Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae

Discovery of mannose as an alternative non-nutrient-deficient regulator of lipid accumulation in microalgae

INTRODUCTION

Microalgae are considered promising bioenergy producers, but their commercial potential is limited by low lipid yields. Nutrient deprivation, particularly nitrogen starvation, is a primary strategy to enhance lipid synthesis efficiency in microalgae. However, controlling this process flexibly, effectively, and accurately remains challenging. Moreover, nutrient deficiency triggers expression changes of numerous genes, complicating the identification of key lipid biosynthesis regulators.

OBJECTIVES

For the first time, we investigated mannose as a novel non-nutrient-deficient regulator of lipid accumulation in microalgae and explored its potential underlying mechanisms.

METHODS

We examined how mannose induction affectslipid accumulation in Chlorella sorokiniana W1 under various culture conditions and compared its effects with nitrogen-starvation. Transcriptome analysis and genome-scale metabolic modeling were used to elucidate the regulatory mechanisms underlying mannose-induced lipid synthesis. Additionally, potential transcription factors were identified using weighted gene co-expression network analysis.

RESULTS

Mannose drives rapid and sustained lipid accumulation in C. sorokiniana under various cultivation conditions, independent of nutrient deficiencies. Under autotrophic conditions, mannose increased lipid content of microalgae by 80.1 %. Notably, mannose was not consumed during cultivation, supporting its role as an inducer. Transcriptomic analysis revealed that mannose increased carbon flux by upregulating genes associated with the Calvin cycle, glycolysis, the TCA cycle, and starch degradation. It also redirected carbon towards lipid accumulation by upregulating lipid synthesis pathways and downregulating lipid degradation pathways. Additionally, two SBP1 transcription factors specifically responsive to mannose were identified and may regulate carbon metabolism in microalgae.

CONCLUSION

Our study introduces mannose as a novel non-nutrient-deficiency regulatory factor for lipid accumulation in C. sorokiniana W1, and explores its metabolic and regulatory mechanisms under various nutrient conditions. The research demonstrates that mannose induction has significant potential for improving microalgal lipid production in practical applications.

Enhanced growth and metabolite production from a novel strain of Porphyridium sp

Microalgae are capable of generating numerous metabolites that possess notable biological activities and hold substantial promise for various industrial applications. Nevertheless, the taxonomic diversity of these photosynthetic microorganisms has not received thorough investigation. Using the 18S rRNA encoding gene, a recently discovered strain originating from the Tunisian coast (the governorate of Mahdia) was identified as a member of the Porphyridium genus. The growth response as well as the metabolite accumulation of Porphyridium sp. to different culture media (Pm, F/2, and Hemerick) was investigated over a period of 52 days. The highest biomass production was recorded with Pm medium (2 × 107 cell/mL). The apparent growth rates (µ) and the doubling time (Dt) were about 0.081 day-1 and 12.34 days, respectively. The highest chlorophyll a (0.678 ± 0.005 pg/cell), total carotenoids (0.18 ± 0.003 pg/cell), phycoerythrin (3.88 ± 0.003 pg/cell), and proteins (14.58 ± 0.35 pg/cell) contents were observed with F/2 medium. Cultivating Porphyridium sp. in both F/2 and Hemerick media yielded similar levels of starch accumulation. The Hemerick medium has proven to be the most suitable for the production of lipids (2.23% DW) and exopolysaccharides (5.41 ± 0.56 pg/cell).

Global Profiling of Protein Phosphorylation, Acetylation, and β-Hydroxybutyrylation in Nannochloropsis oceanica

Protein post-translational modifications (PTMs) regulate protein functions but remain poorly characterized in Nannochloropsis. This study examined three PTMs: lysine acetylation (Kac), lysine β-hydroxybutyrylation (Kbhb), and phosphorylation. Using LC-MS/MS, we identified 4571 Kac sites, 7812 Kbhb sites, and 6237 phosphorylation sites across 2455, 3109, and 2786 proteins, respectively. Subcellular localization analysis revealed significant overlaps between Kac and Kbhb proteins, primarily in the chloroplast, cytosol, and nucleus, while phosphorylated proteins were predominantly located in the nucleus and chloroplast. Motif analysis highlighted specific amino acid enrichments around modification sites, with several motifs conserved. Additionally, 529 proteins harbored all three PTMs, underscoring the potential regulatory interplay. Kac, Kbhb, and phosphorylated proteins were particularly abundant in glycolysis, the TCA cycle, carbon fixation, and lipid metabolism pathways, influencing energy production and lipid accumulation. Based on previous transcriptome data under nutrient-limited conditions, these frequently modified key enzymes appear to be vital components in the response to abiotic stress. The presence of histone modifications related to Kac and Kbhb might also point to the epigenetic regulation in gene expression and stress adaptation. This comprehensive PTM landscape in N. oceanica provides a foundation of valuable insights into future metabolic engineering and biotechnological applications.

Physiological and transcriptomic response of dinoflagellate Gymnodinium catenatum to nitrate deficiency

The paralytic shellfish toxin producing dinoflagellate Gymnodinium catenatum is a globally distributed species and often forms massive blooms. However, the physiological and molecular responses of G. catenatum to nitrate starvation have not been thoroughly investigated. Our results showed that multiple forms of N could be utilized by G. catenatum under nitrate-deficient conditions. Nitrate deficiency adversely affected the growth, cellular Chlorophyll a (Chl a) content, and toxin production of G. catenatum. Transcriptomic analysis revealed significant down-regulation of gene expressions involved in the light reaction of photosynthesis, while genes related to fatty acids synthesis and antioxidation were significantly upregulated in the N-depleted cultures. Our results suggested that excess carbon was channeled into lipid synthesis for energy storage, and antioxidant reactions were upregulated to eliminate toxic peroxides caused by nitrate limitation. These findings highlight the adaptative strategy of G. catenatum in low-nitrate environments, which are crucial factors driving its bloom formation.

Nutritional Quality of Basal Resource in Stream Food Webs Increased with Light Reduction-Implications for Riparian Revegetation

Biofilms are considered a basal resource with high nutritional quality in stream food webs, as periphytic algae are abundant of polyunsaturated fatty acids (PUFAs). PUFAs are essential for growth and reproduction of consumers who cannot or have very limited capacity to biosynthesize. Yet, how the nutritional quality based on PUFA of basal food sources changes with light intensity remains unclear. We conducted a manipulative experiment in mesocosms to explore the response and mechanisms of nutritional quality to shading, simulating riparian restoration. We found a significant increase in PUFA% (including arachidonic acid, ARA) under shading conditions. The increased PUFA is caused by the algal community succession from Cyanobacteria and Chlorophyta to Bacillariophyta which is abundant of PUFA (especially eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA). On the other hand, shading increased PUFA via upregulating enzymes such as Δ12 desaturase (FAD2, EC:1.14.19.6) and 3-ketoacyl-CoA synthase (KCS, EC:2.3.1.199) in the biosynthesis of unsaturated fatty acid elongation pathways. Our findings imply that riparian reforestation by decreasing light intensity increases the nutritional quality of basal resources in streams, which may enhance transfer of good quality carbon to consumers in higher trophic levels through bottom-up effects.

