Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779

Systematic approach for dissecting promoters and designing transform systems in microalgae

The rapidly expanding catalog of sequenced genomes has revolutionized the pace and scale of microalgal cellular metabolism delineation. However, knowledge of the gene regulation in these genomes is lacking. This is true even for Chlamydomonas reinhardtii , the laboratory model species where transcriptional regulation is best understood, although systematic knowledge of regulatory elements (e.g., promoters) remains elusive. This leads to limitations in microalgae for engineering system designs, which currently rely mainly on characterizing the molecular mechanisms of individual regulatory sequences via low-throughput methods. Here, we take a first step toward multi-promoter dissection and demonstrate systematic dissection of multiple microalgal promoters through quantitative genome-wide comparisons and sequence-based structural annotations. We demonstrate this approach on both well-studied and previously uncharacterized promoters in the oleaginous microalga Nannochloropsis oceanica IMET1. Using in silico design, representative regulatory elements were synthesized and assembled as building blocks for transgene circuits. Assessment of the in vivo activity revealed the maximum transformation efficiency (414 ± 102 transformants/µg DNA) in the plasmid pHN5-2 containing lhp promoter and α-tub terminator. Therefore, the present synthetic approach for establishing engineering systems is superior to the conventional empirical methods. Applying these transforming circuits to the creation and characterization of a gene-indexed loss-of-function mutagenesis library verifies the applicability of this strategy to the discovery and standardization of regulatory parts for microalgae. Moreover, the generality of the approach presented here provides the possibility of quantitative promoter dissection and rational transform system design in N. oceanica and a wide range of other microalgae.

Nannochloropsis oceanica IMET1 and its bacterial symbionts for carbon capture, utilization, and storage: biomass and calcium carbonate production under high pH and high alkalinity

To combat the increasing levels of carbon dioxide (CO2) released from the combustion of fossil fuels, microalgae have emerged as a promising strategy for biological carbon capture, utilization, and storage. This study used a marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO2 concentrations. A high-pH, high-alkalinity culture was designed for CO2 capture through algal biomass production as well as permanent sequestration through calcium carbonate (CaCO3) precipitation. This was accomplished by timed pH elevation and the addition of sodium bicarbonate to cultures of N. oceanica grown at lab scale (1 L) and pilot scale (500 L) with 10% and 5% CO2, respectively. Our data showed that 0.02 M NaHCO3 promoted algal growth and that sparging cultures with ambient air after 12 days raised pH and created favorable CaCO3 formation conditions. At the 1 L scale, we reached 1.52 g L-1 biomass after 12 days and an extra 9.3% CO2 was captured in the form of CaCO3 precipitates. At the 500 L pilot scale, an extra 60% CO2 was captured (Day 40) with a maximum CO2 capture rate of 63.2 g m-2 day-1 (Day 35). Bacterial communities associated with the microalgae were dominated by two novel Patescibacteria. Functional analysis revealed that genes for several plant growth-promotion traits (PGPTs) were enriched within this group. The microalgal-bacterial coculture system offers advantages for enhanced carbon mitigation through biomass production and simultaneous precipitation of recalcitrant CaCO3 for long-term CO2 storage.IMPORTANCECapturing carbon dioxide (CO2) released from fossil fuel combustion is of the utmost importance as the impacts of climate change continue to worsen. Microalgae can remove CO2 through their natural photosynthetic pathways and are additionally able to convert CO2 into a stable, recalcitrant form as calcium carbonate (CaCO3). We demonstrate that microalgae-based carbon capture systems can be greatly improved with high pH and high alkalinity by providing optimal conditions for carbonate precipitation. Our results with the microalga, Nannochloropsis oceanica strain IMET1, show an extra 9.3% CO2 captured as CaCO3 at the 1 L scale and an extra 60% CO2 captured at the 500 L (pilot) scale. Our optimized system provides a novel approach to capture CO2 through two mechanisms: (i) as organic carbon within microalgal biomass and (ii) as inorganic carbon stored permanently in the form of CaCO3.

Metabolic regulation strategies for enhancing microbial docosahexaenoic acid production by Schizochytrium sp

Docosahexaenoic acid (DHA), one of the most important ω-3 long-chain polyunsaturated fatty acids, has attracted great attention in recent years because of its significant health benefits for human beings. Traditionally, DHA is obtained from marine fish oil, but this approach depends on marine fishing and has suffered a dramatic fall in the past few years due to overfishing and climate change, which cannot meet the increasing market demand. Microbial DHA production by oleaginous microorganisms has become the current research hotspot. Schizochytrium sp., a heterotrophic thraustochytrid, has become one of the most promising DHA producers because of its safety, fast growth and high DHA content. However, industrial DHA production by Schizochytrium sp. is severely hindered by the high production cost. Many regulation strategies have been developed to enhance DHA production through fermentation optimization and metabolic regulation. In this review, recent advances in metabolic regulation for enhancing DHA production by Schizochytrium sp. are reviewed, from the aspects of key lipogenic enzymes, precursors, transcription factors, lipid peroxidation, transport of non-esterified DHA and stress environment.

