Dynamics of protein and polar lipid recruitment during lipid droplet assembly in Chlamydomonas reinhardtii

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.

Acyl-CoA binding protein is required for lipid droplet degradation in the diatom Phaeodactylum tricornutum

Diatoms (Bacillariophyceae) accumulate neutral storage lipids in lipid droplets during stress conditions, which can be rapidly degraded and recycled when optimal conditions resume. Since nutrient and light availability fluctuate in marine environments, storage lipid turnover is essential for diatom dominance of marine ecosystems. Diatoms have garnered attention for their potential to provide a sustainable source of omega-3 fatty acids. Several independent proteomic studies of lipid droplets isolated from the model oleaginous pennate diatom Phaeodactylum tricornutum have identified a previously uncharacterized protein with an acyl-CoA binding (ACB) domain, Phatrdraft_48778, here referred to as Phaeodactylum tricornutum acyl-CoA binding protein (PtACBP). We report the phenotypic effects of CRISPR-Cas9 targeted genome editing of PtACBP. ptacbp mutants were defective in lipid droplet and triacylglycerol degradation, as well as lipid and eicosapentaenoic acid synthesis, during recovery from nitrogen starvation. Transcription of genes responsible for peroxisomal β-oxidation, triacylglycerol lipolysis, and eicosapentaenoic acid synthesis was inhibited. A lipid-binding assay using a synthetic ACB domain from PtACBP indicated preferential binding specificity toward certain polar lipids. PtACBP fused to eGFP displayed an endomembrane-like pattern, which surrounded the periphery of lipid droplets. PtACBP is likely responsible for intracellular acyl transport, affecting cell division, development, photosynthesis, and stress response. A deeper understanding of the molecular mechanisms governing storage lipid turnover will be crucial for developing diatoms and other microalgae as biotechnological cell factories.

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.

Expression of Chlamydomonas reinhardtii chloroplast diacylglycerol acyltransferase 3 is induced by light in concert with triacylglycerol accumulation

Considerable progress has been made towards the understanding of triacylglycerol (TAG) accumulation in algae. One key aspect is finding conditions that trigger TAG production without reducing cell division. Previously, we identified a soluble diacylglycerol acyltransferase (DGAT), related to plant DGAT3, with heterologous DGAT activity. In this work, we demonstrate that Chlamydomonas reinhardtii DGAT3 localizes to the chloroplast and that its expression is induced by light, in correspondence with TAG accumulation. Dgat3 mRNAs and TAGs increase in both wild-type and starch-deficient cells grown with acetate upon transferring them from dark or low light to higher light levels, albeit affected by the particularities of each strain. The response of dgat3 mRNAs and TAGs to light depends on the pre-existing levels of TAGs, suggesting the existence of a negative regulatory loop in the synthesis pathway, although an effect of TAG turnover cannot be ruled out. Altogether, these results hint towards a possible role of DGAT3 in light-dependent TAG accumulation in C. reinhardtii.

Multiplexed Genome Editing via an RNA Polymerase II Promoter-Driven sgRNA Array in the Diatom Phaeodactylum tricornutum: Insights Into the Role of StLDP

CRISPR/Cas9-mediated genome editing has been demonstrated in the model diatom P. tricornutum, yet the currently available genetic tools do not combine the various advantageous features into a single, easy-to-assemble, modular construct that would allow the multiplexed targeting and creation of marker-free genome-edited lines. In this report, we describe the construction of the first modular two-component transcriptional unit system expressing SpCas9 from a diatom episome, assembled using the Universal Loop plasmid kit for Golden Gate assembly. We compared the editing efficiency of two constructs with orthogonal promoter-terminator combinations targeting the StLDP gene, encoding the major lipid droplet protein of P. tricornutum. Multiplexed targeting of the StLDP gene was confirmed via PCR screening, and lines with homozygous deletions were isolated from primary exconjugants. An editing efficiency ranging from 6.7 to 13.8% was observed in the better performing construct. Selected gene-edited lines displayed growth impairment, altered morphology, and the formation of lipid droplets during nutrient-replete growth. Under nitrogen deprivation, oversized lipid droplets were observed; the recovery of cell proliferation and degradation of lipid droplets were impaired after nitrogen replenishment. The results are consistent with the key role played by StLDP in the regulation of lipid droplet size and lipid homeostasis.

The disassembly of lipid droplets in Chlamydomonas

Lipid droplets (LDs) are ubiquitous and specialized organelles in eukaryotic cells. Consisting of a triacylglycerol core surrounded by a monolayer of membrane lipids, LDs are decorated with proteins and have myriad functions, from carbon/energy storage to membrane lipid remodeling and signal transduction. The biogenesis and turnover of LDs are therefore tightly coordinated with cellular metabolic needs in a fluctuating environment. Lipid droplet turnover requires remodeling of the protein coat, lipolysis, autophagy and fatty acid β-oxidation. Several key components of these processes have been identified in Chlamydomonas (Chlamydomonas reinhardtii), including the major lipid droplet protein, a CXC-domain containing regulatory protein, the phosphatidylethanolamine-binding DTH1 (DELAYED IN TAG HYDROLYSIS1), two lipases and two enzymes involved in fatty acid β-oxidation. Here, we review LD turnover and discuss its physiological significance in Chlamydomonas, a major model green microalga in research on algal oil.

