Epigenetic silencing of a foreign gene in nuclear transformants of Chlamydomonas

Proteomic analysis reveals molecular changes following genetic engineering in Chlamydomonas reinhardtii

BACKGROUND

Chlamydomonas reinhardtii is gaining recognition as a promising expression system for the production of recombinant proteins. However, its performance as a cellular biofactory remains suboptimal, especially with respect to consistent expression of heterologous genes. Gene silencing mechanisms, position effect, and low nuclear transgene expression are major drawbacks for recombinant protein production in this model system. To unveil the molecular changes following transgene insertion, retention, and expression in this species, we genetically engineered C. reinhardtii wild type strain 137c (strain cc-125 mt+) to express the fluorescent protein mVenus and subsequently analysed its intracellular proteome.

RESULTS

The obtained transgenic cell lines showed differences in abundance in more than 400 proteins, with multiple pathways altered post-transformation. Proteins involved in chromatin remodelling, translation initiation and elongation, and protein quality control and transport were found in lower abundance. On the other hand, ribosomal proteins showed higher abundance, a signal of ribosomal stress response.

CONCLUSIONS

These results provide new insights into the modifications of C. reinhardtii proteome after transformation, highlighting possible pathways involved in gene silencing. Moreover, this study identifies multiple protein targets for future genetic engineering approaches to improve the prospective use of C. reinhardtii as cell biofactory for industrial applications.

Optimized transgene expression in the red alga Porphyridium purpureum and efficient recombinant protein secretion into the culture medium

Microalgae represent a promising but yet underexplored production platform for biotechnology. The vast majority of studies on recombinant protein expression in algae have been conducted in a single species, the green alga Chlamydomonas reinhardtii. However, due to epigenetic silencing, transgene expression in Chlamydomonas is often inefficient. Here we have investigated parameters that govern efficient transgene expression in the red microalga Porphyridium purpureum. Porphyridium is unique in that the introduced transformation vectors are episomally maintained as autonomously replicating plasmids in the nucleus. We show that full codon optimization to the preferred codon usage in the Porphyridium genome confers superior transgene expression, not only at the level of protein accumulation, but also at the level of mRNA accumulation, indicating that high translation rates increase mRNA stability. Our optimized expression constructs resulted in YFP accumulation to unprecedented levels of up to 5% of the total soluble protein. We also designed expression cassettes that target foreign proteins to the secretory pathway and lead to efficient protein secretion into the culture medium, thus simplifying recombinant protein harvest and purification. Our study paves the way to the exploration of red microalgae as expression hosts in molecular farming for recombinant proteins and metabolites.

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

Successful reversal of transgene silencing in Chlamydomonas reinhardtii

Chlamydomonas reinhardtii has been successfully engineered to produce compounds of interest following transgene integration and heterologous protein expression. The advantages of this model include the availability of validated tools for bioengineering, its photosynthetic ability, and its potential use as biofuel. Despite this, breakthroughs have been hindered by its ability to silence transgene expression through epigenetic changes. Histone deacetylases (HDAC) are main players in gene expression. We hypothesized that transgene silencing can be reverted with chemical treatments using HDAC inhibitors. To analyze this, we transformed C. reinhardtii, integrating into its genome the mVenus reporter gene under the HSP70-rbcs2 promoter. From 384 transformed clones, 88 (22.9%) displayed mVenus positive (mVenus+ ) cells upon flow-cytometry analysis. Five clones with different fluorescence intensities were selected. The number of integrated copies was measured by qPCR. Transgene expression levels were followed over the growth cycle and upon SAHA treatment, using a microplate reader, flow cytometry, RT-qPCR, and western blot analysis. First, we observed that expression varies with the cell cycle, reaching a maximum level just before the stationary phase in all clones. Second, we uncovered that supplementation with HDAC inhibitors of the hydroxamate family, such as vorinostat (suberoylanilide-hydroxamic-acid, SAHA) at the initiation of culture increases the frequency (% of mVenus+ cells) and the level of transgene expression per cell over the whole growth cycle, through histone deacetylase inhibition. Thus, we propose a new tool to successfully trigger the expression of heterologous proteins in the green algae C. reinhardtii, overcoming its main obstacle as an expression platform.

