis

Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and intercellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how CME functions in planta To facilitate the direct quantitative study of plant CME, we review current routinely used methods and present refined, standardized quantitative imaging protocols that allow the detailed characterization of CME at multiple scales in plant tissues. These protocols include: (1) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultrastructure of clathrin-coated vesicles; (2) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (3) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (4) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.This article has an associated First Person interview with the first author of the paper.

Sticking With It: ER-PM Membrane Contact Sites as a Coordinating Nexus for Regulating Lipids and Proteins at the Cell Cortex

Membrane contact sites between the cortical endoplasmic reticulum (ER) and the plasma membrane (PM) provide a direct conduit for small molecule transfer and signaling between the two largest membranes of the cell. Contact is established through ER integral membrane proteins that physically tether the two membranes together, though the general mechanism is remarkably non-specific given the diversity of different tethering proteins. Primary tethers including VAMP-associated proteins (VAPs), Anoctamin/TMEM16/Ist2p homologs, and extended synaptotagmins (E-Syts), are largely conserved in most eukaryotes and are both necessary and sufficient for establishing ER-PM association. In addition, other species-specific ER-PM tether proteins impart unique functional attributes to both membranes at the cell cortex. This review distils recent functional and structural findings about conserved and species-specific tethers that form ER-PM contact sites, with an emphasis on their roles in the coordinate regulation of lipid metabolism, cellular structure, and responses to membrane stress.

Light microscopy of the endoplasmic reticulum-membrane contact sites in plants

The existence of membrane contact sites (MCS) has been reported in different systems in the past decade, and their importance has been recognised by the cell biology community. Amongst all endomembrane structures, the endoplasmic reticulum (ER) plays vital roles in organising the organelle interaction network with the plasma membrane (PM), Golgi bodies, mitochondria, plastids, endosomes and autophagosomes. A number of methods have been used to study the establishment and functions of these interactions, among them, light microscopy appears to be one of the most effective approaches. Here, we present an overview of the discovery of ER-PM contact sites, and highlight the latest developments in light microscopical-based techniques that can be used for their study.

Functions of Anionic Lipids in Plants

Anionic phospholipids, which include phosphatidic acid, phosphatidylserine, and phosphoinositides, represent a small percentage of membrane lipids. They are able to modulate the physical properties of membranes, such as their surface charges, curvature, or clustering of proteins. Moreover, by mediating interactions with numerous membrane-associated proteins, they are key components in the establishment of organelle identity and dynamics. Finally, anionic lipids also act as signaling molecules, as they are rapidly produced or interconverted by a set of dedicated enzymes. As such, anionic lipids are major regulators of many fundamental cellular processes, including cell signaling, cell division, membrane trafficking, cell growth, and gene expression. In this review, we describe the functions of anionic lipids from a cellular perspective. Using the localization of each anionic lipid and its related metabolic enzymes as starting points, we summarize their roles within the different compartments of the endomembrane system and address their associated developmental and physiological consequences.

Membrane Contact Sites and Organelles Interaction in Plant Autophagy

Autophagy is an intracellular trafficking and degradation system for recycling of damaged organelles, mis-folded proteins and cytoplasmic constituents. Autophagy can be divided into non-selective autophagy and selective autophagy according to the cargo specification. Key to the process is the timely formation of the autophagosome, a double-membrane structure which is responsible for the delivery of damaged organelles and proteins to lysosomes or vacuoles for their turnover. Autophagosomes are formed by the closure of cup-shaped phagophore which depends on the proper communication with membrane contributors. The endoplasmic reticulum (ER) is a major membrane source for autophagosome biogenesis whereby the ER connects with phagophore through membrane contact sites (MCSs). MCSs are closely apposed domains between organelle membranes where lipids and signals are exchanged. Lipid transfer proteins (LTPs) are a large family of proteins including Oxysterol-binding protein related proteins (ORP) which can be found at MCSs and mediate lipid transfer in mammals and yeast. In addition, interaction between autophagosomes and other organelles can also be detected in selective autophagy for selection and degradation of various damaged organelles. Selective autophagy is mediated by the binding of a receptor or an adaptor between a cargo and an autophagosome. Here we summarize what we know about the MCS between autophagosomes and other organelles in eukaryotes. We then discuss progress in our understanding about ORPs at MCSs in plants and the underlying mechanisms of selective autophagy in plants with a focus on receptors/adaptors that are involved in the interaction of the autophagosome with other cytoplasmic constituents, including the Neighbor of BRCA1 gene 1 (NBR1), ATG8-interacting protein 1 (ATI1), Regulatory Particle Non-ATPase 10 (RPN10), and Dominant Suppressor of KAR2 (DSK2).