The oleaginous astaxanthin-producing alga Chromochloris zofingiensis: potential from production to an emerging model for studying lipid metabolism and carotenogenesis

The algal lipids-based biodiesel, albeit having advantages over plant oils, still remains high in the production cost. Co-production of value-added products with lipids has the potential to add benefits and is thus believed to be a promising strategy to improve the production economics of algal biodiesel. Chromochloris zofingiensis, a unicellular green alga, has been considered as a promising feedstock for biodiesel production because of its robust growth and ability of accumulating high levels of triacylglycerol under multiple trophic conditions. This alga is also able to synthesize high-value keto-carotenoids and has been cited as a candidate producer of astaxanthin, the strongest antioxidant found in nature. The concurrent accumulation of triacylglycerol and astaxanthin enables C. zofingiensis an ideal cell factory for integrated production of the two compounds and has potential to improve algae-based production economics. Furthermore, with the advent of chromosome-level whole genome sequence and genetic tools, C. zofingiensis becomes an emerging model for studying lipid metabolism and carotenogenesis. In this review, we summarize recent progress on the production of triacylglycerol and astaxanthin by C. zofingiensis. We also update our understanding in the distinctive molecular mechanisms underlying lipid metabolism and carotenogenesis, with an emphasis on triacylglycerol and astaxanthin biosynthesis and crosstalk between the two pathways. Furthermore, strategies for trait improvements are discussed regarding triacylglycerol and astaxanthin synthesis in C. zofingiensis.

Lipid Droplets in Unicellular Photosynthetic Stramenopiles

The Heterokonta or Stramenopile phylum comprises clades of unicellular photosynthetic species, which are promising for a broad range of biotechnological applications, based on their capacity to capture atmospheric CO₂ via photosynthesis and produce biomolecules of interest. These molecules include triacylglycerol (TAG) loaded inside specific cytosolic bodies, called the lipid droplets (LDs). Understanding TAG production and LD biogenesis and function in photosynthetic stramenopiles is therefore essential, and is mostly based on the study of a few emerging models, such as the pennate diatom Phaeodactylum tricornutum and eustigmatophytes, such as Nannochloropsis and Microchloropsis species. The biogenesis of cytosolic LD usually occurs at the level of the endoplasmic reticulum. However, stramenopile cells contain a complex plastid deriving from a secondary endosymbiosis, limited by four membranes, the outermost one being connected to the endomembrane system. Recent cell imaging and proteomic studies suggest that at least some cytosolic LDs might be associated to the surface of the complex plastid, via still uncharacterized contact sites. The carbon length and number of double bonds of the acyl groups contained in the TAG molecules depend on their origin. De novo synthesis produces long-chain saturated or monounsaturated fatty acids (SFA, MUFA), whereas subsequent maturation processes lead to very long-chain polyunsaturated FA (VLC-PUFA). TAG composition in SFA, MUFA, and VLC-PUFA reflects therefore the metabolic context that gave rise to the formation of the LD, either via an early partitioning of carbon following FA de novo synthesis and/or a recycling of FA from membrane lipids, e.g., plastid galactolipids or endomembrane phosphor- or betaine lipids. In this review, we address the relationship between cytosolic LDs and the complex membrane compartmentalization within stramenopile cells, the metabolic routes leading to TAG accumulation, and the physiological conditions that trigger LD production, in response to various environmental factors.

A Lipid Bodies-Associated Galactosyl Hydrolase Is Involved in Triacylglycerol Biosynthesis and Galactolipid Turnover in the Unicellular Green Alga Chlamydomonas reinhardtii

Monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) are the main constituent lipids of thylakoid and chloroplast envelop membranes. Many microalgae can accumulate large amounts of triacylglycerols (TAGs) under adverse environmental conditions, which is accompanied by degradation of the photosynthetic membrane lipids. However, the process mediating the conversion from galactolipids to TAG remains largely unknown. In this study, we performed genetic and biochemical analyses of galactosyl hydrolases (CrGH) identified in the proteome of lipid bodies of the green microalga Chlamydomonas reinhardtii. The recombinant CrGH was confirmed to possess galactosyl hydrolase activity by using o-nitrophenyl-β-D-galactoside as the substrate, and the Michaelis constant (Km) and Kcat of CrGH were 13.98 μM and 3.62 s^-1, respectively. Comparative lipidomic analyses showed that the content of MGDG and DGDG increased by 14.42% and 24.88%, respectively, in the CrGH-deficient mutant as compared with that of the wild type cc4533 grown under high light stress conditions, and meanwhile, the TAG content decreased by 32.20%. Up-regulation of CrGH at both a gene expression and protein level was observed under high light stress (HL) conditions. In addition, CrGH was detected in multiple subcellular localizations, including the chloroplast envelope, mitochondria, and endoplasmic reticulum membranes. This study uncovered a new paradigm mediated by the multi-localized CrGH for the conversion of the photosynthetic membranes to TAGs.