Overexpression of a MYB1 Transcription Factor Enhances Triacylglycerol and Starch Accumulation and Biomass Production in the Green Microalga Chlamydomonas reinhardtii

Microalgae are promising platforms for biofuel production. Transcription factors (TFs) are emerging as key regulators of lipid metabolism for biofuel production in microalgae. We previously identified a novel TF MYB1, which mediates lipid accumulation in the green microalga Chlamydomonas under nitrogen depletion. However, the function of MYB1 on lipid metabolism in microalgae under standard growth conditions remains poorly understood. Here, we examined the effects of MYB1 overexpression (MYB1-OE) on lipid metabolism and physiological changes in Chlamydomonas. Under standard growth conditions, MYB1-OE transformants accumulated 1.9 to 3.2-fold more triacylglycerols (TAGs) than that in the parental line (PL), and total fatty acids (FAs) also significantly increased. Moreover, saturated FA (C16:0) was enriched in TAGs and total FAs in MYB1-OE transformants. Notably, starch and protein content and biomass production also significantly increased in MYB1-OE transformants compared with that in PL. Furthermore, RT-qPCR results showed that the expressions of key genes involved in TAG, FA, and starch biosynthesis were upregulated. In addition, MYB1-OE transformants showed higher biomass production without a compromised cell growth rate and photosynthetic activity. Overall, our results indicate that MYB1 overexpression not only enhanced lipid content but also improved starch and protein content and biomass production under standard growth conditions. TF MYB1 engineering is a promising genetic engineering tool for biofuel production in microalgae.

Cell Type-Specific Promoters of Volvox carteri for Molecular Cell Biology Studies

The multicellular green alga Volvox carteri has emerged as a valuable model organism for investigating various aspects of multicellularity and cellular differentiation, photoreception and phototaxis, cell division, biogenesis of the extracellular matrix and morphogenetic movements. While a range of molecular tools and bioinformatics resources have been made available for exploring these topics, the establishment of cell type-specific promoters in V. carteri has not been achieved so far. Therefore, here, we conducted a thorough screening of transcriptome data from RNA sequencing analyses of V. carteri in order to identify potential cell type-specific promoters. Eventually, we chose two putative strong and cell type-specific promoters, with one exhibiting specific expression in reproductive cells (gonidia), the PCY1 promoter, and the other in somatic cells, the PFP promoter. After cloning both promoter regions, they were introduced upstream of a luciferase reporter gene. By using particle bombardment, the DNA constructs were stably integrated into the genome of V. carteri. The results of the expression analyses, which were conducted at both the transcript and protein levels, demonstrated that the two promoters drive cell type-specific expression in their respective target cell types. Transformants with considerably diverse expression levels of the chimeric genes were identifiable. In conclusion, the screening and analysis of transcriptome data from RNA sequencing allowed for the identification of potential cell type-specific promoters in V. carteri. Reporter gene constructs demonstrated the actual usability of two promoters. The investigated PCY1 and PFP promoters were proven to be potent molecular tools for genetic engineering in V. carteri.

Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR

In the present study, we applied the HDR (homology-directed DNA repair) CRISPR-Cas9-mediated knock-in system to accurately insert an optimized foreign bacterial phytase gene at a specific site of the nitrate reductase (NR) gene (exon 2) to achieve homologous recombination with the stability of the transgene and reduce insertion site effects or gene silencing. To this end, we successfully knocked-in the targeted NR gene of Chlamydomonas reinhardtii using the bacterial phytase gene cassette through direct delivery of the CRISPR/Cas9 system as the ribonucleoprotein (RNP) complex consisting of Cas9 protein and the specific single guide RNAs (sgRNAs). The NR insertion site editing was confirmed by PCR and sequencing of the transgene positive clones. Moreover, 24 clones with correct editing were obtained, where the phytase gene cassette was located in exon 2 of the NR gene, and the editing efficiency was determined to be 14.81%. Additionally, site-specific gene expression was analyzed and confirmed using RT-qPCR. Cultivation of the positive knocked-in colonies on the selective media during 10 generations indicated the stability of the correct editing without gene silencing or negative insertion site effects. Our results demonstrated that CRISPR-Cas9-mediated knock-in could be applied for nuclear expression of the heterologous gene of interest, and also confirmed its efficacy as an effective tool for site-specific gene knock-in, avoiding nuclear positional effects and gene silencing in C. reinhardtii. These findings could also provide a new perspective on the advantageous application of RNP-CRISPR/Cas9 gene-editing to accelerate the commercial production of complex recombinant proteins in the food-grade organism "C. reinhardtii".