A novel strategy of bloom forming cyanobacteria Microcystis sp. in response to phosphorus deficiency: Using non-phosphorus lipids substitute phospholipids

Despite significant reductions in phosphorus (P) loads, lakes still experience cyanobacterial blooms. Little is known regarding cellular P regulation in response to P deficiency in widely distributed bloom causing species such as Microcystis. In this study, we investigated changes in P containing and non-P lipids contents and their ratios concomitantly with the determinations of expression levels of genes encoding these lipids in cultural and field Microcystis samples. In the culture, the content of phosphatidylglycerol (PG) decreased from 2.1 μg g-1 in P replete control to 1.2 μg g-1 in P-deficient treatment, while non-P lipids, like sulfoquinovosyldiacylglycerol (SQDG) and monogalactosyldiacylglycerol (MGDG), increased dramatically from 13.6 μg g-1 to 142.3 μg g-1, and from 0.9 μg g-1 to 16.74 μg g-1, respectively. The expression of the MGDG synthesis gene, mgdE, also increased under low P conditions. Significant positive relationships between soluble reactive phosphorus (SRP) and ratios of P-containing lipids (PG) to non-P lipids, including SQDG, MGDG and digalactosyldiacylglycerol (DGDG) (P < 0.05) were observed in the field investigations. Both cultural and field data indicated that Microcystis sp. might increase non-P lipids proportion to lower P demand when suffering from P deficiency. Furthermore, despite lipid remodeling, photosynthetic activity remained stable, as indicated by comparable chlorophyll fluorescence and Fv/Fm ratios among cultural treatments. These findings suggested that Microcystis sp. may dominate in P-limited environments by substituting glycolipids and sulfolipids for phospholipids to reduce P demand without compromising the photosynthetic activity. This effective strategy in response to P deficiency meant a stricter P reduction threshold is needed in terms of Microcystis bloom control.

Low-dose ionizing radiation generates a hormetic response to modify lipid metabolism in Chlorella sorokiniana

Algal biomass is a viable source of chemicals and metabolites for various energy, nutritional, medicinal and agricultural uses. While stresses have commonly been used to induce metabolite accumulation in microalgae in attempts to enhance high-value product yields, this is often very detrimental to growth. Therefore, understanding how to modify metabolism without deleterious consequences is highly beneficial. We demonstrate that low-doses (1-5 Gy) of ionizing radiation in the X-ray range induces a non-toxic, hormetic response in microalgae to promote metabolic activation. We identify specific radiation exposure parameters that give reproducible metabolic responses in Chlorella sorokiniana caused by transcriptional changes. This includes up-regulation of >30 lipid metabolism genes, such as genes encoding an acetyl-CoA carboxylase subunit, phosphatidic acid phosphatase, lysophosphatidic acid acyltransferase, and diacylglycerol acyltransferase. The outcome is an increased lipid yield in stationary phase cultures by 25% in just 24 hours, without any negative effects on cell viability or biomass.

Ameliorating microalgal OMEGA production using omics platforms

Over the past decade, the focus on omega (ω)-3 fatty acids from microalgae has intensified due to their diverse health benefits. Bioprocess optimization has notably increased ω-3 fatty acid yields, yet understanding of the genetic architecture and metabolic pathways of high-yielding strains remains limited. Leveraging genomics, transcriptomics, proteomics, and metabolomics tools can provide vital system-level insights into native ω-3 fatty acid-producing microalgae, further boosting production. In this review, we explore 'omics' studies uncovering alternative pathways for ω-3 fatty acid synthesis and genome-wide regulation in response to cultivation parameters. We also emphasize potential targets to fine-tune in order to enhance yield. Despite progress, an integrated omics platform is essential to overcome current bottlenecks in optimizing the process for ω-3 fatty acid production from microalgae, advancing this crucial field.

Physiological Functions of Phospholipid:Diacylglycerol Acyltransferases

Triacylglycerol (TAG) is among the most energy dense storage forms of reduced carbon in living systems. TAG metabolism plays critical roles in cellular energy balance, lipid homeostasis, cell growth and stress responses. In higher plants, microalgae and fungi, TAG is assembled by acyl-CoA-dependent and acyl-CoA-independent pathways catalyzed by diacylglycerol (DAG) acyltransferase and phospholipid:DAG acyltransferase (PDAT), respectively. This review contains a summary of the current understanding of the physiological functions of PDATs. Emphasis is placed on their role in lipid remodeling and lipid homeostasis in response to abiotic stress or perturbations in lipid metabolism.

Transcriptomic Analysis Reveals the Effect of Urea on Metabolism of Nannochloropsis oceanica

The eukaryotic microalga Nannochloropsis oceanica represents a promising bioresource for the production of biofuels and pharmaceuticals. Urea, a crucial nutrient for the photosynthetic N. oceanica, stimulates the accumulation of substances such as lipids, which influence growth and physiology. However, the specific mechanisms by which N. oceanica responds and adapts to urea addition remain unknown. High-throughput mRNA sequencing and differential gene expression analysis under control and urea-added conditions revealed significant metabolic changes. This involved the differential expression of 2104 genes, with 1354 being upregulated and 750 downregulated, resulting in the reprogramming of crucial pathways such as carbon and nitrogen metabolism, photosynthesis, and lipid metabolism. The results specifically showed that genes associated with photosynthesis in N. oceanica were significantly downregulated, particularly those related to light-harvesting proteins. Interestingly, urea absorption and transport may depend not only on specialized transport channels such as urease but also on alternative transport channels such as the ABC transporter family and the CLC protein family. In addition, urea caused specific changes in carbon and lipid metabolism. Genes associated with the Calvin cycle and carbon concentration mechanisms were significantly upregulated. In lipid metabolism, the expression of genes associated with lipases and polyunsaturated fatty acid synthesis was highly activated. Furthermore, the expression of several genes involved in the tricarboxylic acid cycle and folate metabolism was enhanced, making important contributions to energy supply and the synthesis and modification of genes and macromolecules. Our observations indicate that N. oceanica actively and dynamically regulates the redistribution of carbon and nitrogen after urea addition, providing references for further research on the effects of urea on N. oceanica.

Integration of Epigenome and Lactylome Reveals the Regulation of Lipid Production in Nannochloropsis oceanica

Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM) that participates in gene expression and various metabolic processes. Nannochloropsis has a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions. Moreover, a total of 5375 differential Kla peaks were identified, including 5331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (≤1 kb) (71.07%), 5'UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research offers a new perspective for the investigation of lipid biosynthesis in Nannochloropsis.

Toward the Exploitation of Sustainable Green Factory: Biotechnology Use of Nannochloropsis spp

Securing food, energy, and raw materials for a growing population is one of the most significant challenges of our century. Algae play a central role as an alternative to plants. Wastewater and flue gas can secure nutrients and CO2 for carbon fixation. Unfortunately, algae domestication is necessary to enhance biomass production and reduce cultivation costs. Nannochloropsis spp. have increased in popularity among microalgae due to their ability to accumulate high amounts of lipids, including PUFAs. Recently, the interest in the use of Nannochloropsis spp. as a green bio-factory for producing high-value products increased proportionally to the advances of synthetic biology and genetic tools in these species. In this review, we summarized the state of the art of current nuclear genetic manipulation techniques and a few examples of their application. The industrial use of Nannochloropsis spp. has not been feasible yet, but genetic tools can finally lead to exploiting this full-of-potential microalga.