The phosphatidylethanolamine-binding protein DTH1 mediates degradation of lipid droplets in Chlamydomonas reinhardtii

Lipid droplets (LDs) are intracellular organelles found in a wide range of organisms and play important roles in stress tolerance. During nitrogen (N) starvation, Chlamydomonas reinhardtii stores large amounts of triacylglycerols (TAGs) inside LDs. When N is resupplied, the LDs disappear and the TAGs are degraded, presumably providing carbon and energy for regrowth. The mechanism by which cells degrade LDs is poorly understood. Here, we isolated a mutant (dth1-1, Delayed in TAG Hydrolysis 1) in which TAG degradation during recovery from N starvation was compromised. Consequently, the dth1-1 mutant grew poorly compared to its parental line during N recovery. Two additional independent loss-of-function mutants (dth1-2 and dth1-3) also exhibited delayed TAG remobilization. DTH1 transcript levels increased sevenfold upon N resupply, and DTH1 protein was localized to LDs. DTH1 contains a putative lipid-binding domain (DTH1^LBD) with alpha helices predicted to be structurally similar to those in apolipoproteins E and A-I. Recombinant DTH1^LBD bound specifically to phosphatidylethanolamine (PE), a major phospholipid coating the LD surface. Overexpression of DTH1^LBD in Chlamydomonas phenocopied the dth1 mutant's defective TAG degradation, suggesting that the function of DTH1 depends on its ability to bind PE. Together, our results demonstrate that the lipid-binding DTH1 plays an essential role in LD degradation and provide insight into the molecular mechanism of protein anchorage to LDs at the LD surface in photosynthetic cells.

Oil crop genetic modification for producing added value lipids

Plant lipids, mainly stored in seeds and other plant parts, are not only a crucial resource for food and fodder but are also a promising alternative to fossil oils as a chemical industry feedstock. Oil crop cultivation and processing are always important parts of agriculture worldwide. Vegetable oils containing polyunsaturated fatty acids, very long chain fatty acids, conjugated fatty acids, hydroxy fatty acids and wax esters, have outstanding nutritional, lubricating, surfactant, and artificial-fibre-synthesis properties, amongst others. Enhancing the production of such specific lipid components is of economic interest. There has been a considerable amount of information reported about plant lipid biosynthesis, including identification of the pathway map of carbon flux, key enzymes (and the coding genes), and substrate affinities. Plant lipid biosynthesis engineering to produce special oil compounds has become feasible, although until now, only limited progress has been made in the laboratory. It is relatively easy to achieve the experimental objectives, for example, accumulating novel lipid compounds in given plant tissues facilitated by genetic modification. Applying such technologies to agricultural production is difficult, and the challenge is to make engineered crops economically attractive, which is impeded by only moderate success. To achieve this goal, more complicated and systematic strategies should be developed and discussed based on the relevant results currently available.

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.

A Review of Diatom Lipid Droplets

The dynamic nutrient availability and photon flux density of diatom habitats necessitate buffering capabilities in order to maintain metabolic homeostasis. This is accomplished by the biosynthesis and turnover of storage lipids, which are sequestered in lipid droplets (LDs). LDs are an organelle conserved among eukaryotes, composed of a neutral lipid core surrounded by a polar lipid monolayer. LDs shield the intracellular environment from the accumulation of hydrophobic compounds and function as a carbon and electron sink. These functions are implemented by interconnections with other intracellular systems, including photosynthesis and autophagy. Since diatom lipid production may be a promising objective for biotechnological exploitation, a deeper understanding of LDs may offer targets for metabolic engineering. In this review, we provide an overview of diatom LD biology and biotechnological potential.

CrABCA2 Facilitates Triacylglycerol Accumulation in Chlamydomonas reinhardtii under Nitrogen Starvation

The microalga Chlamydomonas reinhardtii accumulates triacylglycerols (TAGs) in lipid droplets under stress conditions, such as nitrogen starvation. TAG biosynthesis occurs mainly at the endoplasmic reticulum (ER) and requires fatty acid (FA) substrates supplied from chloroplasts. How FAs are transferred from chloroplast to ER in microalgae was unknown. We previously reported that an Arabidopsis thaliana ATP-binding cassette (ABC) transporter, AtABCA9, facilitates FA transport at the ER during seed development. Here we identified a gene homologous to AtABCA9 in the C. reinhardtii genome, which we named CrABCA2. Under nitrogen deprivation conditions, CrABCA2 expression was upregulated, and the CrABCA2 protein level also increased. CrABCA2 knockdown lines accumulated less TAGs and CrABCA2 overexpression lines accumulated more TAGs than their untransformed parental lines. Transmission electron microscopy showed that CrABCA2 was localized in swollen ER. These results suggest that CrABCA2 transports substrates for TAG biosynthesis to the ER during nitrogen starvation . Our study provides a potential tool for increasing lipid production in microalgae.

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.

New Insights Into the Role of Seed Oil Body Proteins in Metabolism and Plant Development

Oil bodies (OBs) are ubiquitous dynamic organelles found in plant seeds. They have attracted increasing attention recently because of their important roles in plant physiology. First, the neutral lipids stored within these organelles serve as an initial, essential source of energy and carbon for seed germination and post-germinative growth of the seedlings. Secondly, they are involved in many other cellular processes such as stress responses, lipid metabolism, organ development, and hormone signaling. The biological functions of seed OBs are dependent on structural proteins, principally oleosins, caleosins, and steroleosins, which are embedded in the OB phospholipid monolayer. Oleosin and caleosin proteins are specific to plants and mainly act as OB structural proteins and are important for the biogenesis, stability, and dynamics of the organelle; whereas steroleosin proteins are also present in mammals and play an important role in steroid hormone metabolism and signaling. Significant progress using new genetic, biochemical, and imaging technologies has uncovered the roles of these proteins. Here, we review recent work on the structural or metabolic roles of these proteins in OB biogenesis, stabilization and degradation, lipid homeostasis and mobilization, hormone signal transduction, stress defenses, and various aspects of plant growth and development.