In Vitro Culture, Genetic Transformation and the Production of Biopharmaceuticals in Microalgae

Microalgae represent a promising platform for the synthesis of recombinant proteins, particularly in the context of biopharmaceutical applications. Their unique combination of eukaryotic cellular machinery and prokaryotic-like simplicity offers several advantages, including the ability to perform complex post-translational modifications, rapid growth rates, and cost-effective culture conditions. Advances in genome sequencing, genetic engineering tools, and omics technologies have significantly enhanced the feasibility and efficiency of using microalgae for therapeutic protein production. These advancements, coupled with the development of well-established transformation methods and optimized vectors, have enabled the successful expression of various biopharmaceuticals, ranging from vaccines to enzymes. Here, the main stages and current status of the production of exogenic recombinant proteins dedicated to human therapy are presented.

Progress and challenges in CRISPR/Cas applications in microalgae

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.

Enhanced Eicosapentaenoic Acid Production via Synthetic Biological Strategy in Nannochloropsis oceanica

The rational dietary ratio of docosahexaenoic acid (DHA) to eicosapentaenoic acid (EPA) can exert neurotrophic and cardiotrophic effects on the human body. The marine microalga Nannochloropsis oceanica produces EPA yet no DHA, and thus, it is considered an ideal EPA-only model to pursue a rational DHA/EPA ratio. In this study, synthetic biological strategy was applied to improve EPA production in N. oceanica. Firstly, to identify promoters and terminators, fifteen genes from N. oceanica were isolated using a transcriptomic approach. Compared to α-tubulin, NO08G03500, NO03G03480 and NO22G01450 exhibited 1.2~1.3-fold increases in transcription levels. Secondly, to identify EPA-synthesizing modules, putative desaturases (NoFADs) and elongases (NoFAEs) were overexpressed by the NO08G03500 and NO03G03480 promoters/terminators in N. oceanica. Compared to the wild type (WT), NoFAD1770 and NoFAE0510 overexpression resulted in 47.7% and 40.6% increases in EPA yields, respectively. Thirdly, to store EPA in triacylglycerol (TAG), NoDGAT2K was overexpressed using the NO22G01450 promoter/terminator, along with NoFAD1770-NoFAE0510 stacking, forming transgenic line XS521. Compared to WT, TAG-EPA content increased by 154.8% in XS521. Finally, to inhibit TAG-EPA degradation, a TAG lipase-encoding gene NoTGL1990 was knocked out in XS521, leading to a 49.2-65.3% increase in TAG-EPA content. Our work expands upon EPA-enhancing approaches through synthetic biology in microalgae and potentially crops.

Engineering Nannochloropsis oceanica for concurrent production of canthaxanthin and eicosapentaenoic acid

The marine alga Nannochloropsis oceanica can synthesize the high-value ketocarotenoid canthaxanthin yet at an extremely low level. Introducing a β-carotenoid ketolase from Chlamydomonas reinhardtii into the chloroplast for expression, enabled N. oceanica to synthesize substantial amounts of canthaxanthin and grow better under high light. Compared to wild type, the engineered strain had higher levels of primary carotenoids and chlorophyll a as well, and synthesized more eicosapentaenoic acid (EPA, an ω3 polyunsaturated fatty acids). Further metabolic engineering by enhancing the flux to carotenoids or suppressing competing pathways allowed for a considerable increase of canthaxanthin, reaching 4.7 mg g-1 dry weight. A fed-batch culture strategy with nitrate and phosphate replenishment was developed for the co-production of canthaxanthin and EPA, which within a 10-day period reached 37.6 and 268.8 mg/L, respectively. This study sheds light on manipulating the industrially relevant alga for efficient co-production of high-value biochemicals from CO2.

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.

A synthetic biology approach for the treatment of pollutants with microalgae

The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.

Knocking Out Chloroplastic Aldolases/Rubisco Lysine Methyltransferase Enhances Biomass Accumulation in Nannochloropsis oceanica under High-Light Stress

Rubisco large-subunit methyltransferase (LSMT), a SET-domain protein lysine methyltransferase, catalyzes the formation of trimethyl-lysine in the large subunit of Rubisco or in fructose-1,6-bisphosphate aldolases (FBAs). Rubisco and FBAs are both vital proteins involved in CO2 fixation in chloroplasts; however, the physiological effect of their trimethylation remains unknown. In Nannochloropsis oceanica, a homolog of LSMT (NoLSMT) is found. Phylogenetic analysis indicates that NoLSMT and other algae LSMTs are clustered in a basal position, suggesting that algal species are the origin of LSMT. As NoLSMT lacks the His-Ala/ProTrp triad, it is predicted to have FBAs as its substrate instead of Rubisco. The 18-20% reduced abundance of FBA methylation in NoLSMT-defective mutants further confirms this observation. Moreover, this gene (nolsmt) can be induced by low-CO2 conditions. Intriguingly, NoLSMT-knockout N. oceanica mutants exhibit a 9.7-13.8% increase in dry weight and enhanced growth, which is attributed to the alleviation of photoinhibition under high-light stress. This suggests that the elimination of FBA trimethylation facilitates carbon fixation under high-light stress conditions. These findings have implications in engineering carbon fixation to improve microalgae biomass production.