Genome-wide adenine N6-methylation map reveals epigenomic regulation of lipid accumulation in Nannochloropsis

Epigenetic marks on histones and DNA, such as DNA methylation at N6-adenine (6mA), play crucial roles in gene expression and genome maintenance, but their deposition and function in microalgae remain largely uncharacterized. Here, we report a genome-wide 6mA map for the model industrial oleaginous microalga Nannochloropsis oceanica produced by single-molecule real-time sequencing. Found in 0.1% of adenines, 6mA sites are mostly enriched at the AGGYV motif, more abundant in transposons and 3' untranslated regions, and associated with active transcription. Moreover, 6mA gradually increases in abundance along the direction of gene transcription and shows special positional enrichment near splicing donor and transcription termination sites. Highly expressed genes tend to show greater 6mA abundance in the gene body than do poorly expressed genes, indicating a positive interaction between 6mA and general transcription factors. Furthermore, knockout of the putative 6mA methylase NO08G00280 by genome editing leads to changes in methylation patterns that are correlated with changes in the expression of molybdenum cofactor, sulfate transporter, glycosyl transferase, and lipase genes that underlie reductions in biomass and oil productivity. By contrast, knockout of the candidate demethylase NO06G02500 results in increased 6mA levels and reduced growth. Unraveling the epigenomic players and their roles in biomass productivity and lipid metabolism lays a foundation for epigenetic engineering of industrial microalgae.

Nannochloropsis as an Emerging Algal Chassis for Light-Driven Synthesis of Lipids and High-Value Products

In light of the escalating global energy crisis, microalgae have emerged as highly promising producers of biofuel and high-value products. Among these microalgae, Nannochloropsis has received significant attention due to its capacity to generate not only triacylglycerol (TAG) but also eicosapentaenoic acid (EPA) and valuable carotenoids. Recent advancements in genetic tools and the field of synthetic biology have revolutionized Nannochloropsis into a powerful biofactory. This comprehensive review provides an initial overview of the current state of cultivation and utilization of the Nannochloropsis genus. Subsequently, our review examines the metabolic pathways governing lipids and carotenoids, emphasizing strategies to enhance oil production and optimize carbon flux redirection toward target products. Additionally, we summarize the utilization of advanced genetic manipulation techniques in Nannochloropsis. Together, the insights presented in this review highlight the immense potential of Nannochloropsis as a valuable model for biofuels and synthetic biology. By effectively integrating genetic tools and metabolic engineering, the realization of this potential becomes increasingly feasible.

Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities

The development of microalgal biofuels is of significant importance in advancing the energy transition, alleviating food pressure, preserving the natural environment, and addressing climate change. Numerous countries and regions across the globe have conducted extensive research and strategic planning on microalgal bioenergy, investing significant funds and manpower into this field. However, the microalgae biofuel industry has faced a downturn due to the constraints of high costs. In the past decade, with the development of new strains, technologies, and equipment, the feasibility of large-scale production of microalgae biofuel should be re-evaluated. Here, we have gathered research results from the past decade regarding microalgae biofuel production, providing insights into the opportunities and challenges faced by this industry from the perspectives of microalgae selection, modification, and cultivation. In this review, we suggest that highly adaptable microalgae are the preferred choice for large-scale biofuel production, especially strains that can utilize high concentrations of inorganic carbon sources and possess stress resistance. The use of omics technologies and genetic editing has greatly enhanced lipid accumulation in microalgae. However, the associated risks have constrained the feasibility of large-scale outdoor cultivation. Therefore, the relatively controllable cultivation method of photobioreactors (PBRs) has made it the mainstream approach for microalgae biofuel production. Moreover, adjusting the performance and parameters of PBRs can also enhance lipid accumulation in microalgae. In the future, given the relentless escalation in demand for sustainable energy sources, microalgae biofuels should be deemed a pivotal constituent of national energy planning, particularly in the case of China. The advancement of synthetic biology helps reduce the risks associated with genetically modified (GM) microalgae and enhances the economic viability of their biofuel production.

Evaluating nutrient limitation in co-culture of Chlorella pyrenoidosa and Rhodobacter sphaeroides

The influence of nitrogen deficiency on microalgae-bacteria co-culture has been studied mostly with nitrogen-fixing bacteria. Photosynthetic bacteria (PSB), which are non-nitrogen-fixing bacteria, the impact of N deficiency on its co-culture with microalgae is unknown. In this study, Chlorella pyrenoidosa and Rhodobacter sphaeroides co-culture was cultivated photoheterotrophically with acetate. The impact of N starvation and different P supply levels on oil production were examined. When phosphorus was sufficient, N starvation increased the fatty acid methyl ester (FAME) content from 21.7 % to 28.2 %, and also increased the FAME yield (g CODFAME/g CODAcetate) from 0.17 to 0.22. However, the biomass and FAME productivities decreased. Sufficient phosphorus was also essential for a high growth rate and FAME productivity. Deficiencies in either N or P led to a decrease in the proportion of unsaturated FAMEs. iTRAQ analysis indicated N starvation promoted oil accumulation by driving the carbon flow to fatty acid synthesis in microalgae from co-culture. This study improves the understanding of biomass and lipid production via microalgae-PSB co-culture in photoheterotrophic cultivation. The mechanism of interaction between microalgae and bacteria needs further study.

Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica

Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.

Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1

BACKGROUND

Cottonseed oil is a promising edible plant oil with abundant unsaturated fatty acids. However, few studies have been conducted to explore the characteristics of cottonseed oil. The molecular mechanism of cottonseed oil accumulation remains unclear.

RESULTS

In the present study, we conducted comparative transcriptome and weighted gene co-expression network (WGCNA) analysis for two G. hirsutum materials with significant difference in cottonseed oil content. Results showed that, between the high oil genotype 6053 (H6053) and the low oil genotype 2052 (L2052), a total of 412, 507, 1,121, 1,953, and 2,019 differentially expressed genes (DEGs) were detected at 10, 15, 20, 25, and 30 DPA, respectively. Remarkably, a large number of the down-regulated DEGs were enriched in the phenylalanine metabolic processes. Investigation into the dynamic changes of expression profiling of genes associated with both phenylalanine metabolism and oil biosynthesis has shed light on a significant competitive relationship in substrate allocation during cottonseed development. Additionally, the WGCNA analysis of all DEGs identified eight distinct modules, one of which includes GhPXN1, a gene closely associated with oil accumulation. Through phylogenetic analysis, we hypothesized that GhPXN1 in G. hirsutum might have been introgressed from G. arboreum. Overexpression of the GhPXN1 gene in tobacco leaf suggested a significant reduction in oil content compared to the empty-vector transformants. Furthermore, ten other crucial oil candidate genes identified in this study were also validated using quantitative real-time PCR (qRT-PCR).

CONCLUSIONS

Overall, this study enhances our comprehension of the molecular mechanisms underlying cottonseed oil accumulation.

Strategies of NaCl Tolerance in Saline-Alkali-Tolerant Green Microalga Monoraphidium dybowskii LB50

Studying how freshwater cells modify metabolism and membrane lipids in response to salt stress is important for understanding how freshwater organisms adapt to salt stress and investigating new osmoregulatory ways. Physiological, biochemical, metabolic, and proteomic analyses were applied in a novel saline-alkali-tolerant microalga Monoraphidium dybowskii LB50 under different NaCl concentrations. Cells adopt a variety of strategies to adapt to salt stress, including increasing ion transport and osmolytes, regulating cell cycle and life history, and accumulating triacylglycerol (TAG). A large number of metabolic activities point to TAG accumulation. With increasing NaCl concentration, the C resource for TAG accumulation went from photosynthetically fixed C and a small amount of lipid remodeling to macromolecule degradation and a mass of lipid remodeling, respectively. The energy for TAG accumulation went from linear electron transfer and oxidative phosphate pentose pathway to cyclic electron flow, substrate phosphorylation, oxidation phosphorylation, and FA oxidation. Additionally, digalacturonic acid and amino acids of the N-acetyl group, which usually were the osmotica for marine organisms, were important for M. dybowskii LB50. Freshwater organisms evolved many biological ways to adapt to salt stress. This insight enriches our understanding of the adaptation mechanisms underlying abiotic stress.

Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation

BACKGROUND

Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.

