Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions

Maize lipid droplet-associated protein 2 is recruited by a virus to enhance viral multiplication and infection through regulating cellular fatty acid metabolism

Pathogen infection induces massive reprogramming of host primary metabolism. Lipid and fatty acid (FA) metabolism is generally disrupted by pathogens and co-opted for their proliferation. Lipid droplets (LDs) that play important roles in regulating cellular lipid metabolism are utilized by a variety of pathogens in mammalian cells. However, the function of LDs during pathogenic infection in plants remains unknown. We show here that infection by rice black streaked dwarf virus (RBSDV) affects the lipid metabolism of maize, which causes elevated accumulation of C18 polyunsaturated fatty acids (PUFAs) leading to viral proliferation and symptom development. The overexpression of one of the two novel LD-associated proteins (LDAPs) of maize (ZmLDAP1 and ZmLDAP2) induces LD clustering. The core capsid protein P8 of RBSDV interacts with ZmLDAP2 and prevents its degradation through the ubiquitin-proteasome system mediated by a UBX domain-containing protein, PUX10. In addition, silencing of ZmLDAP2 downregulates the expression of FA desaturase genes in maize, leading to a decrease in C18 PUFAs levels and suppression of RBSDV accumulation. Our findings reveal that plant virus may recruit LDAP to regulate cellular FA metabolism to promote viral multiplication and infection. These results expand the knowledge of LD functions and viral infection mechanisms in plants.

Genome-wide identification and evolution of the tubulin gene family in Camelina sativa

BACKGROUND

Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa.

RESULTS

We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome.

CONCLUSIONS

For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.

Lipid droplets in Arabidopsis thaliana leaves contain myosin-binding proteins and enzymes associated with furan-containing fatty acid biosynthesis

Lipid droplets (LDs) are lipid storage organelles in plant leaves and seeds. Seed LD proteins are well known, and their functions in lipid metabolism have been characterized; however, many leaf LD proteins remain to be identified. We therefore isolated LDs from leaves of the leaf LD-overaccumulating mutant high sterol ester 1 (hise1) of Arabidopsis thaliana by centrifugation or co-immunoprecipitation. We then performed LD proteomics by mass spectrometry and identified 3,206 candidate leaf LD proteins. In this study, we selected 31 candidate proteins for transient expression assays using a construct encoding the candidate protein fused with green fluorescent protein (GFP). Fluorescence microscopy showed that MYOSIN BINDING PROTEIN14 (MYOB14) and two uncharacterized proteins localized to LDs labeled with the LD marker. Subcellular localization analysis of MYOB family members revealed that MYOB1, MYOB2, MYOB3, and MYOB5 localized to LDs. LDs moved along actin filaments together with the endoplasmic reticulum. Co-immunoprecipitation of myosin XIK with MYOB2-GFP or MYOB14-GFP suggested that LD-localized MYOBs are involved in association with the myosin XIK-LDs. The two uncharacterized proteins were highly similar to enzymes for furan fatty acid biosynthesis in the photosynthetic bacterium Cereibacter sphaeroides, suggesting a relationship between LDs and furan fatty acid biosynthesis. Our findings thus reveal potential molecular functions of LDs and provide a valuable resource for further studies of the leaf LD proteome.

Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy

The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.

The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration

Quantitative analyses and models are required to connect a plant's cellular organisation with its metabolism. However, quantitative data are often scattered over multiple studies, and finding such data and converting them into useful information is time-consuming. Consequently, there is a need to centralise the available data and to highlight the remaining knowledge gaps. Here, we present a step-by-step approach to manually extract quantitative data from various information sources, and to unify the data format. First, data from Arabidopsis leaf were collated, checked for consistency and correctness and curated by cross-checking sources. Second, quantitative data were combined by applying calculation rules. They were then integrated into a unique comprehensive, referenced, modifiable and reusable data compendium representing an Arabidopsis reference leaf. This atlas contains the metrics of the 15 cell types found in leaves at the cellular and subcellular levels.

Degeneration of oil bodies by rough endoplasmic reticulum -associated protein during seed germination in Cannabis sativa

Oil bodies serve as a vital energy source of embryos during germination and contribute to sustaining the initial growth of seedlings until photosynthesis initiation. Despite high stability in chemical properties, how oil bodies break down and go into the degradation process during germination is still unknown. This study provides a morphological understanding of the mobilization of stored compounds in the seed germination of Cannabis. The achenes of fibrous hemp cultivar (Cannabis sativa cv. 'Chungsam') were examined in this study using light microscopy, scanning electron microscopy and transmission electron microscopy. Oil bodies in Cannabis seeds appeared spherical and sporadically distributed in the cotyledonary cells. Protein bodies contained electron-dense globoid and heterogeneous protein matrices. During seed germination, rough endoplasmic reticulum (rER) and high electron-dense substances were present adjacent to the oil bodies. The border of the oil bodies became a dense cluster region and appeared as a sinuous outline. Later, irregular hyaline areas were distributed throughout oil bodies, showing the destabilized emulsification of oil bodies. Finally, the oil bodies lost their morphology and fused with each other. The storage proteins were concentrated in the centre of the protein body as a dense homogenous circular mass surrounded by a light heterogeneous area. Some storage proteins are considered emulsifying agents on the surface region of oil bodies, enabling them to remain stable and distinct within and outside cotyledon cells. At the early germination stage, rER appeared and dense substances aggregated adjacent to the oil bodies. Certain proteins were synthesized within the rER and then translocated into the oil bodies by crossing the half membrane of oil bodies. Our data suggest that rER-associated proteins function as enzymes to lyse the emulsifying proteins, thereby weakening the emulsifying agent on the surface of the oil bodies. This process plays a key role in the degeneration of oil bodies and induces coalescence during seed germination.