Cloning and expression of an anti-cancerous cytokine: human IL-29 gene in Chlamydomonas reinhardtii

Green algae, Chlamydomonas reinhardtii, with low cultivation cost, absence of endotoxins and insusceptibility to human pathogens is emerging as a potential system for the future production of recombinant proteins. The recent development of molecular tools enabling recombinant protein expression in algae chloroplast has provided new research and advance opportunities for developing low-cost therapeutic proteins. In the present study, algae chloroplast expression system was evaluated for the recombinant production of an anti-cancerous therapeutic protein, Interleukin 29 (IL29). The IL29 gene was cloned into algae chloroplast expression vector (pSRSapI). After the transformation, the positive clones were screened for homoplasmy and the presence of the IL29 gene by spot test and PCR analysis, respectively. The expressed SDS-PAGE and western blotting assay characterized IL-29. The algae expressed IL-29 was biologically active in an anti-proliferating bioassay using HepG2 cells. The results suggest that the Chlamydomonas reinhardtii expression system is convenient, low-cost, eco-friendly, and safe to express IL29.

DNA Methylation in Algae and Its Impact on Abiotic Stress Responses

Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.

Expression of a mosquito larvicidal gene in chloroplast and nuclear compartments of Chlamydomonas reinhardtii

As a part of the search for environment-friendly biocontrol of mosquito-borne diseases, mosquito larvicidal potential of Bacillus thuringiensis subsp. jegathesan (Btj) Cry toxins is explored for toxins with increased toxicity. Safe delivery of the Cry toxins to mosquito larvae in aquatic habitats is a major concern. This is because in water bodies Bacillus thuringiensis (Bt) protein formulations degrade by sunlight, can sink down and get adsorbed by the silt. So, because of its short persistence the toxin requires repeated applications at the given site. Therefore, an upcoming approach is incorporating the Bt toxins in Chlamydomonas reinhardtii (C. reinhardtii) because it is a food of mosquito larvae in water and its molecular toolkit is well investigated for foreign gene expression. The present work aimed to compare the feasibility of C. reinhardtii chloroplast and nuclear compartments for stable expression of Cry11Ba toxin as this is the most toxic Btj protein to date, lethal to different mosquito species. With chloroplast expression of cry11Ba gene we were able to generate marker-free C. reinhardtii strain stably expressing Cry11Ba protein and demonstrating mortality against Aedes aegypti larvae. Moreover, for nuclear expression linking the cry11Ba gene to zeocin via foot and mouth disease virus (FMDV) 2A peptide resulted in the selection of transformants with increased cry11Ba mRNA expression levels by semi-quantitative reverse transcriptase PCR. Obtained results lay a foundation for the C. reinhardtii chloroplast expression system to be used for genetic engineering with Bt toxins which possess enhanced toxicity^.

Trait drift in microalgae and applications for strain improvement

Microalgae are increasingly used to generate a wide range of commercial products, and there is growing evidence that microalgae-based products can be produced sustainably. However, industrial production of microalgal biomass is not as developed as other biomanufacturing platform technologies. In addition, results of bench-scale research often fail to translate to large-scale or mass production systems. This disconnect may result from trait drift and evolution occurring, through time, in response to unique drivers in each environment, such as cultivation regimes, weather, and pests. Moreover, outdoor and indoor cultivation of microalgae has the potential to impose negative selection pressures, which makes the maintenance of desired traits a challenge. In this context, this review sheds the light on our current understanding of trait drift and evolution in microalgae. We delineate the basics of phenotype plasticity and evolution, with a focus on how microalgae respond under various conditions. In addition, we review techniques that exploit phenotypic plasticity and evolution for strain improvement in view of industrial commercial applications, highlighting associated advantages and shortcomings. Finally, we suggest future research directions and recommendations to overcome unwanted trait drift and evolution in microalgae cultivation.

Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.

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.

Novel cis-regulatory elements as synthetic promoters to drive recombinant protein expression from the Chlamydomonas reinhardtii nuclear genome

Eukaryotic green microalgae represent a sustainable, photosynthetic biotechnology platform for generating high-value products. The model green alga Chlamydomonas reinhardtii has already been used to generate high value bioproducts such as recombinant proteins and terpenoids. However, low, unstable, and variable nuclear transgene expression has limited the ease and speed of metabolic engineering and recombinant protein expression in this system. Here, novel genetic devices for transgene expression in C. reinhardtii have been developed by identifying cis-regulatory DNA elements capable of driving high transgene expression in C. reinhardtii promoters using de novo motif discovery informatics approaches. Thirteen putative motifs were synthesized as concatemers, linked to a common minimal basal promoter, and assayed for their activity to drive expression of a yellow fluorescent protein reporter gene. Following transformation of the vectors into C. reinhardtii by electroporation, in vivo measurements of yellow fluorescent protein expression by flow cytometry revealed that five of the DNA motifs analyzed displayed significantly higher reporter expression compared to the basal promoter control. Two of the concatemerized motifs, despite being much smaller minimal cis-regulatory elements, drove reporter expression at levels approaching that of the conventionally-used AR1 promoter. This analysis provides insight into C. reinhardtii promoter structure and gene regulation, and provides a new toolbox of cis-regulatory elements that can be used to drive transgene expression at a variety of expression levels.