An efficient and comprehensive plant glycerolipids analysis approach based on high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer

In past two decades, numerous lipidomics approaches based on mass spectrometry with or without liquid chromatography separation have been established for identification and quantification of lipids in plants. In this study, we developed an efficient and comprehensive lipidomics approach based on UPLC with an Acquity UPLCTM BEH C18 column coupled to TripleTOF using ESI in positive ion mode and MS/MSALL scan for data collection. Lipid extract was prepared to 2 mg/ml solution according to dry tissue weight and mixed with 13 kinds of internal standards including PA, PC, PE, and PG. Each analysis required single injection of 5-10 μl lipid solvent and completed in 32 min. A target method dataset was generated using the LipidView software for prediction of the accurate mass of target lipid species. The dataset was uploaded into the PeakView to create processing datasets to search target lipid species, which achieved batch data processing of multiple samples for lipid species-specific identification and quantification. As proof of concept, we profiled the lipids of different tissues of rapeseed. Thirteen lipid classes including 218 glycerolipids were identified including 46 TAGs, 15 DAGs, 20 PCs, 24 PEs, 13 PGs, 14 PIs, 26 PSs, 12 PAs, 16 MGDGs, 16 DGDGs, 6 LysoPCs, 5 LysoPEs, and 5 LysoPGs. Together, our approach permits the analysis of glycerolipids in plant tissues with simplicity in sample analysis and data processing using UPLC-TripleTOF.

Proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism

Chromochloris zofingiensis represents an industrially relevant and unique green alga, given its capability of synthesizing triacylglycerol (TAG) and astaxanthin simultaneously for storage in lipid droplets (LDs). To further decipher lipid metabolism, the nitrogen deprivation (ND)-induced LDs from C. zofingiensis were isolated, purified, and subjected to proteomic analysis. Intriguingly, many C. zofingiensis LD proteins had no orthologs present in LD proteome of the model alga Chlamydomonas reinhardtii. Seven novel LD proteins (i.e., two functionally unknown proteins, two caleosins, two lipases, and one l-gulonolactone oxidase) and the major LD protein (MLDP), which were all transcriptionally up-regulated by ND, were selected for further investigation. Heterologous expression in yeast demonstrated that all tested LD proteins were localized to LDs and all except the two functionally unknown proteins enabled yeast to produce more TAG. MLDP could restore the phenotype of mldp mutant strain and enhance TAG synthesis in wild-type strain of C. reinhardtii. Although MLDP and caleosins had a comparable abundance in LDs, they responded distinctly to ND at the transcriptional level. The two lipases, instead of functioning as TAG lipases, likely recycled polar lipids to support TAG synthesis. For the first time, we reported that l-gulonolactone oxidase was abundant in LDs and facilitated TAG accumulation. Moreover, we also proposed a novel working model for C. zofingiensis LDs. Taken together, our work unravels the unique characteristics of C. zofingiensis LDs and provides insights into algal LD biogenesis and TAG synthesis, which would facilitate genetic engineering of this alga for TAG improvement.

LIP4 Is Involved in Triacylglycerol Degradation in Chlamydomonas reinhardtii

Degradation of the storage compound triacylglycerol (TAG) is a crucial process in response to environmental stimuli. In microalgae, this process is important for re-growth when conditions become favorable after cells have experienced stresses. Mobilization of TAG is initiated by actions of lipases causing the release of glycerol and free fatty acids, which can be further broken down for energy production or recycled to synthesize membrane lipids. Although key enzymes in the process, TAG lipases remain to be characterized in the model green alga Chlamydomonas reinhardtii. Here, we describe the functional analysis of a putative TAG lipase, i.e. LIP4, which shares 44% amino acid identity with the major TAG lipase in Arabidopsis (SUGAR DEPENDENT1-SDP1). The LIP4 transcript level was downregulated during nitrogen deprivation when TAG accumulates, but was upregulated during nitrogen resupply (NR) when TAG was degraded. Both artificial microRNA and insertional mutants showed a delay in TAG mobilization during NR. The difference in TAG degradation was more pronounced when the cultures were incubated without acetate in the dark. Furthermore, the lip4 insertional mutants over-accumulated TAG during optimal growth conditions. Taken together, the results suggest to us that LIP4 likely acts as a TAG lipase and plays a role in TAG homeostasis in Chlamydomonas.

Ultrastructural patterns of photoacclimation and photodamage to photosynthetic algae cell under environmental stress

In oxygenic phototrophs including unicellular algae, acclimation to and damage by diverse environmental stresses induce profound changes in the ultrastructural organization of the cell. These alterations reflect acclimation of the photosynthetic apparatus to unfavorable conditions (mainly reduction of the chloroplast and its membranal system) and rewiring of the photo-fixed carbon fluxes in the cell. These changes, eventually pursuing mitigation of the photooxidative damage risk, are manifested by the formation of diverse carbon-rich inclusions. Although the physiological and molecular basis of these processes are well understood, the ultrastructural manifestations of the stress responses are often fragmented and frequently controversial. This minireview attempts to generalize on the ultrastructural patterns accompanying stresses in the photosynthetic cell, involving the concerted rearrangements of its assimilatory and storage compartments. The changes characteristic of normal functioning and emergency reduction of the chloroplast thylakoids under harsh stress are also addressed. Special attention is paid to the manifestations of the engagement of photoprotection via active (energy-dependent non-photochemical quenching) and passive mechanisms (e.g. optical shielding by secondary carotenoids). We also underline the potentially important role of autophagy-like processes and provide a more integral view of ultrastructural rearrangements under stress.