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.

Pioneering DNA assembling techniques and their applications in eukaryotic microalgae

Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.

Engineering Nannochloropsis oceanica for the production of diterpenoid compounds

Photosynthetic microalgae like Nannochloropsis hold enormous potential as sustainable, light-driven biofactories for the production of high-value natural products such as terpenoids. Nannochloropsis oceanica is distinguished as a particularly robust host with extensive genomic and transgenic resources available. Its capacity to grow in wastewater, brackish, and sea waters, coupled with advances in microalgal metabolic engineering, genome editing, and synthetic biology, provides an excellent opportunity. In the present work, we demonstrate how N. oceanica can be engineered to produce the diterpene casbene-an important intermediate in the biosynthesis of pharmacologically relevant macrocyclic diterpenoids. Casbene accumulated after stably expressing and targeting the casbene synthase from Daphne genkwa (DgTPS1) to the algal chloroplast. The engineered strains yielded production titers of up to 0.12 mg g-1 total dry cell weight (DCW) casbene. Heterologous overexpression and chloroplast targeting of two upstream rate-limiting enzymes in the 2-C-methyl- d-erythritol 4-phosphate pathway, Coleus forskohlii 1-deoxy- d-xylulose-5-phosphate synthase and geranylgeranyl diphosphate synthase genes, further enhanced the yield of casbene to a titer up to 1.80 mg g-1 DCW. The results presented here form a basis for further development and production of complex plant diterpenoids in microalgae.

A potential paradigm in CRISPR/Cas systems delivery: at the crossroad of microalgal gene editing and algal-mediated nanoparticles

Microalgae as the photosynthetic organisms offer enormous promise in a variety of industries, such as the generation of high-value byproducts, biofuels, pharmaceuticals, environmental remediation, and others. With the rapid advancement of gene editing technology, CRISPR/Cas system has evolved into an effective tool that revolutionised the genetic engineering of microalgae due to its robustness, high target specificity, and programmability. However, due to the lack of robust delivery system, the efficacy of gene editing is significantly impaired, limiting its application in microalgae. Nanomaterials have become a potential delivery platform for CRISPR/Cas systems due to their advantages of precise targeting, high stability, safety, and improved immune system. Notably, algal-mediated nanoparticles (AMNPs), especially the microalgae-derived nanoparticles, are appealing as a sustainable delivery platform because of their biocompatibility and low toxicity in a homologous relationship. In addition, living microalgae demonstrated effective and regulated distribution into specified areas as the biohybrid microrobots. This review extensively summarised the uses of CRISPR/Cas systems in microalgae and the recent developments of nanoparticle-based CRISPR/Cas delivery systems. A systematic description of the properties and uses of AMNPs, microalgae-derived nanoparticles, and microalgae microrobots has also been discussed. Finally, this review highlights the challenges and future research directions for the development of gene-edited microalgae.

Biomanufacturing of γ-linolenic acid-enriched galactosyldiacylglycerols: Challenges in microalgae and potential in oleaginous yeasts

γ-Linolenic acid-enriched galactosyldiacylglycerols (GDGs-GLA), as the natural form of γ-linolenic acid in microalgae, have a range of functional activities, including anti-inflammatory, antioxidant, and anti-allergic properties. The low abundance of microalgae and the structural stereoselectivity complexity impede microalgae extraction or chemical synthesis, resulting in a lack of supply of GDGs-GLA with a growing demand. At present, there is a growing interest in engineering oleaginous yeasts for mass production of GDGs-GLA based on their ability to utilize a variety of hydrophobic substrates and a high metabolic flux toward fatty acid and lipid (triacylglycerol, TAG) production. Here, we first introduce the GDGs-GLA biosynthetic pathway in microalgae and challenges in the engineering of the native host. Subsequently, we describe in detail the applications of oleaginous yeasts with Yarrowia lipolytica as the representative for GDGs-GLA biosynthesis, including the development of synthetic biology parts, gene editing tools, and metabolic engineering of lipid biosynthesis. Finally, we discuss the development trend of GDGs-GLA biosynthesis in Y. lipolytica.

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.