Exploring the Impact of Terminators on Transgene Expression in Chlamydomonas reinhardtii with a Synthetic Biology Approach

Chlamydomonas reinhardtii has many attractive features for use as a model organism for both fundamental studies and as a biotechnological platform. Nonetheless, despite the many molecular tools and resources that have been developed, there are challenges for its successful engineering, in particular to obtain reproducible and high levels of transgene expression. Here we describe a synthetic biology approach to screen several hundred independent transformants using standardised parts to explore different parameters that might affect transgene expression. We focused on terminators and, using a standardised workflow and quantitative outputs, tested 9 different elements representing three different size classes of native terminators to determine their ability to support high level expression of a GFP reporter gene. We found that the optimal size reflected the median size of element found in the C. reinhardtii genome. The behaviour of the terminator parts was similar with different promoters, in different host strains and with different transgenes. This approach is applicable to the systematic testing of other genetic elements, facilitating comparison to determine optimal transgene design.

Novel transgenic Chlamydomonas reinhardtii strain with retargetable genomic transgene integration using Cre-loxP system

The use of Chlamydomonas for biofuel and biopharmaceutical production has been anticipated. However, the genetic engineering technology for Chlamydomonas is not as advanced as that for other organisms. Here, we established transgenic Chlamydomonas strains capable of high and stable transgene expression. The established cells exhibited stable reporter gene expression at a high level throughout long-term culture (∼60 days), even in the absence of drug pressure. The transgene insertion sites in the cell genome that may be suitable for exogenous gene expression were identified. Because the transgene contains a loxP site, the cells can be used as founders for retargeting other transgenes using the Cre-loxP system to generate transgenic Chlamydomonas producing useful substances. As a model biopharmaceutical gene, an interferon expression cassette was integrated into the genomic locus of the cells using Cre recombinase. The transgenic cells stably produced interferon protein in medium for 12 passages under non-selective conditions. These results indicate that the Chlamydomonas cells established in this study can serve as valuable and powerful tools not only for basic research on microalgae but also for the rapid establishment of cell lines expressing exogenous genes.

Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly

Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that scaffolds organelle formation. The importance of this architecture has been difficult to decipher notably because of the lack of precise tools to modulate the underlying assembly reaction. Here, we developed monobodies against Chlamydomonas reinhardtii SAS-6, characterizing three in detail with X-ray crystallography, atomic force microscopy and cryo-electron microscopy. This revealed distinct monobody-target interaction modes, as well as specific consequences on ring assembly and stacking. Of particular interest, monobody MB_CRS6-15 induces a conformational change in CrSAS-6, resulting in the formation of a helix instead of a ring. Furthermore, we show that this alteration impairs centriole biogenesis in human cells. Overall, our findings identify monobodies as powerful molecular levers to alter the architecture of multi-protein complexes and tune centriole assembly.

A novel, robust and mating-competent Chlamydomonas reinhardtii strain with an enhanced transgene expression capacity for algal biotechnology

In the future, algae biotechnology could play an important role in sustainable development, especially with regard to the production of valuable chemicals. Among the established laboratory strains with efficient transgene expression, there are none that have demonstrated the required robustness for industrial applications, which generally require growth at larger scale. Here, we created a robust and mating-competent cell line of the green microalga Chlamydomonas reinhardtii, which also possesses a high transgene expression capacity. This strain shows a comparably high resistance to shear stress by accumulating increased amounts of biomass under these conditions. As a proof-of-concept, a high phototrophic productivity of cadaverine from CO₂ and nitrate was demonstrated by efficiently expressing a bacterial l-lysine decarboxylase. In contrast to other established strains, this novel chassis strain for phototrophic production schemes is equipped with the traits required for industrial applications, by combining mating-competence, cell wall-mediated robustness and high level transgene expression.