Molecular characterization of oleosin genes in Cyperus esculentus, a Cyperaceae plant producing oil in underground tubers

KEY MESSAGE

CeOLE genes exhibit a tuber-predominant expression pattern and their mRNA/protein abundances are positively correlated with oil accumulation during tuber development. Overexpression could significantly increase the oil content of tobacco leaves. Oleosins (OLEs) are abundant structural proteins of lipid droplets (LDs) that function in LD formation and stabilization in seeds of oil crops. However, little information is available on their roles in vegetative tissues. In this study, we present the first genome-wide characterization of the oleosin family in tigernut (Cyperus esculentus L., Cyperaceae), a rare example accumulating high amounts of oil in underground tubers. Six members identified represent three previously defined clades (i.e. U, SL and SH) or six out of seven orthogroups (i.e. U, SL1, SL2, and SH1-3) proposed in this study. Comparative genomics analysis reveals that lineage-specific expansion of Clades SL and SH was contributed by whole-genome duplication and dispersed duplication, respectively. Moreover, presence of SL2 and SH3 in Juncus effuses implies their appearance sometime before Cyperaceae-Juncaceae divergence, whereas SH2 appears to be Cyperaceae specific. Expression analysis showed that CeOLE genes exhibit a tuber-predominant expression pattern and transcript levels are considerably more abundant than homologs in the close relative Cyperus rotundus. Moreover, CeOLE mRNA and protein abundances were shown to positively correlate with oil accumulation during tuber development. Additionally, two dominant isoforms (i.e. CeOLE2 and -5) were shown to locate in LDs as well as the endoplasmic reticulum of tobacco (Nicotiana benthamiana) leaves, and are more likely to function in homo and heteromultimers. Furthermore, overexpression of CeOLE2 and -5 in tobacco leaves could significantly increase the oil content, supporting their roles in oil accumulation. These findings provide insights into lineage-specific family evolution and putative roles of CeOLE genes in oil accumulation of vegetative tissues, which facilitate further genetic improvement for tigernut.

Cell wall polysaccharide and glycoprotein content tracks growth-form diversity and an aridity gradient in the leaf-succulent genus Crassula

Cell wall traits are believed to be a key component of the succulent syndrome, an adaptive syndrome to drought, yet the variability of such traits remains largely unknown. In this study, we surveyed the leaf polysaccharide and glycoprotein composition in a wide sampling of Crassula species that occur naturally along an aridity gradient in southern Africa, and we interpreted its adaptive significance in relation to growth form and arid adaptation. To study the glycomic diversity, we sampled leaf material from 56 Crassula taxa and performed comprehensive microarray polymer profiling to obtain the relative content of cell wall polysaccharides and glycoproteins. This analysis was complemented by the determination of monosaccharide composition and immunolocalization in leaf sections using glycan-targeting antibodies. We found that compact and non-compact Crassula species occupy distinct phenotypic spaces in terms of leaf glycomics, particularly in regard to rhamnogalacturonan I, its arabinan side chains, and arabinogalactan proteins (AGPs). Moreover, these cell wall components also correlated positively with increasing aridity, which suggests that they are likely advantageous in terms of arid adaptation. These differences point to compact Crassula species having more elastic cell walls with plasticizing properties, which can be interpreted as an adaptation toward increased drought resistance. Furthermore, we report an intracellular pool of AGPs associated with oil bodies and calcium oxalate crystals, which could be a peculiarity of Crassula and could be linked to increased drought resistance. Our results indicate that glycomics may be underlying arid adaptation and drought resistance in succulent plants.

Golgi-localized MORN1 promotes lipid droplet abundance and enhances tolerance to multiple stresses in Arabidopsis

Lipid droplet (LD) in vegetative tissues has recently been implicated in environmental responses in plants, but its regulation and its function in stress tolerance are not well understood. Here, we identified a Membrane Occupation and Recognition Nexus 1 (MORN1) gene as a contributor to natural variations of stress tolerance through genome-wide association study in Arabidopsis thaliana. Characterization of its loss-of-function mutant and natural variants revealed that the MORN1 gene is a positive regulator of plant growth, disease resistance, cold tolerance, and heat tolerance. The MORN1 protein is associated with the Golgi and is also partly associated with LD. Protein truncations that disrupt these associations abolished the biological function of the MORN1 protein. Furthermore, the MORN1 gene is a positive regulator of LD abundance, and its role in LD number regulation and stress tolerance is highly linked. Therefore, this study identifies MORN1 as a positive regulator of LD abundance and a contributor to natural variations of stress tolerance. It implicates a potential involvement of Golgi in LD biogenesis and strongly suggests a contribution of LD to diverse processes of plant growth and stress responses.

Lipid droplets are versatile organelles involved in plant development and plant response to environmental changes

Since decades plant lipid droplets (LDs) are described as storage organelles accumulated in seeds to provide energy for seedling growth after germination. Indeed, LDs are the site of accumulation for neutral lipids, predominantly triacylglycerols (TAGs), one of the most energy-dense molecules, and sterol esters. Such organelles are present in the whole plant kingdom, from microalgae to perennial trees, and can probably be found in all plant tissues. Several studies over the past decade have revealed that LDs are not merely simple energy storage compartments, but also dynamic structures involved in diverse cellular processes like membrane remodeling, regulation of energy homeostasis and stress responses. In this review, we aim to highlight the functions of LDs in plant development and response to environmental changes. In particular, we tackle the fate and roles of LDs during the plant post-stress recovery phase.

Wound-induced triacylglycerol biosynthesis is jasmonoy-l-isoleucin and abscisic acid independent

Triacylglycerol (TAG) plays a significant role during plant stress - it maintains lipid homeostasis. Upon wounding plants accumulate TAG, likely as a storage form of fatty acids (FAs) that originate from damaged membranes. This study asked if this process depends on the two phytohormones jasmonoyl-isoleucine (JA-Ile) and abscisic acid (ABA), which are involved in wound signalling. To analyse regulation of wound-induced TAG accumulation, we used mutants deficient in JA-Ile, with reduced ABA and the myb96 mutant, which is deficient in an ABA-dependent transcription factor. The expression of genes involved in TAG biosynthesis, and TAG content after wounding were analysed via LC-MS and GC-FID, plastidial lipid content in all mentioned mutant lines was also determined. The localization of newly synthesized TAG was investigated using lipid droplet staining. TAG accumulation upon wounding was confirmed as well as the fact that the newly synthesized TAG are mostly composed of polyunsaturated fatty acids. Nevertheless, all tested mutant lines were able to accumulate TAG similar to the WT. We observed differences in reduction of plastidial lipids - in WT plants this was higher than in mutant lines. Newly synthesized TAGs were stored in lipid droplets at and around the wounded area. Our results show that TAG accumulation upon wounding is not dependent on JA-Ile or ABA. The newly synthesized TAG species are composed of unsaturated fatty acids of membrane origin, and most likely serves as a transient energy store.