Genome engineering via gene editing technologies in microalgae

CRISPR-Cas has revolutionized genetic modification with its comparative simplicity and accuracy, and it can be used even at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals because they contain high levels of fatty acids, carotenoids, and other metabolites; however, genome engineering for microalgae is not yet as developed as for other model organisms. Microalgal engineering at the genetic and metabolic levels is relatively well established, and a few genomic resources are available. Their genomic information was used for a "safe harbor" site for stable transgene expression in microalgae. This review proposes further genome engineering schemes including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, which can together be developed into synthetic biology for carbon-based engineering in microalgae. Acetyl-CoA is at the center of carbon metabolic pathways and is further reviewed for the production of molecules including terpenoids in microalgae.

Plant Synthetic Promoters: Advancement and Prospective

Native/endogenous promoters have several fundamental limitations in terms of their size, Cis-elements distribution/patterning, and mode of induction, which is ultimately reflected in their insufficient transcriptional activity. Several customized synthetic promoters were designed and tested in plants during the past decade to circumvent such constraints. Such synthetic promoters have a built-in capacity to drive the expression of the foreign genes at their maximum amplitude in plant orthologous systems. The basic structure and function of the promoter has been discussed in this review, with emphasis on the role of the Cis-element in regulating gene expression. In addition to this, the necessity of synthetic promoters in the arena of plant biology has been highlighted. This review also provides explicit information on the two major approaches for developing plant-based synthetic promoters: the conventional approach (by utilizing the basic knowledge of promoter structure and Cis-trans interaction) and the advancement in gene editing technology. The success of plant genetic manipulation relies on the promoter efficiency and the expression level of the transgene. Therefore, advancements in the field of synthetic promoters has enormous potential in genetic engineering-mediated crop improvement.

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.

Microalgal Carotenoids: Therapeutic Application and Latest Approaches to Enhance the Production

Microalgae are microscopic photosynthetic organisms frequently found in fresh and marine water ecosystems. Various microalgal species have been considered a reservoir of diverse health-value products, including vitamins, proteins, lipids, and polysaccharides, and are broadly utilized as food and for the treatment of human ailments such as cancer, cardiovascular diseases, allergies, and immunodeficiency. Microalgae-derived carotenoids are the type of accessory pigment that possess light-absorbing potential and play a significant role in metabolic functions. To date, nearly a thousand carotenoids have been reported, but a very less number of microalgae have been used for the commercial production of carotenoids. This review article briefly discussed the carotenoids of microalgal origin and their therapeutic application. In addition, we have briefly compiled the optimization of culture parameters used to enhance microalgal carotenoid production. In addition, the latest biotechnological approaches used to improve the yields of carotenoid has also been discussed.

A review on design-build-test-learn cycle to potentiate progress in isoprenoid engineering of photosynthetic microalgae

Currently, the generation of isoprenoid factories in microalgae relies on two strategies: 1) enhanced production of endogenous isoprenoids; or 2) production of heterologous terpenes by metabolic engineering. Nevertheless, low titers and productivity are still a feature of isoprenoid biotechnology and need to be addressed. In this context, the mechanisms underlying isoprenoid biosynthesis in microalgae and its relationship with central carbon metabolism are reviewed. Developments in microalgal biotechnology are discussed, and a new approach of integrated "design-build-test-learn" cycle is advocated to the trends, challenges and prospects involved in isoprenoid engineering. The emerging and promising strategies and tools are discussed for microalgal engineering in the future. This review encourages a systematic engineering perspective aimed at potentiating progress in isoprenoid engineering of photosynthetic microalgae.

Production of a viral surface protein in Nannochloropsis oceanica for fish vaccination against infectious pancreatic necrosis virus

Nannochloropsis oceanica is a unicellular oleaginous microalga of emerging biotechnological interest with a sequenced, annotated genome, available transcriptomic and proteomic data, and well-established basic molecular tools for genetic engineering. To establish N. oceanica as a eukaryotic host for recombinant protein synthesis and develop molecular technology for vaccine production, we chose the viral surface protein 2 (VP2) of a pathogenic fish virus that causes infectious pancreatic necrosis as a model vaccine. Upon stable nuclear transformation of N. oceanica strain CCMP1779 with the codon-optimized VP2 gene, a Venus reporter fusion served to evaluate the strength of different endogenous promoters in transformant populations by qPCR and flow cytometry. The highest VP2 yields were achieved for the elongation factor promoter, with enhancer effects by its N-terminal leader sequence. Individual transformants differed in their production capability of reporter-free VP2 by orders of magnitude. When subjecting the best candidates to kinetic analyses of growth and VP2 production in photobioreactors, recombinant protein integrity was maintained until the early stationary growth phase, and a high yield of 4.4% VP2 of total soluble protein was achieved. The maximum yield correlated with multiple integrations of the expression vector into the nuclear genome. The results demonstrate that N. oceanica was successfully engineered to constitute a robust platform for high-level production of a model subunit vaccine. The molecular methodology established here can likely be adapted in a straightforward manner to the production of further vaccines in the same host, allowing their distribution to fish, vertebrates, or humans via a microalgae-containing diet. KEY POINTS: • We engineered N. oceanica for recombinant protein production. • The antigenic surface protein 2 of IPN virus could indeed be expressed in the host. • A high yield of 4.4% VP2 of total soluble protein was achieved in N. oceanica.