RESULTS

Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the 'fatty acid metabolism', 'response to stress', 'carbon fixation' and 'photosynthesis' functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.

CONCLUSIONS

Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

Overview and Challenges of Large-Scale Cultivation of Photosynthetic Microalgae and Cyanobacteria

Microalgae and cyanobacteria are diverse groups of organisms with great potential to benefit societies across the world. These organisms are currently used in food, feed, pharmaceutical and cosmetic industries. In addition, a variety of novel compounds are being isolated. Commercial production of photosynthetic microalgae and cyanobacteria requires cultivation on a large scale with high throughput. However, scaling up production from lab-based systems to large-scale systems is a complex and potentially costly endeavor. In this review, we summarise all aspects of large-scale cultivation, including aims of cultivation, species selection, types of cultivation (ponds, photobioreactors, and biofilms), water and nutrient sources, temperature, light and mixing, monitoring, contamination, harvesting strategies, and potential environmental risks. Importantly, we also present practical recommendations and discuss challenges of profitable large-scale systems associated with economical design, effective operation and maintenance, automation, and shortage of experienced phycologists.

Biodiesel Production from the Marine Alga Nannochloropsis oceanica Grown on Yeast Wastewater and the Effect on Its Biochemical Composition and Gene Expression

Microalgae-based biodiesel synthesis is currently not commercially viable due to the high costs of culture realizations and low lipid yields. The main objective of the current study was to determine the possibility of growing Nannochloropsis oceanica on Saccharomyces cerevisiae yeast wastewater for biodiesel generation at an economical rate. N. oceanica was grown in Guillard F/2 synthetic medium and three dilutions of yeast wastewater (1, 1.25, and 1.5%). Biodiesel properties, in addition to carbohydrate, protein, lipid, dry weight, biomass, lipid productivity, amino acids, and fatty acid methyl ester (FAMEs) content, were analyzed and the quality of the produced biodiesel is assessed. The data revealed the response of N. oceanica to nitrogen-deficiency in the three dilutions of yeast wastewater. N. oceanica in Y2 (1.25%) yeast wastewater dilution exhibited the highest total carbohydrate and lipid percentages (21.19% and 41.97%, respectively), and the highest lipid productivity (52.46 mg L-1 day -1) under nitrogen deficiency in yeast wastewater. The fatty acids profile shows that N. oceanica cultivated in Y2 (1.25%) wastewater dilution provides a significant level of TSFA (47.42%) and can be used as a feedstock for biodiesel synthesis. In addition, N. oceanica responded to nitrogen shortage in wastewater dilutions by upregulating the gene encoding delta-9 fatty acid desaturase (Δ9FAD). As a result, the oleic and palmitoleic acid levels increased in the fatty acid profile of Y2 yeast wastewater dilution, highlighting the increased activity of Δ9FAD enzyme in transforming stearic acid and palmitic acid into oleic acid and palmitoleic acid. This study proved that the Y2 (1.25%) yeast wastewater dilution can be utilized as a growth medium for improving the quantity of specific fatty acids and lipid productivity in N. oceanica that affect biodiesel quality to satisfy global biodiesel requirements.

Chemical cues in the interaction of herbivory-prey induce consumer-specific morphological and chemical defenses in Phaeocystis globosa

Bloom-forming algae Phaeocystis globosa is one of the most successful blooming algae in the oceans due to its capacity to sense grazer-associated chemical cues and respond adaptively to these grazer-specific cues with opposing shifts in phenotype. P. globosa produces toxic and deterrent compounds as chemical defenses. However, the origin of the signals and underlying mechanisms that triggered the morphological and chemical defenses remain enigmatic. Rotifer was chosen to establish an herbivore-phytoplankton interaction with P. globosa. The influences of rotifer kairomone and conspecific-grazed cue on morphological and chemical defenses in P. globosa were investigated. As a result, rotifer kairomones elicited morphological defenses and broad-spectrum chemical defenses, whereas algae-grazed cues elicited morphological defenses and consumer-specific chemical defenses. According to multi-omics findings, the difference in hemolytic toxicity caused by different stimuli may be related to the upregulation of lipid metabolism pathways and increased lipid metabolite content, while the inhibition of colonial formation and development of P. globosa may be caused by the downscaled production and secretion of glycosaminoglycans. The study demonstrated that zooplankton consumption cues were recognized by intraspecific prey and elicited consumer-specific chemical defenses, highlighting the chemical ecology of herbivore-phytoplankton interactions in the marine ecosystem.

Zeaxanthin epoxidase is involved in the carotenoid biosynthesis and light-dependent growth of the marine alga Nannochloropsis oceanica

BACKGROUND

The marine alga Nannochloropsis oceanica, an emerging model belonging to Heterokont, is considered as a promising light-driven eukaryotic chassis for transforming carbon dioxide to various compounds including carotenoids. Nevertheless, the carotenogenic genes and their roles in the alga remain less understood and to be further explored.

RESULTS

Here, two phylogenetically distant zeaxanthin epoxidase (ZEP) genes from N. oceanica (NoZEP1 and NoZEP2) were functionally characterized. Subcellular localization experiment demonstrated that both NoZEP1 and NoZEP2 reside in the chloroplast yet with differential distribution patterns. Overexpression of NoZEP1 or NoZEP2 led to increases of violaxanthin and its downstream carotenoids at the expense of zeaxanthin in N. oceanica, with the extent of changes mediated by NoZEP1 overexpression being greater as compared to NoZEP2 overexpression. Suppression of NoZEP1 or NoZEP2, on the other hand, caused decreases of violaxanthin and its downstream carotenoids as well as increases of zeaxanthin; similarly, the extent of changes mediated by NoZEP1 suppression was larger than that by NoZEP2 suppression. Interestingly, chlorophyll a dropped following violaxanthin decrease in a well-correlated manner in response to NoZEP suppression. The thylakoid membrane lipids including monogalactosyldiacylglycerol also correlated with the violaxanthin decreases. Accordingly, NoZEP1 suppression resulted in more attenuated algal growth than NoZEP2 suppression did under either normal light or high light stage.

CONCLUSIONS

The results together support that both NoZEP1 and NoZEP2, localized in the chloroplast, have overlapping roles in epoxidating zeaxanthin to violaxanthin for the light-dependent growth, yet with NoZEP1 being more functional than NoZEP2 in N. oceanica. Our study provides implications into the understanding of carotenoid biosynthesis and future manipulation of N. oceanica for carotenoid production.

Different Responses of Photosynthesis to Nitrogen Starvation Between Highly Oil-Accumulative Diatoms, Fistulifera solaris and Mayamaea sp. JPCC CTDA0820

Highly oil-accumulative diatoms are expected to be a promising biomass for the production of biofuel. To harvest the diatom oils at high yields, it is critical to elucidate the relationship of oil accumulation with photosynthesis under fluctuating environmental conditions. Here, we characterized the physiological responses of the growth and photosynthesis in the mesophilic diatom Fistulifera solaris and the cold-tolerant one Mayamaea sp. JPCC CTDA0820 to nitrogen starvation, one of the most notable abiotic stresses, where most eukaryotic algae decrease their photosynthetic activity and accumulate oil in the cells. While F. solaris started showing growth retardation at NaNO₃ levels less than 50% of a normal F/2 artificial seawater (ASW) medium, Mayamaea sp. sustained normal growth even at a NaNO₃ level 10% of normal F/2ASW, indicating the sharp contrast of nitrogen requirement between these two diatom species. In the transition from 100 to 0% nitrogen conditions in the modified F/2ASW, F. solaris showed a clear suppression of chlorophyll (Chl)-based photosynthetic O₂ evolution rate and relative electron transport rate at photosystem II, which were negatively correlated to the capacity of non-photochemical quenching. Meanwhile, there was no change in these Chl-based parameters observed in nitrogen-starved Mayamaea sp. Instead, Mayamaea sp. showed a significant decrease in the Chl a amount per cells. These data suggested the occurrence of two types of photosynthetic responses to nitrogen starvation in oleaginous diatoms; that is, (1) suppression of photosynthetic activity per Chl with enhancing heat dissipation of excess light energy and (2) synchronous suppression of cellular photosynthetic activity with Chl amounts.