Possible Roles of Membrane Trafficking Components for Lipid Droplet Dynamics in Higher Plants and Green Algae

Lipid droplets are ubiquitous dynamic organelles that contain neutral lipids surrounded by a phospholipid monolayer. They can store and supply lipids for energy metabolism and membrane synthesis. In addition, protein transport and lipid exchange often occur between LDs and various organelles to control lipid homeostasis in response to multiple stress responses and cellular signaling. In recent years, multiple membrane trafficking proteins have been identified through LD proteomics and genetic analyses. These membrane trafficking machineries are emerging as critical regulators to function in different LD-organelle interactions, e.g., for LD dynamics, biogenesis and turnover. In this review, we will summarize recent advances in regard to LD-related membrane trafficking proteins and discuss future investigations in higher plants and green algae.

Triacylglycerol accumulates exclusively outside the chloroplast in short-term nitrogen-deprived Chlamydomonas reinhardtii

In microalgae, triacylglycerol (TAG) biosynthesis occurs by parallel pathways involving both the chloroplast and endoplasmic reticulum. A better understanding of contribution of each pathway to TAG assembly facilitates enhanced TAG production via rational genetic engineering of microalgae. Here, using a UPLC-MS(/MS) coupled with TLC-GC-based lipidomic platform, the early response of the major glycerolipids to nitrogen stress was analyzed at both the cellular and chloroplastidic levels in the model green alga Chlamydomonas reinhardtii. Subcellular lipidomic analysis demonstrated that TAG was accumulated exclusively outside the chloroplast, and remained unaltered inside the chloroplast after 4 h of nitrogen starvation. This study ascertained the existence of the glycolipid, digalactosyldiacylglycerol (DGDG), outside the chloroplast and the betaine lipid, diacylglycerol-N,N,N-trimethylhomoserine (DGTS), inside the chloroplast. The newly synthesized DGDG and DGTS prominently increased at the extra-chloroplastidic compartments and served as the major precursors for TAG biosynthesis. In particular, DGDG contributed to the extra-chloroplastidic TAG assembly in form of diacylglycerol (DAG) and DGTS in form of acyl groups. The chloroplastidic membrane lipid, monogalactosyldiacylglycerol (MGDG), was proposed to primarily offer DAG for TAG formation outside the chloroplast. This study provides valuable insights into the subcellular glycerolipidomics and unveils the acyl flux into the extra-chloroplastidic TAG in microalgae.

3D Reconstruction of Lipid Droplets in the Seed of Brassica napus

Rapeseed is one of the most important and widely cultured oilseed crops for food and nonfood purposes worldwide. Neutral lipids are stored in lipid droplets (LDs) as fuel for germination and subsequent seedling growth. Most of the LD detection in seeds was still in 2D levels, and some of the details might have been lost in previous studies. In the present work, the configuration of LDs in seeds was obtained by confocal imaging combined with 3D reconstruction technology in Brassica napus. The size and shape of LDs, LD numbers, cell interval spaces and cell size were observed and compared at 3D levels in the seeds of different materials with high and low oil content. It was also revealed that different cells located in the same tissue exhibited various oil contents according to the construction at the 3D level, which was not previously reported in B. napus. The present work provides a new way to understand the differential in cell populations and enhance the seed oil content at the single cell level within seeds.

Leveraging algal omics to reveal potential targets for augmenting TAG accumulation

Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.

Autophagic flux is required for the synthesis of triacylglycerols and ribosomal protein turnover in Chlamydomonas

Autophagy is an intracellular catabolic process that allows cells to recycle unneeded or damaged material to maintain cellular homeostasis. This highly dynamic process is characterized by the formation of double-membrane vesicles called autophagosomes, which engulf and deliver the cargo to the vacuole. Flow of material through the autophagy pathway and its degradation in the vacuole is known as autophagic flux, and reflects the autophagic degradation activity. A number of assays have been developed to determine autophagic flux in yeasts, mammals, and plants, but it has not been examined yet in algae. Here we analyzed autophagic flux in the model green alga Chlamydomonas reinhardtii. By monitoring specific autophagy markers such as ATG8 lipidation and using immunofluorescence and electron microscopy techniques, we show that concanamycin A, a vacuolar ATPase inhibitor, blocks autophagic flux in Chlamydomonas. Our results revealed that vacuolar lytic function is needed for the synthesis of triacylglycerols and the formation of lipid bodies in nitrogen- or phosphate-starved cells. Moreover, we found that concanamycin A treatment prevented the degradation of ribosomal proteins RPS6 and RPL37 under nitrogen or phosphate deprivation. These results indicate that autophagy might play an important role in the regulation of lipid metabolism and the recycling of ribosomal proteins under nutrient limitation in Chlamydomonas.

Endoplasmic reticulum acyltransferase with prokaryotic substrate preference contributes to triacylglycerol assembly in Chlamydomonas

Understanding the unique features of triacylglycerol (TAG) metabolism in microalgae may be necessary to realize the full potential of these organisms for biofuel and biomaterial production. In the unicellular green alga Chlamydomonas reinhardtii a chloroplastic (prokaryotic) pathway has been proposed to play a major role in TAG precursor biosynthesis. However, as reported here, C. reinhardtii contains a chlorophyte-specific lysophosphatidic acid acyltransferase, CrLPAAT2, that localizes to endoplasmic reticulum (ER) membranes. Unlike canonical, ER-located LPAATs, CrLPAAT2 prefers palmitoyl-CoA over oleoyl-CoA as the acyl donor substrate. RNA-mediated suppression of CrLPAAT2 indicated that the enzyme is required for TAG accumulation under nitrogen deprivation. Our findings suggest that Chlamydomonas has a distinct glycerolipid assembly pathway that relies on CrLPAAT2 to generate prokaryotic-like TAG precursors in the ER.