The mysterious life of the plant trans-Golgi network: advances and tools to understand it better

By being at the interface of the exocytic and endocytic pathways, the plant trans-Golgi network (TGN) is a multitasking and highly diversified organelle. Despite governing vital cellular processes, the TGN remains one of the most uncharacterized organelle of plant cells. In this review, we highlight recent studies that have contributed new insights and to the generation of markers needed to answer several important questions on the plant TGN. Several drugs specifically affecting proteins critical for the TGN functions have been extremely useful for the identification of mutants of the TGN in the pursuit to understand how the morphology and the function of this organelle are controlled. In addition to these chemical tools, we review emerging microscopy techniques that help visualize the TGN at an unpreceded resolution and appreciate the heterogeneity and dynamics of this organelle in plant cells.

Analysis of Endoplasmic Reticulum-Endosome Association Using Live-Cell Imaging in Plant Cells

The endoplasmic reticulum (ER) is one of the most abundant endomembrane compartments and is in close association with most of the other organelles. In mammalian and yeast cells, the physiological roles and the molecular machineries underlying such association have only recently begun to emerge. In plant cells, recent live-cell confocal imaging and electron microscopy studies have established that endosomes are associated with the ER [1]. Here, we describe confocal imaging methods and software to analyze ER-endosome association in plant cells.

CesA6 and PGIP2 Endocytosis Involves Different Subpopulations of TGN-Related Endosomes

Endocytosis is an essential process for the internalization of plasma membrane proteins, lipids and extracellular molecules into the cells. The mechanisms underlying endocytosis in plant cells involve several endosomal organelles whose origins and specific role needs still to be clarified. In this study we compare the internalization events of a GFP-tagged polygalacturonase-inhibiting protein of Phaseolus vulgaris (PGIP2-GFP) to that of a GFP-tagged subunit of cellulose synthase complex of Arabidopsis thaliana (secGFP-CesA6). Through the use of endocytic traffic chemical inhibitors (tyrphostin A23, salicylic acid, wortmannin, concanamycin A, Sortin 2, Endosidin 5 and BFA) it was evidenced that the two protein fusions were endocytosed through distinct endosomes with different mechanisms. PGIP2-GFP endocytosis is specifically sensitive to tyrphostin A23, salicylic acid and Sortin 2; furthermore, SYP51, a tSNARE with interfering effect on late steps of vacuolar traffic, affects its arrival in the central vacuole. SecGFP-CesA6, specifically sensitive to Endosidin 5, likely reaches the plasma membrane passing through the trans Golgi network (TGN), since the BFA treatment leads to the formation of BFA bodies, compatible with the aggregation of TGNs. BFA treatments determine the accumulation and tethering of the intracellular compartments labeled by both proteins, but PGIP2-GFP aggregated compartments overlap with those labeled by the endocytic dye FM4-64 while secGFP-CesA6 fills different compartments. Furthermore, secGFP-CesA6 co-localization with RFP-NIP1.1, marker of the direct ER-to-Vacuole traffic, in small compartments separated from ER suggests that secGFP-CesA6 is sorted through TGNs in which the direct contribution from the ER plays an important role. All together the data indicate the existence of a heterogeneous population of Golgi-independent TGNs.

Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery

The Arabidopsis EH proteins (AtEH1/Pan1 and AtEH2/Pan1) are components of the endocytic TPLATE complex (TPC) which is essential for endocytosis. Both proteins are homologues of the yeast ARP2/3 complex activator, Pan1p. Here, we show that these proteins are also involved in actin cytoskeleton regulated autophagy. Both AtEH/Pan1 proteins localise to the plasma membrane and autophagosomes. Upon induction of autophagy, AtEH/Pan1 proteins recruit TPC and AP-2 subunits, clathrin, actin and ARP2/3 proteins to autophagosomes. Increased expression of AtEH/Pan1 proteins boosts autophagosome formation, suggesting independent and redundant pathways for actin-mediated autophagy in plants. Moreover, AtEHs/Pan1-regulated autophagosomes associate with ER-PM contact sites (EPCS) where AtEH1/Pan1 interacts with VAP27-1. Knock-down expression of either AtEH1/Pan1 or VAP27-1 makes plants more susceptible to nutrient depleted conditions, indicating that the autophagy pathway is perturbed. In conclusion, we identify the existence of an autophagy-dependent pathway in plants to degrade endocytic components, starting at the EPCS through the interaction among AtEH/Pan1, actin cytoskeleton and the EPCS resident protein VAP27-1.

Arabidopsis EH/Pan1 proteins are part of the TPLATE complex (TPC) that is required for endocytosis in plants. Here, the authors show AtEH/Pan1 proteins also act in actin-mediated autophagy, by interacting with VAP27-1 at ER-PM contact sites and recruiting TPLATE and AP-2 complex subunits, clathrin and ARP2/3/ proteins to autophagosomes.