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.

Genetic compensation of triacylglycerol biosynthesis in the green microalga Chlamydomonas reinhardtii

Genetic compensation has been proposed to explain phenotypic differences between gene knockouts and knockdowns in several metazoan and plant model systems. With the rapid development of reverse genetic tools such as CRISPR/Cas9 and RNAi in microalgae, it is increasingly important to assess whether genetic compensation affects the phenotype of engineered algal mutants. While exploring triacylglycerol (TAG) biosynthesis pathways in the model alga Chlamydomonas reinhardtii, it was discovered that knockout of certain genes catalyzing rate-limiting steps of TAG biosynthesis, type-2 diacylglycerol acyltransferase genes (DGTTs), triggered genetic compensation under abiotic stress conditions. Genetic compensation of a DGTT1 null mutation by a related PDAT gene was observed regardless of the strain background or mutagenesis approach, for example, CRISPR/Cas 9 or insertional mutagenesis. However, no compensation was found in the PDAT knockout mutant. The effect of PDAT knockout was evaluated in a Δvtc1 mutant, in which PDAT was upregulated under stress, resulting in a 90% increase in TAG content. Knockout of PDAT in the Δvtc1 background induced a 12.8-fold upregulation of DGTT1 and a 272.3% increase in TAG content in Δvtc1/pdat1 cells, while remaining viable. These data suggest that genetic compensation contributes to the genetic robustness of microalgal TAG biosynthetic pathways, maintaining lipid and redox homeostasis in the knockout mutants under abiotic stress. This work demonstrates examples of genetic compensation in microalgae, implies the physiological relevance of genetic compensation in TAG biosynthesis under stress, and provides guidance for future genetic engineering and mutant characterization efforts.

Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica

Nannochloropsis oceanica, like other stramenopile microalgae, is rich in long-chain polyunsaturated fatty acids (LC-PUFAs) such as eicosapentaenoic acid (EPA). We observed that fatty acid desaturases (FADs) involved in LC-PUFA biosynthesis were among the strongest blue light-induced genes in N. oceanica CCMP1779. Blue light was also necessary for maintaining LC-PUFA levels in CCMP1779 cells, and growth under red light led to a reduction in EPA content. Aureochromes are stramenopile-specific proteins that contain a light-oxygen-voltage (LOV)-sensing domain that associates with a flavin mononucleotide and is able to sense blue light. These proteins also contain a basic leucine zipper DNA-binding motif and can act as blue light-regulated transcription factors by associating with an E-box like motif, which we found enriched in the promoters of blue light-induced genes. We demonstrated that, in vitro, two CCMP1779 aureochromes were able to absorb blue light. Moreover, the loss or reduction of the expression of any of the three aureochrome genes led to a decrease in the blue light-specific induction of several FADs in CCMP1779. EPA content was also significantly reduced in NoAUREO2 and NoAUREO4 mutants. Taken together, our results indicate that aureochromes mediate blue light-dependent regulation of LC-PUFA content in N. oceanica CCMP1779 cells.

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.

Genome editing with removable TALEN vectors harboring a yeast centromere and autonomous replication sequence in oleaginous microalga

Algal lipids are expected to become a basis for sustainable fuels because of the highly efficient lipid production by photosynthesis accompanied by carbon dioxide assimilation. Molecular breeding of microalgae has been studied to improve algal lipid production, but the resultant gene-modified algae containing transgenes are rarely used for outdoor culture because the use of genetically modified organisms (GMOs) is strictly restricted under biocontainment regulations. Recently, it was reported that plasmids containing yeast centromere and autonomous replication sequence (CEN/ARS) behaved as episomes in Nannochloropsis species. We previously reported that the Platinum TALEN (PtTALEN) system exhibited high activity in Nannochloropsis oceanica. Therefore, we attempted to develop a genome editing system in which the expression vectors for PtTALEN can be removed from host cells after introduction of mutations. Using all-in-one PtTALEN plasmids containing CEN/ARS, targeted mutations and removal of all-in-one vectors were observed in N. oceanica, suggesting that our all-in-one PtTALEN vectors enable the construction of mutated N. oceanica without any transgenes. This system will be a feasible method for constructing non-GMO high-performance algae.

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.

Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects

In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement. CRISPR/Cas is a powerful genome-editing tool with a wide range of applications for the genetic improvement of crops. However, the constitutive genome editing of vital genes is often associated with pleiotropic effects on other genes, needless metabolic burden, or interference in the cellular machinery. Tissue-specific genome editing (TSGE), on the other hand, enables researchers to study those genes in specific cells, tissues, or organs without disturbing neighboring groups of cells. Until recently, there was only limited proof of the TSGE concept, where the CRISPR-TSKO tool was successfully used in Arabidopsis, tomato, and cotton, laying a solid foundation for crop improvement. In this review, we have laid out valuable insights into the concept and application of TSGE on relatively unexplored areas such as grain trait improvement under favorable or unfavorable conditions. We also enlisted some of the prominent tissue-specific promoters and described the procedure of their isolation with several TSGE promoter expression systems in detail. Moreover, we highlighted potential negative regulatory genes that could be targeted through TSGE using tissue-specific promoters. In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement.

Comprehensive Genome Engineering Toolbox for Microalgae Nannochloropsis oceanica Based on CRISPR-Cas Systems

Microalgae can produce industrially relevant metabolites using atmospheric CO₂ and sunlight as carbon and energy sources, respectively. Developing molecular tools for high-throughput genome engineering could accelerate the generation of tailored strains with improved traits. To this end, we developed a genome editing strategy based on Cas12a ribonucleoproteins (RNPs) and homology-directed repair (HDR) to generate scarless and markerless mutants of the microalga Nannochloropsis oceanica. We also developed an episomal plasmid-based Cas12a system for efficiently introducing indels at the target site. Additionally, we exploited the ability of Cas12a to process an associated CRISPR array to perform multiplexed genome engineering. We efficiently targeted three sites in the host genome in a single transformation, thereby making a major step toward high-throughput genome engineering in microalgae. Furthermore, a CRISPR interference (CRISPRi) tool based on Cas9 and Cas12a was developed for effective downregulation of target genes. We observed up to 85% reduction in the transcript levels upon performing CRISPRi with dCas9 in N. oceanica. Overall, these developments substantially accelerate genome engineering efforts in N. oceanica and potentially provide a general toolbox for improving other microalgal strains.

Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet

Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.

Metabolic engineering of the oleaginous alga Nannochloropsis for enriching eicosapentaenoic acid in triacylglycerol by combined pulling and pushing strategies

The marine alga Nannochloropsis oceanica has been considered as a promising photosynthetic cell factory for synthesizing eicosapentaenoic acid (EPA), yet the accumulation of EPA in triacylglycerol (TAG) is restricted to an extreme low level. Poor channeling of EPA to TAG was observed in N. oceanica under TAG induction conditions, likely due to the weak activity of endogenous diacylglycerol acyltransferases (DGATs) on EPA-CoA. Screening over thirty algal DGATs revealed potent enzymes acting on EPA-CoA. Whilst overexpressing endogenous DGATs had no or slight effect on EPA abundance in TAG, introducing selected DGATs with strong activity on EPA-CoA, particularly the Chlamydomonas-derived CrDGTT1, which resided at the outermost membrane of the chloroplast and provided a strong pulling power to divert EPA to TAG for storage and protection, led to drastic increases in EPA abundance in TAG and TAG-derived EPA level in N. oceanica. They were further promoted by additional overexpression of an elongase gene involved in EPA biosynthesis, reaching 5.9- and 12.3-fold greater than the control strain, respectively. Our results together demonstrate the concept of applying combined pulling and pushing strategies to enrich EPA in algal TAG and provide clues for the enrichment of other desired fatty acids in TAG as well.

CRISPRa/i with Adaptive Single Guide Assisted Regulation DNA (ASGARD) mediated control of Chlorella sorokiniana to enhance lipid and protein production

Chlorella species are indispensable microalgae for biorefinery but are hardly in DNA manipulation due to the high guanine-cytosine (GC) contents of DNA. In this study, we established a new approach via 20 guanines for sgRNA design, which is annotated as "Adaptive Single Guide Assisted Regulation DNA (ASGARD)" and coupling with CRISPR interference associated dCas9 system to overcome the difficulties. At first, C. sorokiniana was predominate as its faster growth rate when compared to C. vulgaris and C. variabilis in the culture using Tris-acetate-phosphate (TAP) medium. Among all the genetic transformants, gene regulation via CRISPRa-VP64 (CRISPRa) enhanced the protein contents up to 60% (w/w) of dry cell weight, where the highest concentration was 570 mg L^-1 . Meanwhile, CRISPRi-KRAB (CRISPRi) with ASGARD increased protein content to 65% and lipid formed in the range of 150-250 mg L^-1 . From the transcriptome analysis, we deciphered 468 genes down-regulated and 313 genes up-regulated via CRISPRi, while less difference existed in CRISPRa. This novel design and technology reveal a high potential of gene-regulating approach to other species for the biorefinery and bio-industry.

Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae

Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

Safe-Harboring based novel genetic toolkit for Nannochloropsis salina CCMP1776: Efficient overexpression of transgene via CRISPR/Cas9-Mediated Knock-in at the transcriptional hotspot

Transgene expression in microalgae can be hampered by transgene silencing and unstable expression due to position effects. To overcome this, "safe harboring" transgene expression system was established for Nannochloropsis. Initially, transformants were obtained expressing a sfGFP reporter, followed by screening for high expression of sfGFP with fluorescence-activated cell sorter (FACS). 'T1' transcriptional hotspot was identified from a mutant showing best expression of sfGFP, but did not affect growth or lipid contents. By using a Cas9 editor strain, FAD12 gene, encoding Δ12-fatty acid desaturase (FAD12), was successfully knocked-in at the T1 locus, resulting in significantly higher expression of FAD12 than those of random integration. Importantly, the "safe harbored" FAD12 transformants showed four-fold higher production of linoleic acid (LA), the product of FAD12, leading to 1.5-fold increase in eicosapentaenoic acid (EPA). This safe harboring principle provide excellent proof of the concept for successful genetic/metabolic engineering of microalgae and other organisms.

Doing synthetic biology with photosynthetic microorganisms

The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.

Stramenopile microalgae as "green biofactories" for recombinant protein production

Photoautotrophic microalgae have become intriguing hosts for recombinant protein production because they offer important advantages of both prokaryotic and eukaryotic expression systems. Advanced molecular tools have recently been established for the biotechnologically relevant group of stramenopile microalgae, particularly for several Nannochloropsis species and diatoms. Strategies for the selection of powerful genetic elements and for optimization of protein production have been reported. Much needed high-throughput techniques required for straight-forward identification and selection of the best expression constructs and transformants have become available and are discussed. The first recombinant proteins have already been produced successfully in stramenopile microalgae and include not only several subunit vaccines but also one antimicrobial peptide, a fish growth hormone, and an antibody. These research results offer interesting future applications in aquaculture and as biopharmaceuticals. In this review we highlight recent progress in genetic technology development for recombinant protein production in the most relevant Nannochloropsis species and diatoms. Diverse realistic biotechnological applications of these proteins are emphasized that have the potential to establish stramenopile algae as sustainable green factories for an economically competitive production of high-value biomolecules.

Engineering microalgae: transition from empirical design to programmable cells

Domesticated microalgae hold great promise for the sustainable provision of various bioresources for human domestic and industrial consumption. Efforts to exploit their potential are far from being fully realized due to limitations in the know-how of microalgal engineering. The associated technologies are not as well developed as those for heterotrophic microbes, cyanobacteria, and plants. However, recent studies on microalgal metabolic engineering, genome editing, and synthetic biology have immensely helped to enhance transformation efficiencies and are bringing new insights into this field. Therefore, this article, summarizes recent developments in microalgal biotechnology and examines the prospects for generating specialty and commodity products through the processes of metabolic engineering and synthetic biology. After a brief examination of empirical engineering methods and vector design, this article focuses on quantitative transformation cassette design, elaborates on target editing methods and emerging digital design of algal cellular metabolism to arrive at high yields of valuable products. These advances have enabled a transition of manners in microalgal engineering from single-gene and enzyme-based metabolic engineering to systems-level precision engineering, from cells created with genetically modified (GM) tags to that without GM tags, and ultimately from proof of concept to tangible industrial applications. Finally, future trends are proposed in microalgal engineering, aiming to establish individualized transformation systems in newly identified species for strain-specific specialty and commodity products, while developing sophisticated universal toolkits in model algal species.

Current perspectives on integrated approaches to enhance lipid accumulation in microalgae

In recent years, research initiatives on renewable bioenergy or biofuels have been gaining momentum, not only due to fast depletion of finite reserves of fossil fuels but also because of the associated concerns for the environment and future energy security. In the last few decades, interest is growing concerning microalgae as the third-generation biofuel feedstock. The CO₂ fixation ability and conversion of it into value-added compounds, devoid of challenging food and feed crops, make these photosynthetic microorganisms an optimistic producer of biofuel from an environmental point of view. Microalgal-derived fuels are currently being considered as clean, renewable, and promising sustainable biofuel. Therefore, most research targets to obtain strains with the highest lipid productivity and a high growth rate at the lowest cultivation costs. Different methods and strategies to attain higher biomass and lipid accumulation in microalgae have been extensively reported in the previous research, but there are fewer inclusive reports that summarize the conventional methods with the modern techniques for lipid enhancement and biodiesel production from microalgae. Therefore, the current review focuses on the latest techniques and advances in different cultivation conditions, the effect of different abiotic and heavy metal stress, and the role of nanoparticles (NPs) in the stimulation of lipid accumulation in microalgae. Techniques such as genetic engineering, where particular genes associated with lipid metabolism, are modified to boost lipid synthesis within the microalgae, the contribution of "Omics" in metabolic pathway studies. Further, the contribution of CRISPR/Cas9 system technique to the production of microalgae biofuel is also briefly described.