Identification and characterization of the LDAP family revealed GhLDAP2_Dt enhances drought tolerance in cotton

Lipid droplet-associated proteins (LDAPs) play essential roles in tissue growth and development and in drought stress responses in plants. Cotton is an important fiber and cash crop; however, the LDAP family has not been characterized in cotton. In this study, a total of 14, six, seven, and seven genes were confirmed as LDAP family members in Gossypium hirsutum, Gossypium raimondii, Gossypium arboreum, and Gossypium stocksii, respectively. Additionally, expansion in the LDAP family occurred with the formation of Gossypium, which is mirrored in the number of LDAPs found in five Malvaceae species (Gossypioides kirkii, Bombax ceiba, Durio zibethinus, Theobroma cacao, and Corchorus capsularis), Arabidopsis thaliana, and Carica papaya. The phylogenetic tree showed that the LDAP genes in cotton can be divided into three groups (I, II, and III). The analysis of gene structure and conserved domains showed that LDAPs derived from group I (LDAP1/2/3) are highly conserved during evolution, while members from groups II and III had large variations in both domains and gene structures. The gene expression pattern analysis of LDAP genes showed that they are expressed not only in the reproductive organs (ovule) but also in vegetative organs (root, stem, and leaves). The expression level of two genes in group III, GhLDAP6_At/Dt, were significantly higher in fiber development than in other tissues, indicating that it may be an important regulator of cotton fiber development. In group III, GhLDAP2_At/Dt, especially GhLDAP2_Dt was strongly induced by various abiotic stresses. Decreasing the expression of GhLDAP2_Dt in cotton via virus-induced gene silencing increased the drought sensitivity, and the over-expression of GhLDAP2_Dt led to increased tolerance to mannitol-simulated osmotic stress at the germination stage. Thus, we conclude that GhLDAP2_Dt plays a positive role in drought tolerance.

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.

Caleosin/peroxygenases: multifunctional proteins in plants

BACKGROUND

Caleosin/peroxygenases (CLO/PXGs) are a family of multifunctional proteins that are ubiquitous in land plants and are also found in some fungi and green algae. CLO/PXGs were initially described as a class of plant lipid-associated proteins with some similarities to the oleosins that stabilize lipid droplets (LDs) in storage tissues, such as seeds. However, we now know that CLO/PXGs have more complex structures, distributions and functions than oleosins. Structurally, CLO/PXGs share conserved domains that confer specific biochemical features, and they have diverse localizations and functions.

SCOPE

This review surveys the structural properties of CLO/PXGs and their biochemical roles. In addition to their highly conserved structures, CLO/PXGs have peroxygenase activities and are involved in several aspects of oxylipin metabolism in plants. The enzymatic activities and the spatiotemporal expression of CLO/PXGs are described and linked with their wider involvement in plant physiology. Plant CLO/PXGs have many roles in both biotic and abiotic stress responses in plants and in their responses to environmental toxins. Finally, some intriguing developments in the biotechnological uses of CLO/PXGs are addressed.

CONCLUSIONS

It is now two decades since CLO/PXGs were first recognized as a new class of lipid-associated proteins and only 15 years since their additional enzymatic functions as a new class of peroxygenases were discovered. There are many interesting research questions that remain to be addressed in future physiological studies of plant CLO/PXGs and in their recently discovered roles in the sequestration and, possibly, detoxification of a wide variety of lipidic xenobiotics that can challenge plant welfare.

Abiotic Stress in Crop Production

The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.

A computational study on the structure-function relationships of plant caleosins

Plant cells store energy in oil bodies constructed by structural proteins such as oleosins and caleosins. Although oil bodies usually accumulate in the seed and pollen of plants, caleosins are present in various organs and organelles. This issue, coupled with the diverse activities of caleosins, complicates the description of these oleo-proteins. Therefore, the current article proposes a new classification based on the bioinformatics analysis of the transmembrane topology of caleosins. Accordingly, the non-membrane class are the most abundant and diverse caleosins, especially in lower plants. Comparing the results with other reports suggests a stress response capacity for these caleosins. However, other classes play a more specific role in germination and pollination. A phylogenetic study also revealed two main clades that were significantly different in terms of caleosin type, expression profile, molecular weight, and isoelectric point (P < 0.01). In addition to the biochemical significance of the findings, predicting the structure of caleosins is necessary for constructing oil bodies used in the food and pharmaceutical industries.

Enhanced proteostasis, lipid remodeling, and nitrogen remobilization define barley flag leaf senescence

Leaf senescence is a developmental process allowing nutrient remobilization to sink organs. We characterized flag leaf senescence at 7, 14, and 21 d past anthesis in two near-isogenic barley lines varying in the allelic state of the HvNAM1 transcription factor gene, which influences senescence timing. Metabolomics and microscopy indicated that, as senescence progressed, thylakoid lipids were transiently converted to neutral lipids accumulating in lipid droplets. Senescing leaves also exhibited an accumulation of sugars including glucose, while nitrogen compounds (nucleobases, nucleotides, and amino acids) decreased. RNA-Seq analysis suggested lipid catabolism via β-oxidation and the glyoxylate cycle, producing carbon skeletons and feeding respiration as a replacement of the diminished carbon supply from photosynthesis. Comparison of the two barley lines highlighted a more prominent up-regulation of heat stress transcription factor- and chaperone-encoding genes in the late-senescing line, suggesting a role for these genes in the control of leaf longevity. While numerous genes with putative roles in nitrogen remobilization were up-regulated in both lines, several peptidases, nucleases, and nitrogen transporters were more highly induced in the early-senescing line; this finding identifies processes and specific candidates which may affect nitrogen remobilization from senescing barley leaves, downstream of the HvNAM1 transcription factor.

A seed-like proteome in oil-rich tubers

There are numerous examples of plant organs or developmental stages that are desiccation-tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation-tolerant. One example are the tubers of yellow nutsedge (Cyperus esculentus), which also store large amounts of lipids similar to seeds. Interestingly, the closest known relative, purple nutsedge (Cyperus rotundus), generates tubers that do not accumulate oil and are not desiccation-tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the close relative purple nutsedge (C. rotundus) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid droplet-enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homologous to ABSCISIC ACID INSENSITIVE3, WRINKLED1, and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.