Arabidopsis lipid droplet-associated protein (LDAP) - interacting protein (LDIP) influences lipid droplet size and neutral lipid homeostasis in both leaves and seeds

Cytoplasmic lipid droplets (LDs) are found in all types of plant cells; they are derived from the endoplasmic reticulum and function as a repository for neutral lipids, as well as serving in lipid remodelling and signalling. However, the mechanisms underlying the formation, steady-state maintenance and turnover of plant LDs, particularly in non-seed tissues, are relatively unknown. Previously, we showed that the LD-associated proteins (LDAPs) are a family of plant-specific, LD surface-associated coat proteins that are required for proper biogenesis of LDs and neutral lipid homeostasis in vegetative tissues. Here, we screened a yeast two-hybrid library using the Arabidopsis LDAP3 isoform as 'bait' in an effort to identify other novel LD protein constituents. One of the candidate LDAP3-interacting proteins was Arabidopsis At5g16550, which is a plant-specific protein of unknown function that we termed LDIP (LDAP-interacting protein). Using a combination of biochemical and cellular approaches, we show that LDIP targets specifically to the LD surface, contains a discrete amphipathic α-helical targeting sequence, and participates in both homotypic and heterotypic associations with itself and LDAP3, respectively. Analysis of LDIP T-DNA knockdown and knockout mutants showed a decrease in LD abundance and an increase in variability of LD size in leaves, with concomitant increases in total neutral lipid content. Similar phenotypes were observed in plant seeds, which showed enlarged LDs and increases in total amounts of seed oil. Collectively, these data identify LDIP as a new player in LD biology that modulates both LD size and cellular neutral lipid homeostasis in both leaves and seeds.

Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation

BACKGROUND

Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering.

RESULTS

An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum. Transcript data were correlated with metabolic data for cellular contents of starch and of different lipid fractions. A pronounced transcriptional down-regulation of photosynthesis became apparent in response to nitrogen starvation, whereas glucose catabolism was found to be up-regulated. An in-depth reconstruction and analysis of the pathways for glycerolipid, central carbon, and starch metabolism revealed that distinct transcriptional changes were generally found only for specific steps within a metabolic pathway. In addition to pathway analyses, the transcript data were also used to refine the current genome annotation. The transcriptome data were integrated into a database and complemented with data for other microalgae which were also subjected to nitrogen starvation. It is available at https://tdbmn.cebitec.uni-bielefeld.de.

CONCLUSIONS

Based on the transcriptional responses to different stages of nitrogen availability, a model for triacylglycerol and lipid hyperaccumulation is proposed, which involves transcriptional induction of thioesterases, differential regulation of lipases, and a re-routing of the central carbon metabolism. Over-expression of distinct thioesterases was identified to be a potential strategy to increase the oleaginous phenotype of M. neglectum, and furthermore specific lipases were identified as potential targets for future metabolic engineering approaches.

Analysis of the lipid body proteome of the oleaginous alga Lobosphaera incisa

BACKGROUND

Lobosphaera incisa (L. incisa) is an oleaginous microalga that stores triacylglycerol (TAG) rich in arachidonic acid in lipid bodies (LBs). This organelle is gaining attention in algal research, since evidence is accumulating that proteins attached to its surface fulfill important functions in TAG storage and metabolism.

RESULTS

Here, the composition of the LB proteome in L incisa was investigated by comparing different cell fractions in a semiquantitative proteomics approach. After applying stringent filters to the proteomics data in order to remove contaminating proteins from the list of possible LB proteins (LBPs), heterologous expression of candidate proteins in tobacco pollen tubes, allowed us to confirm 3 true LBPs: A member of the algal Major Lipid Droplet Protein family, a small protein of unknown function and a putative lipase. In addition, a TAG lipase that belongs to the SUGAR DEPENDENT 1 family of TAG lipases known from oilseed plants was identified. Its activity was verified by functional complementation of an Arabidopsis thaliana mutant lacking the major seed TAG lipases.

CONCLUSIONS

Here we describe 3 LBPs as well as a TAG lipase from the oleaginous microalga L. incisa and discuss their possible involvement in LB metabolism. This study highlights the importance of filtering LB proteome datasets and verifying the subcellular localization one by one, so that contaminating proteins can be recognized as such. Our dataset can serve as a valuable resource in the identification of additional LBPs, shedding more light on the intriguing roles of LBs in microalgae.

A multidomain enzyme, with glycerol-3-phosphate dehydrogenase and phosphatase activities, is involved in a chloroplastic pathway for glycerol synthesis in Chlamydomonas reinhardtii