Genome engineering of Nannochloropsis with hundred-kilobase fragment deletions by Cas9 cleavages

Industrial microalgae are promising photosynthetic cell factories, yet tools for large-scale targeted genome engineering are limited. Here for the model industrial oleaginous microalga Nannochloropsis oceanica, we established a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01 Mb nuclear genome. We started by identifying the 'non-essential' chromosomal regions (i.e. low expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is ~98 kb in size, located near the telomere of the 502.09-kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing the distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also achieved double-deletion of both LER1 and LER2 (from Chr 9) that total ~214 kb at maximum, which can result in slightly higher growth rate and biomass productivity than the wild-type. Therefore, loss of the large, yet 'non-essential' regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions had not been previously reported in microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.

Gene Delivery Technologies with Applications in Microalgal Genetic Engineering

Microalgae and cyanobacteria are photosynthetic microbes that can be grown with the simple inputs of water, carbon dioxide, (sun)light, and trace elements. Their engineering holds the promise of tailored bio-molecule production using sustainable, environmentally friendly waste carbon inputs. Although algal engineering examples are beginning to show maturity, severe limitations remain in the transformation of multigene expression cassettes into model species and DNA delivery into non-model hosts. This review highlights common and emerging DNA delivery methods used for other organisms that may find future applications in algal engineering.

Role of an ancient light-harvesting protein of PSI in light absorption and photoprotection

Diverse algae of the red lineage possess chlorophyll a-binding proteins termed LHCR, comprising the PSI light-harvesting system, which represent an ancient antenna form that evolved in red algae and was acquired through secondary endosymbiosis. However, the function and regulation of LHCR complexes remain obscure. Here we describe isolation of a Nannochloropsis oceanica LHCR mutant, named hlr1, which exhibits a greater tolerance to high-light (HL) stress compared to the wild type. We show that increased tolerance to HL of the mutant can be attributed to alterations in PSI, making it less prone to ROS production, thereby limiting oxidative damage and favoring growth in HL. HLR1 deficiency attenuates PSI light-harvesting capacity and growth of the mutant under light-limiting conditions. We conclude that HLR1, a member of a conserved and broadly distributed clade of LHCR proteins, plays a pivotal role in a dynamic balancing act between photoprotection and efficient light harvesting for photosynthesis.

LHCR proteins are ancient chlorophyll a-binding antennas that evolved in diverse algae of the red lineage. Here Lu et al. characterize a red lineage LHCR mutant and show reduced oxidative damage in high light but attenuated growth under low light, thus demonstrating how LHCR proteins impact the balance between photoprotection and light harvesting.

The NanDeSyn database for Nannochloropsis systems and synthetic biology

Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.

Genome Editing by CRISPR-Cas: A Game Change in the Genetic Manipulation of Chlamydomonas

Microalgae are promising photosynthetic unicellular eukaryotes among the most abundant on the planet and are considered as alternative sustainable resources for various industrial applications. Chlamydomonas is an emerging model for microalgae to be manipulated by multiple biotechnological tools in order to produce high-value bioproducts such as biofuels, bioactive peptides, pigments, nutraceuticals, and medicines. Specifically, Chlamydomonas reinhardtii has become a subject of different genetic-editing techniques adapted to modulate the production of microalgal metabolites. The main nuclear genome-editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and more recently discovered the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) nuclease system. The latter, shown to have an interesting editing capacity, has become an essential tool for genome editing. In this review, we highlight the available literature on the methods and the applications of CRISPR-Cas for C. reinhardtii genetic engineering, including recent transformation methods, most used bioinformatic tools, best strategies for the expression of Cas protein and sgRNA, the CRISPR-Cas mediated gene knock-in/knock-out strategies, and finally the literature related to CRISPR expression and modification approaches.

Novel Insights into Phosphorus Deprivation Boosted Lipid Synthesis in the Marine Alga Nannochloropsis oceanica without Compromising Biomass Production

Nannochloropsis oceanica represents a preferred oleaginous alga for producing lipids. Here we found that phosphorus deprivation (PD) caused a severe decrease in protein and a considerable increase in lipids including triacylglycerol (TAG), yet it had little effect on the carbohydrate level and biomass production of N. oceanica. The combinatorial analysis by integrating physiological, biochemical, and transcriptomic data unraveled the molecular mechanisms underlying PD-induced lipid accumulation. Albeit attenuating the Calvin-Benson cycle, PD stimulated the C4-like pathway to maintain CO₂ fixation for biomass production. PD attenuated nitrogen utilization and enhanced protein catabolism thus leading to protein decrease, from which the carbon was likely salvaged into the stimulated tricarboxylic acid cycle for supplying lipid synthesis with carbon precursors. The impairment of TAG catabolism by downregulating certain lipases rather than the stimulation of TAG assembly pathways contributed to PD-boosted TAG increase. These findings provide novel insights into PD-induced lipogenesis without compromising biomass production by N. oceanica.