Hypes, hopes, and the way forward for microalgal biotechnology

The urge for food security and sustainability has advanced the field of microalgal biotechnology. Microalgae are microorganisms able to grow using (sun)light, fertilizers, sugars, CO₂, and seawater. They have high potential as a feedstock for food, feed, energy, and chemicals. Microalgae grow faster and have higher areal productivity than plant crops, without competing for agricultural land and with 100% efficiency uptake of fertilizers. In comparison with bacterial, fungal, and yeast single-cell protein production, based on hydrogen or sugar, microalgae show higher land-use efficiency. New insights are provided regarding the potential of microalgae replacing soy protein, fish oil, and palm oil and being used as cell factories in modern industrial biotechnology to produce designer feed, recombinant proteins, biopharmaceuticals, and vaccines.

The growth, lipid accumulation and adaptation mechanism in response to variation of temperature and nitrogen supply in psychrotrophic filamentous microalga Xanthonema hormidioides (Xanthophyceae)

BACKGROUND

Microalgae are promising feedstocks for production of renewable biofuels and value-added bioproducts. Temperature and nitrogen supply are important environmental and nutritional factors affecting the growth and metabolism of microalgae, respectively. In this study, the growth and lipid accumulation of filamentous microalgae Xanthonema hormidioides under different temperatures (5, 7, 10, 15, 20, 25, 27 and 30 °C) and initial nitrogen concentrations (3, 9, 18 mM) were investigated, and its adaptive mechanisms of tolerance to low temperature and nitrogen stress were analysis by proteomics.

RESULTS

The optimum temperature range for the growth of X. hormidioides was between 15 and 20 °C, and the algal cells had slow growth rate at 5 °C and could not survive at 30 °C. The maximum biomass concentration was 11.73 g L-1 under the temperature of 20 °C, and the highest total lipid content was 56.63% of dry weight. Low temperature did not change the fatty acids profiles but promoted the accumulation of unsaturated fatty acids of X. hormidioides. The maximum contents of palmitoleic acid, eicosapentaenoic acid and total fatty acid were 23.64%, 2.49% and 41.14% of dry weight, respectively. Proteomics was performed under three temperature (7, 15, 25 °C), two nitrogen concentrations (3 and 18 mM) and two cultivation times (day 3 and 12). A total of 6503 proteins were identified. In the low temperature, photosynthesis-related proteins were down-regulated to protect the photosynthetic apparatus. The up-regulation of key enzymes DGAT and PDAT demonstrated the accumulation of TAGs under low nitrogen treatment. The proteins related to ribosome, phosphatidylinositol signaling system, antioxidant system and cold shock proteins (CSPs) in X. hormidioides were co-upregulated under the treatment of low temperature, which can alleviate the damages induced by temperature stress and maintain the normal growth and metabolism of algal cells.

CONCLUSIONS

X. hormidioides is a psychrotolerant microalga. It is an oleaginous filamentous microalga containing hyper palmitoleic acid and a certain amount of eicosapentaenoic acid with great potential for biofuel development, as well as for applications in nutritional health products and other industries.

Expression of glycerol-3-phosphate acyltransferase increases non-polar lipid accumulation in Nannochloropsis oceanica

Microalgae are considered a suitable production platform for high-value lipids and oleochemicals. Several species including Nannochloropsis oceanica produce large amounts of essential [Formula: see text]-3 polyunsaturated fatty acids (PUFAs) which are integral components of food and feed and have been associated with health-promoting effects. N. oceanica can further accumulate high contents of non-polar lipids with chemical properties that render them a potential replacement for plant oils such as palm oil. However, biomass and lipid productivities obtained with microalgae need to be improved to reach commercial feasibility. Genetic engineering can improve biomass and lipid productivities, for instance by increasing carbon flux to lipids. Here, we report the overexpression of glycerol-3-phosphate acyltransferase (GPAT) in N. oceanica during favorable growth conditions as a strategy to increase non-polar lipid content. Transformants overproducing either an endogenous (NoGPAT) or a heterologous (Acutodesmus obliquus GPAT) GPAT enzyme targeted to the endoplasmic reticulum had up to 42% and 51% increased non-polar lipid contents, respectively, compared to the wild type. Biomass productivities of transformant strains were not substantially impaired, resulting in lipid productivities that were increased by up to 37% and 42% for NoGPAT and AoGPAT transformants, respectively. When exposed to nutrient stress, transformants and wild type had similar lipid contents, suggesting that GPAT enzyme exerts strong flux control on lipid synthesis in N. oceanica under favorable growth conditions. NoGPAT transformants further accumulated PUFAs in non-polar lipids, reaching a total of 6.8% PUFAs per biomass, an increase of 24% relative to the wild type. Overall, our results indicate that GPAT is an interesting target for engineering of lipid metabolism in microalgae, in order to improve non-polar lipid and PUFAs accumulation in microalgae.

Identification and Functional Analysis of Acyl-Acyl Carrier Protein Δ9 Desaturase from Nannochloropsis oceanica

The oleaginous marine microalga Nannochloropsis oceanica strain IMET1 has attracted increasing attention as a promising photosynthetic cell factory due to its unique excellent capacity to accumulate large amounts of triacylglycerols and eicosapentaenoic acid. To complete the genomic annotation for genes in the fatty acid biosynthesis pathway of N. oceanica, we conducted the present study to identify a novel candidate gene encoding the archetypical chloroplast stromal acyl-acyl carrier protein Δ⁹ desaturase. The full-length cDNA was generated using rapid-amplification of cDNA ends, and the structure of the coding region interrupted by four introns was determined. The RT-qPCR results demonstrated the upregulated transcriptional abundance of this gene under nitrogen starvation condition. Fluorescence localization studies using EGFP-fused protein revealed that the translated protein was localized in chloroplast stroma. The catalytic activity of the translated protein was characterized by inducible expression in Escherichia coli and a mutant yeast strain BY4389, indicating its potential desaturated capacity for palmitoyl-ACP (C16:0-ACP) and stearoyl-ACP (C18:0-ACP). Further functional complementation assay using BY4839 on plate demonstrated that the expressed enzyme restored the biosynthesis of oleic acid. These results support the desaturated activity of the expressed protein in chloroplast stroma to fulfill the biosynthesis and accumulation of monounsaturated fatty acids in N. oceanica strain IMET1.

Flashing lights affect the photophysiology and expression of carotenoid and lipid synthesis genes in Nannochloropsis gaditana

Nannochloropsis gaditana is a promising microalga for biotechnology. One of the strategies to stimulate its full potential in metabolite production is exposure to flashing lights. Here, we report how N. gaditana adapts to different flashing light regimes (5, 50, and 500 Hz) by changing its cellular physiology and the relative expression of genes related to critical cellular functions. We analyzed the differential mRNA abundance of genes related to photosynthesis, nitrogen assimilation and biosynthesis of chlorophyll, carotenoids, lipids, fatty acids and starch. Analysis of photosynthetic efficiency and high mRNA abundance of photoprotection genes supported the inference that excess excitation energy provided by light absorbance during photosynthesis was produced under low frequency flashing lights and was dissipated by photopigments via the xanthophyll-cycle. Increased relative expression levels of genes related to the synthesis of carotenoids and chlorophyll confirmed the accumulation of photopigments previously observed at low frequency flashing lights. Higher differential mRNA abundance of genes related to the triacylglycerol biosynthesis were observed at lower frequency flashing lights, possibly triggered by a poor nitrogen assimilation caused by low mRNA abundance of a nitrate reductase gene. This study advances a new understanding of algal physiology and metabolism leading to improved cellular performance and metabolite production.