Transcriptional regulation of triacylglycerol accumulation in plants under environmental stress conditions

Triacylglycerol (TAG), a major energy reserve in lipid form, accumulates mainly in seeds. Although TAG concentrations are usually low in vegetative tissues because of the repression of seed maturation programs, these programs are derepressed upon the exposure of vegetative tissues to environmental stresses. Metabolic reprogramming of TAG accumulation is driven primarily by transcriptional regulation. A substantial proportion of transcription factors regulating seed TAG biosynthesis also participates in stress-induced TAG accumulation in vegetative tissues. TAG accumulation leads to the formation of lipid droplets and plastoglobules, which play important roles in plant tolerance to environmental stresses. Toxic lipid intermediates generated from environmental-stress-induced lipid membrane degradation are captured by TAG-containing lipid droplets and plastoglobules. This review summarizes recent advances in the transcriptional control of metabolic reprogramming underlying stress-induced TAG accumulation, and provides biological insight into the plant adaptive strategy, linking TAG biosynthesis with plant survival.

Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles

Lipid droplets (LDs) have emerged not just as storage sites for lipids but as central regulators of metabolism and organelle quality control. These critical functions are achieved, in part, at membrane contact sites (MCS) between LDs and other organelles. MCS are sites of transfer of cellular constituents to or from LDs for energy mobilization in response to nutrient limitations, as well as LD biogenesis, expansion and autophagy. Here, we describe recent findings on the mechanisms underlying the formation and function of MCS between LDs and mitochondria, ER and lysosomes/vacuoles and the role of the cytoskeleton in promoting LD MCS through its function in LD movement and distribution in response to environmental cues.

Electron microscopy for imaging organelles in plants and algae

Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.

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.

The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource

We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.

LDIP cooperates with SEIPIN and LDAP to facilitate lipid droplet biogenesis in Arabidopsis

Cytoplasmic lipid droplets (LDs) are evolutionarily conserved organelles that store neutral lipids and play critical roles in plant growth, development, and stress responses. However, the molecular mechanisms underlying their biogenesis at the endoplasmic reticulum (ER) remain obscure. Here we show that a recently identified protein termed LD-associated protein [LDAP]-interacting protein (LDIP) works together with both endoplasmic reticulum-localized SEIPIN and the LD-coat protein LDAP to facilitate LD formation in Arabidopsis thaliana. Heterologous expression in insect cells demonstrated that LDAP is required for the targeting of LDIP to the LD surface, and both proteins are required for the production of normal numbers and sizes of LDs in plant cells. LDIP also interacts with SEIPIN via a conserved hydrophobic helix in SEIPIN and LDIP functions together with SEIPIN to modulate LD numbers and sizes in plants. Further, the co-expression of both proteins is required to restore normal LD production in SEIPIN-deficient yeast cells. These data, combined with the analogous function of LDIP to a mammalian protein called LD Assembly Factor 1, are discussed in the context of a new model for LD biogenesis in plant cells with evolutionary connections to LD biogenesis in other eukaryotes.

Functional involvement of caleosin/peroxygenase PdPXG4 in the accumulation of date palm leaf lipid droplets after exposure to dioxins

Dioxins are highly injurious environmental pollutants with proven toxicological effects on both animals and humans, but to date their effects on plants still need to be studied in detail. We identified a dioxin-inducible caleosin/peroxygenase isoform, PdPXG4, that is mostly expressed in leaves of date palm seedlings and exhibits a specific reductase activity towards the 13-hydroperoxide of C18:2 and C18:3 (HpODE and HpOTrE, respectively). After exposure to TCDD, lipid droplets (LDs) isolated from TCDD-exposed leaves were about 6.5-15.7-fold more active in metabolizing 13-HpOTrE compared with those isolated from non-exposed leaves. A characteristic spectrum of leaf dioxin-responsive oxylipins (LDROXYL) was detected in dioxin-exposed seedlings. Of particular importance, a group of these oxylipins, referred to as Class I, comprising six congeners of hydroxides fatty acids derived from C18:2 and C18:3, was exclusively found in leaves after exposure to TCDD. The TCDD-induced oxylipin pattern was confirmed in vitro using terbufos, a typical inhibitor towards the PdPXG4 peroxygenase activity. Of particular interest, the response of terbufos-pretreated protoplasts to TCDD was drastically reduced. Together, these findings suggest that PdPXG4 is implicated in the establishment of a dioxin-specific oxylipin signature in date palm leaves soon after their exposure to these pollutants.

Isolation of Lipid Droplets for Protein and Lipid Analysis

Cytosolic lipid droplets (LDs) are organelles which emulsify a variety of hydrophobic molecules in the aqueous cytoplasm of essentially all plant cells. Most familiar are the LDs from oilseeds or oleaginous fruits that primarily store triacylglycerols and serve a storage function. However, similar hydrophobic particles are found in cells of plant tissues that package terpenoids, sterol esters, wax esters, or other types of nonpolar lipids. The various hydrophobic lipids inside LDs are coated with a phospholipid monolayer, mostly derived from membrane phospholipids during their ontogeny. Various proteins have been identified to be associated with LDs, and these may be cell-type, tissue-type, or even species specific. While major LD proteins like oleosins have been known for decades, more recently a growing list of LD proteins has been identified, primarily by proteomics analyses of isolated LDs and confirmation of their localization by confocal microscopy. LDs, unlike other organelles, have a density less than that of water, and consequently can be isolated and enriched in cellular fractions by flotation centrifugation for composition studies. However, due to its deep coverage, modern proteomics approaches are also prone to identify contaminants, making control experiments necessary. Here, procedures for the isolation of LDs, and analysis of LD components are provided as well as methods to validate the LD localization of proteins.

Lipid Body Dynamics in Shoot Meristems: Production, Enlargement, and Putative Organellar Interactions and Plasmodesmal Targeting

Post-embryonic cells contain minute lipid bodies (LBs) that are transient, mobile, engage in organellar interactions, and target plasmodesmata (PD). While LBs can deliver γ-clade 1,3-β-glucanases to PD, the nature of other cargo is elusive. To gain insight into the poorly understood role of LBs in meristems, we investigated their dynamics by microscopy, gene expression analyzes, and proteomics. In developing buds, meristems accumulated LBs, upregulated several LB-specific OLEOSIN genes and produced OLEOSINs. During bud maturation, the major gene OLE6 was strongly downregulated, OLEOSINs disappeared from bud extracts, whereas lipid biosynthesis genes were upregulated, and LBs were enlarged. Proteomic analyses of the LB fraction of dormant buds confirmed that OLEOSINs were no longer present. Instead, we identified the LB-associated proteins CALEOSIN (CLO1), Oil Body Lipase 1 (OBL1), Lipid Droplet Interacting Protein (LDIP), Lipid Droplet Associated Protein1a/b (LDAP1a/b) and LDAP3a/b, and crucial components of the OLEOSIN-deubiquitinating and degradation machinery, such as PUX10 and CDC48A. All mRFP-tagged LDAPs localized to LBs when transiently expressed in Nicotiana benthamiana. Together with gene expression analyzes, this suggests that during bud maturation, OLEOSINs were replaced by LDIP/LDAPs at enlarging LBs. The LB fraction contained the meristem-related actin7 (ACT7), "myosin XI tail-binding" RAB GTPase C2A, an LB/PD-associated γ-clade 1,3-β-glucanase, and various organelle- and/or PD-localized proteins. The results are congruent with a model in which LBs, motorized by myosin XI-k/1/2, traffic on F-actin, transiently interact with other organelles, and deliver a diverse cargo to PD.