Manipulating Endoplasmic Reticulum-Plasma Membrane Tethering in Plants Through Fluorescent Protein Complementation

The bimolecular fluorescence complementation (BiFC) assay has been widely used to examine interactions between integral and peripheral proteins within putative plasma membrane (PM) microdomains. In the course of using BiFC assays to examine the co-localization of plasma membrane (PM) targeted receptor-like kinases (RLKs), such as FLS2, with PM micro-domain proteins such as remorins, we unexpectedly observed heterogeneous distribution patterns of fluorescence on the PM of Nicotiana benthamiana leaf cortical cells. These patterns appeared to co-localize with the endoplasmic reticulum (ER) and with ER-PM contact sites, and closely resembled patterns caused by over-expression of the ER-PM tether protein Synaptotagmin1 (SYT1). Using domain swap experiments with SYT1, we inferred that non-specific dimerization between FLS2-VenusN and VenusC-StRem1.3 could create artificial ER-PM tether proteins analogous to SYT1. The same patterns of ER-PM tethering were produced when a representative set of integral membrane proteins were partnered in BiFC complexes with PM-targeted peripheral membrane proteins, including PtdIns(4)P-binding proteins. We inferred that spontaneous formation of mature fluorescent proteins caused the BiFC complexes to trap the integral membrane proteins in the ER during delivery to the PM, producing a PM-ER tether. This phenomenon could be a useful tool to deliberately manipulate ER-PM tethering or to test protein membrane localization. However, this study also highlights the risk of using the BiFC assay to study membrane protein interactions in plants, due to the possibility of alterations in cellular structures and membrane organization, or misinterpretation of protein-protein interactions. A number of published studies using this approach may therefore need to be revisited.

Ionic stress enhances ER-PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis

The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)-plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER-PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER-PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P₂] at the PM as a molecular signal associated with the ER-PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER-PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER-PM connectivity in plants.

Dynamic regulation of plasmodesmatal permeability and its application to horticultural research

Effective cell-to-cell communication allows plants to fine-tune their developmental processes in accordance with the prevailing environmental stimuli. Plasmodesmata (PD) are intercellular channels that span the plant cell wall and serve as cytoplasmic bridges to facilitate efficient exchange of signaling molecules between neighboring cells. The identification of PD-associated proteins and the subsequent elucidation of the regulation of PD structure have provided vital insights into the role of PD architecture in enforcing crucial cellular processes, including callose deposition, ER-Golgi-based secretion, cytoskeleton dynamics, membrane lipid raft organization, chloroplast metabolism, and cell wall formation. In this review, we summarize the emerging discoveries from recent studies that elucidated the regulatory mechanisms involved in PD biogenesis and the dynamics of PD opening-closure. Retrospectively, PD-mediated cell-to-cell communication has been implicated in diverse cellular and physiological processes that are fundamental for the development of horticultural plants. The potential application of PD biotechnological engineering represents a powerful approach for improving agronomic traits in horticultural crops in the future.

TGNap1 is required for microtubule-dependent homeostasis of a subpopulation of the plant trans-Golgi network

Defining convergent and divergent mechanisms underlying the biogenesis and function of endomembrane organelles is fundamentally important in cell biology. In all eukaryotes, the Trans-Golgi Network (TGN) is the hub where the exocytic and endocytic pathways converge. To gain knowledge in the mechanisms underlying TGN biogenesis and function, we characterized TGNap1, a protein encoded by a plant gene of unknown function conserved with metazoans. We demonstrate that TGNap1 is a TGN protein required for the homeostasis of biosynthetic and endocytic traffic pathways. We also show that TGNap1 binds Rab6, YIP4 and microtubules. Finally, we establish that TGNap1 contributes to microtubule-dependent biogenesis, tracking and function of a TGN subset, likely through interaction with Rab6 and YIP4. Our results identify an important trafficking determinant at the plant TGN and reveal an unexpected reliance of post-Golgi traffic homeostasis and organelle biogenesis on microtubules in plants.

TGNap1 is required for microtubule-dependent homeostasis of a subpopulation of the plant trans-Golgi network

Defining convergent and divergent mechanisms underlying the biogenesis and function of endomembrane organelles is fundamentally important in cell biology. In all eukaryotes, the Trans-Golgi Network (TGN) is the hub where the exocytic and endocytic pathways converge. To gain knowledge in the mechanisms underlying TGN biogenesis and function, we characterized TGNap1, a protein encoded by a plant gene of unknown function conserved with metazoans. We demonstrate that TGNap1 is a TGN protein required for the homeostasis of biosynthetic and endocytic traffic pathways. We also show that TGNap1 binds Rab6, YIP4 and microtubules. Finally, we establish that TGNap1 contributes to microtubule-dependent biogenesis, tracking and function of a TGN subset, likely through interaction with Rab6 and YIP4. Our results identify an important trafficking determinant at the plant TGN and reveal an unexpected reliance of post-Golgi traffic homeostasis and organelle biogenesis on microtubules in plants.