Understanding the unique features of algal metabolism may be necessary to realize the full potential of algae as feedstock for the production of biofuels and biomaterials. Under nitrogen deprivation, the green alga C. reinhardtii showed substantial triacylglycerol (TAG) accumulation and up-regulation of a gene, GPD2, encoding a multidomain enzyme with a putative phosphoserine phosphatase (PSP) motif fused to glycerol-3-phosphate dehydrogenase (GPD) domains. Canonical GPD enzymes catalyze the synthesis of glycerol-3-phosphate (G3P) by reduction of dihydroxyacetone phosphate (DHAP). G3P forms the backbone of TAGs and membrane glycerolipids and it can be dephosphorylated to yield glycerol, an osmotic stabilizer and compatible solute under hypertonic stress. Recombinant Chlamydomonas GPD2 showed both reductase and phosphatase activities in vitro and it can work as a bifunctional enzyme capable of synthesizing glycerol directly from DHAP. In addition, GPD2 and a gene encoding glycerol kinase were up-regulated in Chlamydomonas cells exposed to high salinity. RNA-mediated silencing of GPD2 revealed that the multidomain enzyme was required for TAG accumulation under nitrogen deprivation and for glycerol synthesis under high salinity. Moreover, a GPD2-mCherry fusion protein was found to localize to the chloroplast, supporting the existence of a GPD2-dependent plastid pathway for the rapid synthesis of glycerol in response to hyperosmotic stress. We hypothesize that the reductase and phosphatase activities of PSP-GPD multidomain enzymes may be modulated by post-translational modifications/mechanisms, allowing them to synthesize primarily G3P or glycerol depending on environmental conditions and/or metabolic demands in algal species of the core Chlorophytes.

Tobacco pollen tubes - a fast and easy tool for studying lipid droplet association of plant proteins

In recent years, lipid droplets have emerged as dynamic organelles rather than inactive storage sites for triacylglycerol. The number of proteins known to be associated with lipid droplets has increased, but remains small in comparison with those found with other organelles. Also the mechanisms of how lipid droplets are recognized and bound by proteins need deeper investigation. Here, we present a fast, simple and inexpensive approach to assay proteins for their association with lipid droplets in vivo that can help to screen protein candidates or mutated variants of proteins for their association in an efficient manner. For this, a system to transiently transform Nicotiana tabacum pollen grains was used because these naturally contain lipid droplets. We designed vectors for fast cloning of genes as fusions with either mVenus or mCherry. This allowed us to assay colocalization with lipid droplets stained with Nile Red and Bodipy 505/515, respectively. We successfully tested our system not only for proteins from Arabidopsis thaliana, but also for proteins from the moss Physcomitrella patens and the alga Chlamydomonas reinhardtii. The small size of the vector used allows easy exchange of codons by site-directed mutagenesis. We used this to show that two proline residues in the proline knot of a caleosin are not essential for the binding of lipid droplets. We also demonstrated that peroxisomes are not associated with the lipid droplets in tobacco pollen tubes, which reduces the risk of false interpretation of microscopic data in our system.

The plant lipidome in human and environmental health

Lipids and oils derived from plant and algal photosynthesis constitute much of human daily caloric intake and provide the basis for high-energy bioproducts, chemical feedstocks for countless applications, and even fossil fuels over geological time scales. Sustainable production of high-energy compounds from plants is essential to preserving fossil fuel sources and ensuring the well-being of future generations. As a result of progress in basic research on plant and algal lipid metabolism, in combination with advances in synthetic biology, we can now tailor plant lipids for desirable biological, physical, and chemical properties. We highlight recent advances in plant lipid translational biology and discuss untapped areas of research that might expand the application of plant lipids.

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

Lipid droplets (LDs) are cell compartments specialized for oil storage. Although their role and biogenesis are relatively well documented in seeds, little is known about their composition, structure and function in senescing leaves where they also accumulate. Here, we used a label free quantitative mass spectrometry approach to define the LD proteome of aging Arabidopsis leaves. We found that its composition is highly different from that of seed/cotyledon and identified 28 proteins including 9 enzymes of the secondary metabolism pathways involved in plant defense response. With the exception of the TRIGALACTOSYLDIACYLGLYCEROL2 protein, we did not identify enzymes implicated in lipid metabolism, suggesting that growth of leaf LDs does not occur by local lipid synthesis but rather through contact sites with the endoplasmic reticulum (ER) or other membranes. The two most abundant proteins of the leaf LDs are the CALEOSIN3 and the SMALL RUBBER PARTICLE1 (AtSRP1); both proteins have structural functions and participate in plant response to stress. CALEOSIN3 and AtSRP1 are part of larger protein families, yet no other members were enriched in the LD proteome suggesting a specific role of both proteins in aging leaves. We thus examined the function of AtSRP1 at this developmental stage and found that AtSRP1 modulates the expression of CALEOSIN3 in aging leaves. Furthermore, AtSRP1 overexpression induces the accumulation of triacylglycerol with an unusual composition compared to wild-type. We demonstrate that, although AtSRP1 expression is naturally increased in wild type senescing leaves, its overexpression in senescent transgenic lines induces an over-accumulation of LDs organized in clusters at restricted sites of the ER. Conversely, atsrp1 knock-down mutants displayed fewer but larger LDs. Together our results reveal that the abundancy of AtSRP1 regulates the neo-formation of LDs during senescence. Using electron tomography, we further provide evidence that LDs in leaves share tenuous physical continuity as well as numerous contact sites with the ER membrane. Thus, our data suggest that leaf LDs are functionally distinct from seed LDs and that their biogenesis is strictly controlled by AtSRP1 at restricted sites of the ER.