Glycerolipid profile differences between perennial and annual stem zones in the perennial model plant Arabis alpina

The perennial life style is a successful ecological strategy, and Arabis alpina is a recently developed model Brassicaceae species for studying it. One aspect, poorly investigated until today, concerns the differing patterns of allocation, storage, and metabolism of nutrients between perennials and annuals and the yet unknown signals that regulate this process. A. alpina has a complex lateral stem architecture with a proximal vegetative perennial (PZ) and a distal annual flowering zone (AZ) inside the same stems. Lipid bodies (LBs) with triacylglycerols (TAGs) accumulate in the PZ. To identify potential processes of lipid metabolism linked with the perennial lifestyle, we analyzed lipid species in the PZ versus AZ. Glycerolipid fractions, including neutral lipids with mainly TAGs, phospholipids, and glycolipids, were present at higher levels in the PZ as compared to AZ or roots. Concomitantly, contents of specific long-chain and very long-chain fatty acids increased during formation of the PZ. Corresponding gene expression data, gene ontology term enrichment, and correlation analysis with lipid species pinpoint glycerolipid-related genes to be active during the development of the PZ. Possibilities that lipid metabolism genes may be targets of regulatory mechanisms specifying PZ differentiation in A. alpina are discussed.

Arabidopsis thaliana EARLY RESPONSIVE TO DEHYDRATION 7 Localizes to Lipid Droplets via Its Senescence Domain

Lipid droplets (LDs) are neutral-lipid-containing organelles found in all kingdoms of life and are coated with proteins that carry out a vast array of functions. Compared to mammals and yeast, relatively few LD proteins have been identified in plants, particularly those associated with LDs in vegetative (non-seed) cell types. Thus, to better understand the cellular roles of LDs in plants, a more comprehensive inventory and characterization of LD proteins is required. Here, we performed a proteomics analysis of LDs isolated from drought-stressed Arabidopsis leaves and identified EARLY RESPONSIVE TO DEHYDRATION 7 (ERD7) as a putative LD protein. mCherry-tagged ERD7 localized to both LDs and the cytosol when ectopically expressed in plant cells, and the protein's C-terminal senescence domain (SD) was both necessary and sufficient for LD targeting. Phylogenetic analysis revealed that ERD7 belongs to a six-member family in Arabidopsis that, along with homologs in other plant species, is separated into two distinct subfamilies. Notably, the SDs of proteins from each subfamily conferred targeting to either LDs or mitochondria. Further, the SD from the ERD7 homolog in humans, spartin, localized to LDs in plant cells, similar to its localization in mammals; although, in mammalian cells, spartin also conditionally localizes to other subcellular compartments, including mitochondria. Disruption of ERD7 gene expression in Arabidopsis revealed no obvious changes in LD numbers or morphology under normal growth conditions, although this does not preclude a role for ERD7 in stress-induced LD dynamics. Consistent with this possibility, a yeast two-hybrid screen using ERD7 as bait identified numerous proteins involved in stress responses, including some that have been identified in other LD proteomes. Collectively, these observations provide new insight to ERD7 and the SD-containing family of proteins in plants and suggest that ERD7 may be involved in functional aspects of plant stress response that also include localization to the LD surface.

Lipid Droplet Isolation from Arabidopsis thaliana Leaves

Lipid droplets (LDs) are neutral lipid aggregates surrounded by a phospholipid monolayer and specific proteins. In plants, they play a key role as energy source after seed germination, but are also formed in vegetative tissues in response to developmental or environmental conditions, where their functions are poorly understood. To elucidate these, it is essential to isolate LDs with good yields, while retaining their protein components. LD isolation protocols are based on their capacity to float after centrifugation in sucrose gradients. Early strategies using stringent conditions and LD-abundant plant tissues produced pure LDs where core proteins were identified. To identify more weakly bound LD proteins, recent protocols have used low stringency buffers, but carryover contaminants and low yields were often a problem. We have developed a sucrose gradient-based protocol to isolate LDs from Arabidopsis leaves, using Tween-20 and fresh tissue to increase yield. In both healthy and bacterially-infected Arabidopsis leaves, this protocol allowed to identify LD proteins that were later confirmed by microscopy analysis.

Connecting moss lipid droplets to patchoulol biosynthesis

Plant-derived terpenoids are extensively used in perfume, food, cosmetic and pharmaceutical industries, and several attempts are being made to produce terpenes in heterologous hosts. Native hosts have evolved to accumulate large quantities of terpenes in specialized cells. However, heterologous cells lack the capacity needed to produce and store high amounts of non-native terpenes, leading to reduced growth and loss of volatile terpenes by evaporation. Here, we describe how to direct the sesquiterpene patchoulol production into cytoplasmic lipid droplets (LDs) in Physcomitrium patens (syn. Physcomitrella patens), by attaching patchoulol synthase (PTS) to proteins linked to plant LD biogenesis. Three different LD-proteins: Oleosin (PpOLE1), Lipid Droplet Associated Protein (AtLDAP1) and Seipin (PpSeipin325) were tested as anchors. Ectopic expression of PTS increased the number and size of LDs, implying an unknown mechanism between heterologous terpene production and LD biogenesis. The expression of PTS physically linked to Seipin increased the LD size and the retention of patchoulol in the cell. Overall, the expression of PTS was lower in the anchored mutants than in the control, but when normalized to the expression the production of patchoulol was higher in the seipin-linked mutants.