Fourth generation biofuel from genetically modified algal biomass for bioeconomic development

Biofuels from microalgae have promising potential for a sustainable bioeconomy. Algal strains' oil content and biomass yield are the most influential cost drivers in the fourth generation biofuel (FGB) production. Genetic modification is the key to improving oil accumulation and biomass yield, consequently developing the bioeconomy. This paper discusses current practices, new insights, and emerging trends in genetic modification and their bioeconomic impact on FGB production. It was demonstrated that enhancing the oil and biomass yield could significantly improve the probability of economic success and the net present value of the FGB production process. The techno-economic and socioeconomic burden of using genetically modified (GM) strains and the preventive control strategies on the bioeconomy of FGB production is reviewed. It is shown that the fully lined open raceway pond could cost up to 25% more than unlined ponds. The cost of a plastic hoop air-supported greenhouse covering cultivation ponds is estimated to be US 60,000$ /ha. The competitiveness and profitability of large-scale cultivation of GM biomass are significantly locked to techno-economic and socioeconomic drivers. Nonetheless, it necessitates further research and careful long-term follow-up studies to understand the mechanism that affects these parameters the most.

A two-prong mutagenesis and adaptive evolution strategy to enhance the temperature tolerance and productivity of Nannochloropsis oculata

Incorporation of microalgae in biorefineries intended to help society reach carbon neutrality is hindered by algal growth inhibition at high temperatures, necessitating the use of costly and carbon-intensive cooling systems. In the present study, a two-prong strategy of random mutagenesis and adaptive laboratory evolution to generate robust thermotolerant strains of Nannochloropsis oculata, was used. The best mutants demonstrated increased productivity at 35 °C, which was 10 °C higher than the optimal temperature of the wild type. In a 2-L photobioreactor at 35 °C, biomass and lipid productivity were 1.43-fold and 2.24-fold higher, respectively, than wild type at 25 °C. Higher pigment and carbohydrate content contributed to the mutants' rapid growth and enhanced photosynthetic efficiency. Metabolomics and lipidomics showed rewiring of the central carbon metabolism and membrane lipid synthesis in thermotolerant strains to ensure cellular homeostasis without compromising productivity. Tagatose and phosphatidylethanolamine upregulation were identified as future genetic targets for further enhancing lipid production.

Medium-chain triglyceride production in Nannochloropsis via a fatty acid chain length discriminating mechanism

Depending on their fatty acid (FA) chain length, triacylglycerols (TAGs) have distinct applications; thus, a feedstock with a genetically designed chain length is desirable to maximize process efficiency and product versatility. Here, ex vivo, in vitro, and in vivo profiling of the large set of type-2 diacylglycerol acyltransferases (NoDGAT2s) in the industrial oleaginous microalga Nannochloropsis oceanica revealed two endoplasmic reticulum-localized enzymes that can assemble medium-chain FAs (MCFAs) with 8-12 carbons into TAGs. Specifically, NoDGAT2D serves as a generalist that assembles C8-C18 FAs into TAG, whereas NoDGAT2H is a specialist that incorporates only MCFAs into TAG. Based on such specialization, stacking of NoDGAT2D with MCFA- or diacylglycerol-supplying enzymes or regulators, including rationally engineering Cuphea palustris acyl carrier protein thioesterase, Cocos nucifera lysophosphatidic acid acyltransferase, and Arabidopsis thaliana WRINKLED1, elevated the medium-chain triacylglycerol (MCT) share in total TAG 66-fold and MCT productivity 64.8-fold at the peak phase of oil production. Such functional specialization of NoDGAT2s in the chain length of substrates and products reveals a dimension of control in the cellular TAG profile, which can be exploited for producing designer oils in microalgae.

Biochemistry and Biotechnology of Lipid Accumulation in the Microalga Nannochloropsis oceanica

Oils are among the most important agricultural commodities and have wide applications in food/nutrition, biofuels, and oleochemicals. The oleaginous microalga Nannochloropsis oceanica can produce large amounts of oils and the high-value ω-3 eicosapentaenoic acid, which represents a promising resource for oil production targeting biodiesel, nutraceutical, and aquaculture industries. In recent years, with the availability of omics databases and the development of genetic tools, N. oceanica has been extensively investigated as a model photosynthetic organism for studying lipid metabolism and as a green cellular factory to produce lipids for industrial applications. This review summarizes the current knowledge on the lipid composition and biosynthetic pathways of N. oceanica and reviews the recent advances in metabolic engineering of lipid production in this microalga.

RNA-seq analysis reveals genes related to photosynthetic carbon partitioning and lipid production in Phaeodactylum tricornutum under alkaline conditions

Alkaline pH can induce triacylglyceride accumulation in microalgae, however its molecular mechanism remains elusive. Here, we investigated the effect of 2-[N-cyclohexylamino]-ethane-sulfonic acid (CHES) -induced intracellular alkalization on the lipid production in Phaeodactylum tricornutum. Intracellular pH was increased upon CHES treatment, displaying a high BCECF fluorescence ratio. CHES treatment significantly induced lipid accumulation but had no change in cell density and biomass. The expression of genes involved in photoreaction, carbon fixation, glycolysis, pentose phosphate pathway, amino acid catabolism, GS/GOGAT cycle, TCA cycle, triacylglyceride assembly, de novo fatty acid synthesis were up-regulated, while that in amino acid biosynthesis were down-regulated under CHES conditions. Correspondingly, the activity of phosphoribulokinase, carbonic anhydrase, pyruvate dehydrogenase and acetaldehyde dehydrogenase were enhanced by CHES treatment. Chloroplast-specific biological processes were activated by CHES treatment in P. tricornutum, which redirects the flux of carbon into lipid biosynthesis, meanwhile stimulates de novo fatty acid biosynthesis, leading to lipid accumulation under CHES conditions. These indicate an enhancement of intermediate metabolism, resulting in lipid accumulation by CHES.

Dissecting Enhanced Carbohydrate and Pigment Productivity in Mutants of Nannochloropsis oculata Using Metabolomics and Lipidomics

Random mutagenesis is an effective strategy for enhancing cellular traits. In this study, we used the mutagen ethyl methanesulfonate to create fast-growing Nannochloropsis oculata mutants. When cultivated in a photobioreactor with a diel cycle, two mutants exhibited 2.2-fold higher carbohydrate productivity and 3.5-4.0-fold higher pigment productivity than the wild type, while one of them also showed 2.5-fold higher lipid productivity. A comprehensive physiological, metabolomic, and lipidomic study showed that the mutants had high levels of glucose-, galactose-, and xylose-based carbohydrates. Their high growth rate was attributed to increased chlorophyll a content, improved nitrogen assimilation, storage, and recycling, and low monogalactosyldiacyl glycerol/digalactosyldiacyl glycerol ratio, which was responsible for higher biomass productivity. The investigation revealed upregulation of lipid precursors, shedding light on high lipid accumulation. The derived algae strains are capable of increasing the biosynthesis of value-added storage molecules without impairing growth, rendering them promising candidates for commercial development in future biorefineries.