Label-free in vivo analysis of intracellular lipid droplets in the oleaginous microalga Monoraphidium neglectum by coherent Raman scattering microscopy

Oleaginous photosynthetic microalgae hold great promise as non-food feedstocks for the sustainable production of bio-commodities. The algal lipid quality can be analysed by Raman micro-spectroscopy, and the lipid content can be imaged in vivo in a label-free and non-destructive manner by coherent anti-Stokes Raman scattering (CARS) microscopy. In this study, both techniques were applied to the oleaginous microalga Monoraphidium neglectum, a biotechnologically promising microalga resistant to commonly applied lipid staining techniques. The lipid-specific CARS signal was successfully separated from the interfering two-photon excited fluorescence of chlorophyll and for the first time, lipid droplet formation during nitrogen starvation could directly be analysed. We found that the neutral lipid content deduced from CARS image analysis strongly correlated with the neutral lipid content measured gravimetrically and furthermore, that the relative degree of unsaturation of fatty acids stored in lipid droplets remained similar. Interestingly, the lipid profile during cellular adaption to nitrogen starvation showed a two-phase characteristic with initially fatty acid recycling and subsequent de novo lipid synthesis. This works demonstrates the potential of quantitative CARS microscopy as a label-free lipid analysis technique for any microalgal species, which is highly relevant for future biotechnological applications and to elucidate the process of microalgal lipid accumulation.

Characterization of type 2 diacylglycerol acyltransferases in Chlamydomonas reinhardtii reveals their distinct substrate specificities and functions in triacylglycerol biosynthesis

Diacylglycerol acyltransferases (DGATs) catalyze a rate-limiting step of triacylglycerol (TAG) biosynthesis in higher plants and yeast. The genome of the green alga Chlamydomonas reinhardtii has multiple genes encoding type 2 DGATs (DGTTs). Here we present detailed functional and biochemical analyses of Chlamydomonas DGTTs. In vitro enzyme analysis using a radiolabel-free assay revealed distinct substrate specificities of three DGTTs: CrDGTT1 preferred polyunsaturated acyl CoAs, CrDGTT2 preferred monounsaturated acyl CoAs, and CrDGTT3 preferred C16 CoAs. When diacylglycerol was used as the substrate, CrDGTT1 preferred C16 over C18 in the sn-2 position of the glycerol backbone, but CrDGTT2 and CrDGTT3 preferred C18 over C16. In vivo knockdown of CrDGTT1, CrDGTT2 or CrDGTT3 resulted in 20-35% decreases in TAG content and a reduction of specific TAG fatty acids, in agreement with the findings of the in vitro assay and fatty acid feeding test. These results demonstrate that CrDGTT1, CrDGTT2 and CrDGTT3 possess distinct specificities toward acyl CoAs and diacylglycerols, and may work in concert spatially and temporally to synthesize diverse TAG species in C. reinhardtii. CrDGTT1 was shown to prefer prokaryotic lipid substrates and probably resides in both the endoplasmic reticulum and chloroplast envelope, indicating its role in prokaryotic and eukaryotic TAG biosynthesis. Based on these findings, we propose a working model for the role of CrDGTT1 in TAG biosynthesis. This work provides insight into TAG biosynthesis in C. reinhardtii, and paves the way for engineering microalgae for production of biofuels and high-value bioproducts.

Antimicrobial cocktails to control bacterial and fungal contamination in Chlamydomonas reinhardtii cultures

Chlamydomonas reinhardtii is a unicellular green alga widely used for research in photosynthesis, cell cycle regulation, ciliary biogenesis, and other physiological processes. Sterile cultures are needed for these studies, but contamination from bacteria and fungi occurs frequently. Although the One-shot Solution cocktail consisting of carbendazim, ampicillin, and cefotaxime has been developed for removing these contaminants from algal cultures, it is not always effective. Here we report two new antimicrobial cocktails for treating mixed bacterial and fungal contamination of Chlamydomonas cultures. A combination of the bactericide nalidixic acid with one of two fungicides, azoxystrobin or tebuconazole, was more effective than the One-shot Solution cocktail. In some of our tests, we find that alternating use of our new cocktails with One-shot Solution is needed to remove obstinate contaminants.

Stress-induced neutral lipid biosynthesis in microalgae - Molecular, cellular and physiological insights

Photosynthetic microalgae have promise as biofuel feedstock. Under certain conditions, they produce substantial amounts of neutral lipids, mainly in the form of triacylglycerols (TAGs), which can be converted to fuels. Much of our current knowledge on the genetic and molecular basis of algal neutral lipid metabolism derives mainly from studies of plants, i.e. seed tissues, and to a lesser extent from direct studies of algal lipid metabolism. Thus, the knowledge of TAG synthesis and the cellular trafficking of TAG precursors in algal cells is to a large extent based on genome predictions, and most aspects of TAG metabolism have yet to be experimentally verified. The biofuel prospects of microalgae have raised the interest in mechanistic studies of algal TAG biosynthesis in recent years and resulted in an increasing number of publications on lipid metabolism in microalgae. In this review we summarize the current findings on genetic, molecular and physiological studies of TAG accumulation in microalgae. Special emphasis is on the functional analysis of key genes involved in TAG synthesis, molecular mechanisms of regulation of TAG biosynthesis, as well as on possible mechanisms of lipid droplet formation in microalgal cells. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.

Fatty Acid and Lipid Transport in Plant Cells

Fatty acids (FAs) and lipids are essential - not only as membrane constituents but also for growth and development. In plants and algae, FAs are synthesized in plastids and to a large extent transported to the endoplasmic reticulum for modification and lipid assembly. Subsequently, lipophilic compounds are distributed within the cell, and thus are transported across most membrane systems. Membrane-intrinsic transporters and proteins for cellular FA/lipid transfer therefore represent key components for delivery and dissemination. In addition to highlighting their role in lipid homeostasis and plant performance, different transport mechanisms for land plants and green algae - in the model systems Arabidopsis thaliana, Chlamydomonas reinhardtii - are compared, thereby providing a current perspective on protein-mediated FA and lipid trafficking in photosynthetic cells.