SEIPIN Isoforms Interact with the Membrane-Tethering Protein VAP27-1 for Lipid Droplet Formation

SEIPIN proteins are localized to endoplasmic reticulum (ER)-lipid droplet (LD) junctions where they mediate the directional formation of LDs into the cytoplasm in eukaryotic cells. Unlike in animal and yeast cells, which have single SEIPIN genes, plants have three distinct SEIPIN isoforms encoded by separate genes. The mechanism of SEIPIN action remains poorly understood, and here we demonstrate that part of the function of two SEIPIN isoforms in Arabidopsis (Arabidopsis thaliana), AtSEIPIN2 and AtSEIPIN3, may depend on their interaction with the vesicle-associated membrane protein (VAMP)-associated protein (VAP) family member AtVAP27-1. VAPs have well-established roles in the formation of membrane contact sites and lipid transfer between the ER and other organelles, and here, we used a combination of biochemical, cell biology, and genetics approaches to show that AtVAP27-1 interacts with the N termini of AtSEIPIN2 and AtSEIPIN3 and likely supports the normal formation of LDs. This insight indicates that the ER membrane tethering machinery in plant cells could play a role with select SEIPIN isoforms in LD biogenesis at the ER, and additional experimental evidence in Saccharomyces cerevisiae supports the possibility that this interaction may be important in other eukaryotic systems.

Protein Profiles of Lipid Droplets during the Hypersensitive Defense Response of Arabidopsis against Pseudomonas Infection

Lipid droplets (LDs) have classically been viewed as seed storage particles, yet they are now emerging as dynamic organelles associated with developmental and stress responses. Nevertheless, their involvement in plant immunity has still been little studied. Here, we found LD accumulation in Arabidopsis thaliana leaves that induced a hypersensitive response (HR) after Pseudomonas infection. We established a protocol to reproducibly isolate LDs and to analyze their protein content. The expression of GFP fusion proteins in Nicotiana benthamiana and in transgenic Arabidopsis lines validated the LD localization of glycerol-3-phosphate acyltransferase 4 (GPAT4) and 8 (GPAT8), required for cutin biosynthesis. Similarly, we showed LD localization of α-dioxygenase1 (α-DOX1) and caleosin3 (CLO3), involved in the synthesis of fatty acid derivatives, and that of phytoalexin-deficient 3 (PAD3), which is involved in camalexin synthesis. We found evidence suggesting the existence of different populations of LDs, with varying protein contents and distributions. GPAT4 and GPAT8 were associated with LDs inside stomata and surrounding cells of untreated leaves, yet they were mainly confined to LDs in guard cells after bacterial inoculation. By contrast, α-DOX1 and PAD3 were associated with LDs in the epidermal cells of HR-responding leaves, with PAD3 mostly restricted to cells near dead tissue, while CLO3 had a more ubiquitous distribution. As such, the nature of the proteins identified, together with the phenotypic examination of selected mutants, suggests that LDs participate in lipid changes and in the production and transport of defense components affecting the interaction of plants with invading pathogens.

Reserve lipids and plant autophagy

Autophagy is a universal mechanism that facilitates the degradation of unwanted cytoplasmic components in eukaryotic cells. In this review, we highlight recent developments in the investigation of the role of autophagy in lipid homeostasis in plants by comparison with algae, yeast, and animals. We consider the storage compartments that form the sources of lipids in plants, and the roles that autophagy plays in the synthesis of triacylglycerols and in the formation and maintenance of lipid droplets. We also consider the relationship between lipids and the biogenesis of autophagosomes, and the role of autophagy in the degradation of lipids in plants.

The complex response of free and bound amino acids to water stress during the seed setting stage in Arabidopsis

Free amino acids (FAAs) and protein-bound amino acids (PBAAs) in seeds play an important role in seed desiccation, longevity, and germination. However, the effect that water stress has on these two functional pools, especially when imposed during the crucial seed setting stage is unclear. To better understand these effects, we exposed Arabidopsis plants at the seed setting stage to a range of water limitation and water deprivation conditions and then evaluated physiological, metabolic, and proteomic parameters, with special focus on FAAs and PBAAs. We found that in response to severe water limitation, seed yield decreased, while seed weight, FAA, and PBAA content per seed increased. Nevertheless, the composition of FAAs and PBAAs remained unaltered. In response to severe water deprivation, however, both seed yield and weight were reduced. In addition, major alterations were observed in both FAA and proteome compositions, which indicated that both osmotic adjustment and proteomic reprogramming occurred in these naturally desiccation-tolerant organs. However, despite the major proteomic alteration, the PBAA composition did not change, suggesting that the proteomic reprogramming was followed by a proteomic rebalancing. Proteomic rebalancing has not been observed previously in response to stress, but its occurrence under stress strongly suggests its natural function. Together, our data show that the dry seed PBAA composition plays a key role in seed fitness and therefore is rigorously maintained even under severe water stress, while the FAA composition is more plastic and adaptable to changing environments, and that both functional pools are distinctly regulated.

Lipid droplets throughout the evolutionary tree

Intracellular lipid droplets are utilized for lipid storage and metabolism in organisms as evolutionarily diverse as animals, fungi, plants, bacteria, and archaea. These lipid droplets demonstrate great diversity in biological functions and protein and lipid compositions, yet fundamentally share common molecular and ultrastructural characteristics. Lipid droplet research has been largely fragmented across the diversity of lipid droplet classes and sub-classes. However, we suggest that there is great potential benefit to the lipid community in better integrating the lipid droplet research fields. To facilitate such integration, we survey the protein and lipid compositions, functional roles, and mechanisms of biogenesis across the breadth of lipid droplets studied throughout the natural world. We depict the big picture of lipid droplet biology, emphasizing shared characteristics and unique differences seen between different classes. In presenting the known diversity of lipid droplets side-by-side it becomes necessary to offer for the first time a consistent system of categorization and nomenclature. We propose a division into three primary classes that reflect their sub-cellular location: i) cytoplasmic lipid droplets (CYTO-LDs), that are present in the eukaryotic cytoplasm, ii) prokaryotic lipid droplets (PRO-LDs), that exist in the prokaryotic cytoplasm, and iii) plastid lipid droplets (PL-LDs), that are found in plant plastids, organelles of photosynthetic eukaryotes. Within each class there is a remarkable array of sub-classes displaying various sizes, shapes and compositions. A more integrated lipid droplet research field will provide opportunities to better build on discoveries and accelerate the pace of research in ways that have not been possible.