A conserved MYB transcription factor is involved in regulating lipid metabolic pathways for oil biosynthesis in green algae

Green algae can accumulate high levels of triacylglycerol (TAG), yet knowledge remains fragmented on the regulation of lipid metabolic pathways by transcription factors (TFs). Here, via bioinformatics and in vitro and in vivo analyses, we revealed the roles of a myeloblastosis (MYB) TF in regulating TAG accumulation in green algae. CzMYB1, an R2R3-MYB from Chromochloris zofingiensis, was transcriptionally upregulated upon TAG-inducing conditions and correlated well with many genes involved in the de novo fatty acid synthesis, fatty acid activation and desaturation, membrane lipid turnover, and TAG assembly. Most promoters of these genes were transactivated by CzMYB1 in the yeast one-hybrid assay and contained the binding elements CNGTTA that were recognized by CzMYB1 through the electrophoretic mobility shift assay. CrMYB1, a close homologue of CzMYB1 from Chlamydomonas reinhardtii that recognized similar elements for binding, also transcriptionally correlated with many lipid metabolic genes. Insertional disruption of CrMYB1 severely suppressed the transcriptional expression of CrMYB1, as well as of key lipogenic genes, and impaired TAG level considerably under stress conditions. Our results reveal that this MYB, conserved in green algae, is involved in regulating global lipid metabolic pathways for TAG biosynthesis and accumulation.

13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in Chlamydomonas

Lipid metabolism in microalgae has attracted much interest due to potential utilization of lipids as feedstocks for biofuels, nutraceuticals, and other high-value compounds. Chlamydomonas reinhardtii is a model organism for characterizing the synthesis of the neutral lipid triacylglycerol (TAG), from which biodiesel is made. While much of TAG accumulation under N-deprivation is the result of de novo fatty acid (FA) synthesis, recent work has revealed that approximately one-third of FAs, especially polyunsaturated FAs (PUFAs), come from preexisting membrane lipids. Here, we used 13C-isotopic labeling and mass spectrometry to analyze the turnover of glycerol backbones, headgroups, FAs, whole molecules, and molecular fragments of individual lipids. About one-third of the glyceryl backbones in TAG are derived from preexisting membrane lipids, as are approximately one-third of FAs. The different moieties of the major galactolipids turn over synchronously, while the FAs of diacylglyceryltrimethylhomoserine (DGTS), the most abundant extraplastidial lipid, turn over independently of the rest of the molecule. The major plastidic lipid monogalactosyldiacylglycerol (MGDG), whose predominant species is 18:3α/16:4, was previously shown to be a major source of PUFAs for TAG synthesis. This study reveals that MGDG turns over as whole molecules, the 18:3α/16:4 species is present in both DAG and TAG, and the positional distribution of these PUFAs is identical in MGDG, DAG, and TAG. We conclude that headgroup removal with subsequent acylation is the mechanism by which the major MGDG species is converted to TAG during N-deprivation. This has noteworthy implications for engineering the composition of microalgal TAG for food, fuel, and other applications.

PDAT regulates PE as transient carbon sink alternative to triacylglycerol in Nannochloropsis

Triacylglycerols (TAGs) are the main storage lipids in photosynthetic organisms under stress. In the oleaginous alga Nannochloropsis oceanica, while multiple acyl CoA:diacylglycerol (DAG) acyltransferases (NoDGATs) are involved in TAG production, the role of the unique phospholipid:DAG acyltransferase (NoPDAT) remains unknown. Here, we performed a functional complementation assay in TAG-deficient yeast (Saccharomyces cerevisiae) and an in vitro assay to probe the acyltransferase activity of NoPDAT. Subcellular localization, overexpression, and knockdown (KD) experiments were also conducted to elucidate the role of NoPDAT in N. oceanica. NoPDAT, residing at the outermost plastid membrane, does not phylogenetically fall into the clades of algae or plants and uses phosphatidylethanolamine (PE) and phosphatidylglycerol with 16:0, 16:1, and 18:1 at position sn-2 as acyl-donors in vivo. NoPDAT KD, not triggering any compensatory mechanism via DGATs, led to an ∼30% decrease of TAG content, accompanied by a vast accumulation of PEs rich in 16:0, 16:1, and 18:1 fatty acids (referred to as "LU-PE") that was positively associated with CO2 availability. We conclude that the NoPDAT pathway is parallel to and independent of the NoDGAT pathway for oil production. LU-PE can serve as an alternative carbon sink for photosynthetically assimilated carbon in N. oceanica when PDAT-mediated TAG biosynthesis is compromised or under stress in the presence of high CO2 levels.

A cheap two-step cultivation of Phaeodactylum tricornutum for increased TAG production and differential expression of TAG biosynthesis associated genes

A cheap cultivation of microalgae greatly reduces the biodiesel production cost. Subsequently in this study, citric acid and effluents from sugar and tannery industries were used as the nutritional supplements for the improvement of biomass and TAG production in Phaeodactylum tricornutum using two-step cultivation. When compared to control (media without supplementation), a considerable increase in biomass and chlorophyll a was obtained with citric acid (CA) and sugar industry effluent (SIE) supplemented media. In the two-step cultivation method, biomass raised from CA (100mg·L^-1) and SIE (1.5mL·L^-1) supplementations in the first step, viz. biomass production (BP) step was allowed for lipid accumulation in the second step, viz. lipid production (LP) step, and thus yielded enhanced lipids of 11.5 ± 0.7mg·L^-1·day^-1 and 13.5 ± 1.9mg·L^-1·day^-1 respectively, with improved TAG synthesis. Further, differential expression analysis of TAG biosynthetic genes of P. tricornutum under single-step and two-step cultivation modes were performed, and the gene expression patterns were studied.

Comparative Proteomics Reveals Evidence of Enhanced EPA Trafficking in a Mutant Strain of Nannochloropsis oculata

The marine microalga Nannochloropsis oculata is a bioproducer of eicosapentaenoic acid (EPA), a fatty acid. EPA is incorporated into monogalactosyldiacylglycerol within N. oculata thylakoid membranes, and there is a biotechnological need to remodel EPA synthesis to maximize production and simplify downstream processing. In this study, random mutagenesis and chemical inhibitor-based selection method were devised to increase EPA production and accessibility for improved extraction. Ethyl methanesulfonate was used as the mutagen with selective pressure achieved by using two enzyme inhibitors of lipid metabolism: cerulenin and galvestine-1. Fatty acid methyl ester analysis of a selected fast-growing mutant strain had a higher percentage of EPA (37.5% of total fatty acids) than the wild-type strain (22.2% total fatty acids), with the highest EPA quantity recorded at 68.5 mg/g dry cell weight, while wild-type cells had 48.6 mg/g dry cell weight. Label-free quantitative proteomics for differential protein expression analysis revealed that the wild-type and mutant strains might have alternative channeling pathways for EPA synthesis. The mutant strain showed potentially improved photosynthetic efficiency, thus synthesizing a higher quantity of membrane lipids and EPA. The EPA synthesis pathways could also have deviated in the mutant, where fatty acid desaturase type 2 (13.7-fold upregulated) and lipid droplet surface protein (LDSP) (34.8-fold upregulated) were expressed significantly higher than in the wild-type strain. This study increases the understanding of EPA trafficking in N. oculata, leading to further strategies that can be implemented to enhance EPA synthesis in marine microalgae.