The Role of Triacylglycerol in Plant Stress Response

Vegetable oil is mainly composed of triacylglycerol (TAG), a storage lipid that serves as a major commodity for food and industrial purposes, as well as an alternative biofuel source. While TAG is typically not produced at significant levels in vegetative tissues, emerging evidence suggests that its accumulation in such tissues may provide one mechanism by which plants cope with abiotic stress. Different types of abiotic stress induce lipid remodeling through the action of specific lipases, which results in various alterations in membrane lipid composition. This response induces the formation of toxic lipid intermediates that cause membrane damage or cell death. However, increased levels of TAG under stress conditions are believed to function, at least in part, as a means of sequestering these toxic lipid intermediates. Moreover, the lipid droplets (LDs) in which TAG is enclosed also function as a subcellular factory to provide binding sites and substrates for the biosynthesis of bioactive compounds that protect against insects and fungi. Though our knowledge concerning the role of TAG in stress tolerance is expanding, many gaps in our understanding of the mechanisms driving these processes are still evident. In this review, we highlight progress that has been made to decipher the role of TAG in plant stress response, and we discuss possible ways in which this information could be utilized to improve crops in the future.

Lipid droplets in plants and algae: Distribution, formation, turnover and function

Plant oils represent an energy-rich and carbon-dense group of hydrophobic compounds. These oils are not only of economic interest, but also play important, fundamental roles in plant and algal growth and development. The subcellular storage compartments of plant lipids, referred to as lipid droplets (LDs), have long been considered relatively inert oil vessels. However, research in the last decade has revealed that LDs play far more dynamic roles in plant biology than previously appreciated, including transient neutral lipid storage, membrane remodeling, lipid signaling, and stress responses. Here we discuss recent developments in the understanding of LD formation, turnover and function in land plants and algae.

Identification of Low-Abundance Lipid Droplet Proteins in Seeds and Seedlings

The developmental program of seed formation, germination, and early seedling growth requires not only tight regulation of cell division and metabolism, but also concerted control of the structure and function of organelles, which relies on specific changes in their protein composition. Of particular interest is the switch from heterotrophic to photoautotrophic seedling growth, for which cytoplasmic lipid droplets (LDs) play a critical role as depots for energy-rich storage lipids. Here, we present the results of a bottom-up proteomics study analyzing the total protein fractions and LD-enriched fractions in eight different developmental phases during silique (seed) development, seed germination, and seedling establishment in Arabidopsis (Arabidopsis thaliana). The quantitative analysis of the LD proteome using LD-enrichment factors led to the identification of six previously unidentified and comparably low-abundance LD proteins, each of which was confirmed by intracellular localization studies with fluorescent protein fusions. In addition to these advances in LD protein discovery and the potential insights provided to as yet unexplored aspects in plant LD functions, our data set allowed for a comparative analysis of the LD protein composition throughout the various developmental phases examined. Among the most notable of the alterations in the LD proteome were those during seedling establishment, indicating a switch in the physiological function(s) of LDs after greening of the cotyledons. This work highlights LDs as dynamic organelles with functions beyond lipid storage.

Arabidopsis LDIP protein locates at a confined area within the lipid droplet surface and favors lipid droplet formation

Lipid droplets (LDs) are cell organelles specialized in neutral lipid storage. Extendedly studied in seeds, LDs also accumulate in leaves during senescence or in response to abiotic stresses. However the mechanisms underlying their biogenesis remain relatively unknown. Here, we deciphered the distinct roles of two proteins during LD biogenesis: LD-associated protein 1 (AtLDAP1) and LDAP-interacting protein (AtLDIP). We demonstrated that AtLDIP overexpression favors the neo-formation of small LDs under growing conditions where LD accumulation is usually not observed. In addition, atldip knock-out mutant displayed fewer but larger LDs, confirming a role of AtLDIP in LD biogenesis. Interestingly, a synergistic effect of the overexpression of both AtLDIP and AtLDAP1 was observed, resulting in an increase of LD cluster occurrence and LD abundance within the clusters and the cells. AtLDIP overexpression has no significant impact on triacylglycerol and steryl ester accumulation but AtLDIP inactivation is associated with an increase of neutral lipid content, that is probably a consequence of the enlarged but less abundant LDs present in this line. Our localization study demonstrated that AtLDIP is localized at specific dotted sites within the LD in contrast to AtLDAP1 that covers the whole LD. In addition, AtLDIP sometimes localized away from the LD marker, but always associated with the ER network, suggesting a location at LD nascent sites within the ER. Taken together, our results suggested that AtLDIP promotes the formation of new LDs from ER localized TAG lenses.

Subcellular localization of chlorophyllase2 reveals it is not involved in chlorophyll degradation during senescence in Arabidopsis thaliana

Chlorophyllase (CLH), which catalyzes the release of the phytol chain from chlorophyll (Chl), has been long considered to catalyze the first step of Chl degradation. Arabidopsis contains two isoforms of CLH (CLH1 and CLH2), and CLH1 was previously demonstrated to be localized in tonoplast and endoplasmic reticulum, and not be involved in Chl degradation. In contrast, CLH2 possesses a predicted signal-peptide for chloroplast localization, and phylogenetic analysis of CLHs in Arabidopsis and other species also indicate that CLH2 forms a different clade than CLH1. Therefore, the possibility remains that CLH2 is involved in the breakdown of Chl. In the current study, clh mutants lacking CLH2 or both CLH isoforms were analyzed after the induction of senescence. Results indicated that the clh knockout lines were still able to degrade Chl at the same rate as wild-type plants. Transgenic Arabidopsis plants were generated that constitutively expressed either CLH2 or CLH2 fused to a yellow fluorescent protein (YFP). Observations made using confocal microscopy indicated that CLH2-YFP was located external to chloroplasts. Additionally, in overexpression plants, CLH2 was enriched in tonoplast and endoplasmic reticulum fractions following membrane fractionation. Based on the collective data, we conclude that CLH2 is not involved in Chl breakdown during senescence in Arabidopsis.

Degradation of Lipid Droplets in Plants and Algae-Right Time, Many Paths, One Goal

In eukaryotic cells, lipids in the form of triacylglycerols (TAGs) are the major reservoir of cellular carbon and energy. These TAGs are packed into specialized organelles called lipid droplets (LDs). They can be found in most, if not all, types of cells, from bacteria to human. Recent data suggest that rather than being simple storage organelles, LDs are very dynamic structures at the center of cellular metabolism. This is also true in plants and algae, where LDs have been implicated in many processes including energy supply; membrane structure, function, trafficking; and signal transduction. Plant and algal LDs also play a vital role in human life, providing multiple sources of food and fuel. Thus, a lot of attention has been paid to metabolism and function of these organelles in recent years. This review summarizes the most recent advances on LDs degradation as a key process for TAGs release. While the initial knowledge on this process came from studies in oilseeds, the findings of the last decade revealed high complexity and specific mechanisms of LDs degradation in plants and algae. This includes identification of numerous novel proteins associated with LDs as well as a prominent role for autophagy in this process. This review outlines, systemizes, and discusses the most current data on LDs catabolism in plants and algae.