Regulation strategy for nutrient-dependent carbon and nitrogen stoichiometric homeostasis in freshwater phytoplankton

Phytoplankton carbon (C) and nitrogen (N) stoichiometric homeostasis plays an important role in aquatic ecosystems. Their C:N ratio is a result of cellular metabolic balance, and the relevant regulatory strategy for its plasticity is still unclear. Therefore, a field survey of seven reservoirs in Tianjin, North China, was conducted to understand variations in phytoplankton C:N ratios, and a laboratory culture of Chlamydomonas reinhardtii was performed to understand the relevant regulation strategy for cellular C-N stoichiometric homeostasis under different C and N availability by using transcriptome sequencing and Nano SIMS and C stable isotope analyses. The results indicated that CO₂ limitation had no significant effect on the phytoplankton C:N ratio in either scene, whereas limitation of dissolved inorganic N induced a 35% higher ratio in the field and a 138% higher ratio in the laboratory. Under CO₂ limitation, algal CO₂-concentrating mechanisms were operated to ensure a C supply, and coupled C-N molecular regulation remained the cellular C:N ratio stable. Under nitrate limitation, differentially expressed gene-regulated intensities increase enormously, and their increasing proportion was comparable to that of the algal C:N ratio; cellular metabolism was reorganized to form a "subhealthy" C-N stoichiometric state with high C:N ratios. In addition, the N transport system had a specific role under CO₂ and nitrate limitations. Our study implies that algal stoichiometric homeostasis depends on the involved limitation element and will help to deepen the understanding of C-N stoichiometric homeostasis in freshwater phytoplankton.

Exploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica

Oleaginous microalgae can produce triacylglycerol (TAG) under stress, yet the underlying mechanism remains largely unknown. Here, we show that, in Nannochloropsis oceanica, a bZIP-family regulator NobZIP77 represses the transcription of a type-2 diacylgycerol acyltransferase encoding gene NoDGAT2B under nitrogen-repletion (N+), while nitrogen-depletion (N−) relieves such inhibition and activates NoDGAT2B expression and synthesis of TAG preferably from C16:1. Intriguingly, NobZIP77 is a sensor of blue light (BL), which reduces binding of NobZIP77 to the NoDGAT2B-promoter, unleashes NoDGAT2B and elevates TAG under N−. Under N+ and white light, NobZIP77 knockout fully preserves cell growth rate and nearly triples TAG productivity. Moreover, exposing the NobZIP77-knockout line to BL under N− can double the peak productivity of TAG. These results underscore the potential of coupling light quality to oil synthesis in feedstock or bioprocess development.

Microalgae are promising feedstock for oil production. The authors report that a transcription factor NobZIP77 can regulate oil synthesis by sensing the blue light, and explore these findings to greatly enhance oil productivity via genetic and process engineering in Nannochloropsis oceanica.

Biochemical and Morphological Changes Triggered by Nitrogen Stress in the Oleaginous Microalga Chlorella vulgaris

Oleaginous microalgae have been considered promising sources of biodiesel due to their high lipid content. Nitrogen limitation/starvation is one of the most prominent strategies to induce lipid accumulation in microalgae. Nonetheless, despite numerous studies, the mechanism underlying this approach is not well understood. The aim of this study was to investigate the effect of nitrogen limitation and starvation on biochemical and morphological changes in the microalga Chlorella vulgaris FACHB-1068, thereby obtaining the optimal nitrogen stress strategy for maximizing the lipid productivity of microalgal biomass. The results showed that nitrogen limitation (nitrate concentration < 21.66 mg/L) and starvation enhanced the lipid content but generally decreased the biomass productivity, pigment concentration, and protein content in algal cells. Comparatively, 3-day nitrogen starvation was found to be a more suitable strategy to produce lipid-rich biomass. It resulted in an increased biomass production and satisfactory lipid content of 266 mg/L and 31.33%, respectively. Besides, nitrogen starvation caused significant changes in cell morphology, with an increase in numbers and total size of lipid droplets and starch granules. Under nitrogen starvation, saturated fatty acids (C-16:0, C-20:0, and C-18:0) accounted for the majority of the total fatty acids (~80%), making C. vulgaris FACHB-1068 a potential feedstock for biodiesel production. Our work may contribute to a better understanding of the biochemical and morphological changes in microalgae under nitrogen stress. Besides, our work may provide valuable information on increasing the lipid productivity of oleaginous microalgae by regulating nitrogen supply.

Identification and expression analysis of genome-wide long noncoding RNA responsive CO2 fluctuated environment in marine microalga Nannochloropsis oceanica

Long non-coding RNAs (lncRNAs) have been demonstrated to participate in plant growth and development as well as response to different biotic and abiotic stresses. However, the knowledge of lncRNA was limited in microalgae. In this study, by RNA deep sequencing, 134 lncRNAs were identified in marine Nannochloropsis oceanica in response to carbon dioxide fluctuation. Among them, there were 51 lncRNAs displayed differentially expressed between low and high CO₂ treatments, including 33 upregulation and 18 downregulation lncRNAs. Cellulose metabolic process, glucan metabolic process, polysaccharide metabolic process, and transmembrane transporter activity were functionally enriched. Multiple potential target genes of lncRNA and lncRNA-mRNA co-located gene network were analyzed. Subsequent analysis had demonstrated that lncRNAs would participate in many biological molecular processes, including gene expression, transcriptional regulation, protein expression and epigenetic regulation. In addition, alternative splicing events were firstly analyzed in response to CO₂ fluctuation. There were 2051 alternative splicing (AS events) identified, which might be associated with lncRNA. These observations will provide a novel insight into lncRNA function in Nannochloropsis and provide a series of targets for lncRNA-based gene editing in future.

The nucleolus as a genomic safe harbor for strong gene expression in Nannochloropsis oceanica

Microalgae are used in food and feed, and they are considered a potential feedstock for sustainably produced chemicals and biofuel. However, production of microalgal-derived chemicals is not yet economically feasible. Genetic engineering could bridge the gap to industrial application and facilitate the production of novel products from microalgae. Here, we report the discovery of a novel gene expression system in the oleaginous microalga Nannochloropsis that exploits the highly efficient transcriptional activity of RNA polymerase I and an internal ribosome entry site for translation. We identified the nucleolus as a genomic safe harbor for Pol I transcription and used it to construct transformant strains with consistently strong transgene expression. The new expression system provides an outstanding tool for genetic and metabolic engineering of microalgae and thus will probably make substantial contributions to microalgal research.

A Novel Bifunctional Wax Ester Synthase Involved in Early Triacylglycerol Accumulation in Unicellular Green Microalga Haematococcus pluvialis Under High Light Stress

The bulk of neutral lipids, including astaxanthin esters and triacylglycerols (TAGs), are accumulated in the green microalga Haematococcus pluvialis under high light (HL) stress. In this study, a novel bifunctional wax ester synthase (WS) gene was cloned from H. pluvialis upon HL stress. The overexpression of HpWS restored the biosynthesis of wax esters and TAGs in neutral lipid-deficient yeast mutant Saccharomyces cerevisiae H1246 fed with C18 alcohol and C18:1/C18:3 fatty acids, respectively. Under HL stress, HpWS was substantially upregulated at the transcript level, prior to that of the type I diacylglycerol:acyl-CoA acyltransferase encoding gene (HpDGAT1). HpDGAT1 is the major TAG synthase in H. pluvialis. In addition, the application of xanthohumol (a DGAT1/2 inhibitor) in the H. pluvialis cells did not completely eliminate the TAG biosynthesis under HL stress at 24 h. These results indicated that HpWS may contribute to the accumulation of TAGs in H. pluvialis at the early stage under HL stress. In addition, the overexpression of HpWS in Chlamydomonas reinhardtii bkt5, which is engineered to produce free astaxanthin, enhanced the production of TAGs and astaxanthin. Our findings broaden the understanding of TAG biosynthesis in microalgae and provide a new molecular target for genetic manipulation in biotechnological applications.