The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes

Membrane compartments are amongst the most fascinating markers of cell evolution from prokaryotes to eukaryotes, some being conserved and the others having emerged via a series of primary and secondary endosymbiosis events. Membrane compartments comprise the system limiting cells (one or two membranes in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal vesicular, subspherical, tubular, or reticulated organelles. In eukaryotes, the internal membranes comprise on the one hand the general endomembrane system, a dynamic network including organelles like the endoplasmic reticulum, the Golgi apparatus, the nuclear envelope, etc. and also the plasma membrane, which are linked via direct lateral connectivity (e.g. between the endoplasmic reticulum and the nuclear outer envelope membrane) or indirectly via vesicular trafficking. On the other hand, semi-autonomous organelles, i.e. mitochondria and chloroplasts, are disconnected from the endomembrane system and request vertical transmission following cell division. Membranes are organized as lipid bilayers in which proteins are embedded. The budding of some of these membranes, leading to the formation of the so-called lipid droplets (LDs) loaded with hydrophobic molecules, most notably triacylglycerol, is conserved in all clades. The evolution of eukaryotes is marked by the acquisition of mitochondria and simple plastids from Gram-positive bacteria by primary endosymbiosis events and the emergence of extremely complex plastids, collectively called secondary plastids, bounded by three to four membranes, following multiple and independent secondary endosymbiosis events. There is currently no consensus view of the evolution of LDs in the Tree of Life. Some features are conserved; others show a striking level of diversification. Here, we summarize the current knowledge on the architecture, dynamics, and multitude of functions of the lipid droplets in prokaryotes and in eukaryotes deriving from primary and secondary endosymbiosis events.

Lipid droplet motility and organelle contacts

Lipid droplets (LDs) are fat storage organelles integral to energy homeostasis and a wide range of cellular processes. LDs physically and functionally interact with many partner organelles, including the ER, mitochondria, lysosomes, and peroxisomes. Recent findings suggest that the dynamics of LD inter-organelle contacts is in part controlled by LD intracellular motility. LDs can be transported directly by motor proteins along either actin filaments or microtubules, via Kinesin-1, Cytoplasmic Dynein, and type V Myosins. LDs can also be propelled indirectly, by hitchhiking on other organelles, cytoplasmic flows, and potentially actin polymerization. Although the anchors that attach motors to LDs remain elusive, other regulators of LD motility have been identified, ranging from modification of the tracks to motor co-factors to members of the perilipin family of LD proteins. Manipulating these regulatory pathways provides a tool to probe whether altered motility affects organelle contacts and has revealed that LD motility can promote interactions with numerous partners, with profound consequences for metabolism. LD motility can cause dramatic redistribution of LDs between a clustered and a dispersed state, resulting in altered organelle contacts and LD turnover. We propose that LD motility can thus promote switches in the metabolic state of a cell. Finally, LD motility is also important for LD allocation during cell division. In a number of animal embryos, uneven allocation results in a large difference in LD content in distinct daughter cells, suggesting cell-type specific LD needs.

Come a little bit closer! Lipid droplet-ER contact sites are getting crowded

Not so long ago, contact sites between the endoplasmic reticulum (ER) and lipid droplets (LDs) were largely unexplored on a molecular level. In recent years however, numerous proteins have been identified that are enriched or exclusively located at the interfaces between LDs and the ER. These comprise members of protein classes typically found in diverse types of contacts, such as organelle tethers and lipid transfer proteins, but also proteins that have no similarities to known contact site machineries. This structurally heterogeneous group of contact site residents might be required to fulfill unique aspects of LD-ER contact biology, such as de novo LD biogenesis, and maintenance of lipidic connections between LDs and ER. Here, we summarize the current knowledge on the molecular components of this special organelle contact site, and discuss their features and functions.

HIGH STEROL ESTER 1 is a key factor in plant sterol homeostasis

Plants strictly regulate the levels of sterol in their cells, as high sterol levels are toxic. However, how plants achieve sterol homeostasis is not fully understood. We isolated an Arabidopsis thaliana mutant that abundantly accumulated sterol esters in structures of about 1 µm in diameter in leaf cells. We designated the mutant high sterol ester 1 (hise1) and called the structures sterol ester bodies. Here, we show that HISE1, the gene product that is altered in this mutant, functions as a key factor in plant sterol homeostasis on the endoplasmic reticulum (ER) and participates in a fail-safe regulatory system comprising two processes. First, HISE1 downregulates the protein levels of the β-hydroxy β-methylglutaryl-CoA reductases HMGR1 and HMGR2, which are rate-limiting enzymes in the sterol synthesis pathway, resulting in suppression of sterol overproduction. Second, if the first process is not successful, excess sterols are converted to sterol esters by phospholipid sterol acyltransferase1 (PSAT1) on ER microdomains and then segregated in SE bodies.

Electron tomography in plant cell biology

Electron tomography (ET) approaches are based on the imaging of a biological specimen at different tilt angles by transmission electron microscopy (TEM). ET can be applied to both plastic-embedded and frozen samples. Technological advancements in TEM, direct electron detection, automated image collection, and imaging processing algorithms allow for 2-7-nm scale axial resolution in tomographic reconstructions of cells and organelles. In this review, we discussed the application of ET in plant cell biology and new opportunities for imaging plant cells by cryo-ET and other 3D electron microscopy approaches.

Mechanisms of lipid droplet biogenesis

Lipid droplets (LDs) are organelles that compartmentalize nonbilayer-forming lipids in the aqueous cytoplasm of cells. They are ubiquitous in most organisms, including in animals, protists, plants and microorganisms. In eukaryotes, LDs are believed to be derived by a budding and scission process from the surface of the endoplasmic reticulum, and this occurs concomitantly with the accumulation of neutral lipids, most often triacylglycerols and steryl esters. Overall, the mechanisms underlying LD biogenesis are difficult to generalize, in part because of the involvement of different sets of both evolutionarily conserved and organism-specific LD-packaging proteins. Here, we briefly compare and contrast these proteins and the allied processes responsible for LD biogenesis in cells of animals, yeasts and plants.