Rational Promoter Engineering Enables Robust Terpene Production in Microalgae

Microalgal biotechnology promises sustainable light-driven production of valuable bioproducts and addresses urgent demands to attain a sustainable economy. However, to unfold its full potential as a platform for biotechnology, new and powerful tools for nuclear engineering need to be established. Chlamydomonas reinhardtii, the model for microalgal synthetic biology and genetic engineering has already been used to produce various bioproducts. Nevertheless, low transgene titers, the lack of potent expression elements, and sparse comparative evaluation prevents further development of C. reinhardtii as a biotechnological host. By systematically evaluating existing expression elements combined with rational promoter engineering, we established novel synthetic expression elements, improved the standardized application of synthetic biology tools, and unveiled an existing synergism between the PSAD 5' UTR and its corresponding chloroplast targeting peptide. Promoter engineering strategies, implemented in a newly designed synthetic algal promoter, increased the production of the sesquiterpene (E)-α-bisabolene by 18-fold compared to its native version and 4-fold to commonly used expression elements. Our results improve the application of synthetic biology in microalgae and display a significant step toward establishing C. reinhardtii as a sustainable green cell-factory.

An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas

Silencing of exogenous DNA can make transgene expression very inefficient. Genetic screens in the model alga Chlamydomonas have demonstrated that transgene silencing can be overcome by mutations in unknown gene(s), thus producing algal strains that stably express foreign genes to high levels. Here, we show that the silencing mechanism specifically acts on transgenic DNA. Once a permissive chromatin structure has assembled, transgene expression can persist even in the absence of mutations disrupting the silencing pathway. We have identified the gene conferring the silencing and show it to encode a sirtuin-type histone deacetylase. Loss of gene function does not appreciably affect endogenous gene expression. Our data suggest that transgenic DNA is recognized and then quickly inactivated by the assembly of a repressive chromatin structure composed of deacetylated histones. We propose that this mechanism may have evolved to provide protection from potentially harmful types of environmental DNA.

Strong transgene suppression has been observed in Chlamydomonas reinhardtii, but the underlying mechanism is unknown. Here, the authors identify a sirtuin-type histone deacetylase that selectively acts on transgenic DNA to repress gene expression by assembling a repressive chromatin structure composed of deacetylated histones.

Nuclear transformation of Chlamydomonas reinhardtii: A review

Chlamydomonas reinhardtii is a model organism with three sequenced genomes capable of genetic transformation. C. reinhardtii has the advantages of being low cost, non-toxic, and having a post-translational modification system that ensures the recombinant proteins have the same activity as natural proteins, thus making it a great platform for application in molecular biology and other fields. In this review, we summarize the existing methods for nuclear transformation of C. reinhardtii, genes for selection, examples of foreign protein expression, and factors affecting transformation efficiency, to provide insights into effective strategies for the nuclear transformation of C. reinhardtii.

Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity

Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism's molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (∼1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2'-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (∼66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.

Development of a species-specific transformation system using the novel endogenous promoter calreticulin from oleaginous microalgae Ettlia sp

Microalgae not only serve as raw materials for biofuel but also have uses in the food, pharmaceutical, and cosmetic industries. However, regulated gene expression in microalgae has only been achieved in a few strains due to the lack of genome information and unstable transformation. This study developed a species-specific transformation system for an oleaginous microalga, Ettlia sp. YC001, using electroporation. The electroporation was optimized using three parameters (waveform, field strength, and number of pulses), and the final selection was a 5 kV cm-1 field strength using an exponential decay wave with one pulse. A new strong endogenous promoter CRT (Pcrt) was identified using transcriptome and quantitative PCR analysis of highly expressed genes during the late exponential growth phase. The activities of this promoter were characterized using a codon optimized cyan fluorescent protein (CFP) as a reporter. The expression of CFP was similar under Pcrt and under the constitutive promoter psaD (PpsaD). The developed transformation system using electroporation with the endogenous promoter is simple to prepare, is easy to operate with high repetition, and utilizes a species-specific vector for high expression. This system could be used not only in molecular studies on microalgae but also in various industrial applications of microalgae.

Good News for Nuclear Transgene Expression in Chlamydomonas

Chlamydomonas reinhardtii is a well-established model system for basic research questions ranging from photosynthesis and organelle biogenesis, to the biology of cilia and basal bodies, to channelrhodopsins and photoreceptors. More recently, Chlamydomonas has also been recognized as a suitable host for the production of high-value chemicals and high-value recombinant proteins. However, basic and applied research have suffered from the inefficient expression of nuclear transgenes. The combined efforts of the Chlamydomonas community over the past decades have provided insights into the mechanisms underlying this phenomenon and have resulted in mutant strains defective in some silencing mechanisms. Moreover, many insights have been gained into the parameters that affect nuclear transgene expression, like promoters, introns, codon usage, or terminators. Here I critically review these insights and try to integrate them into design suggestions for the construction of nuclear transgenes that are to be expressed at high levels.

The Microalgae Biorefinery: A Perspective on the Current Status and Future Opportunities Using Genetic Modification

There is clear scientific evidence that emissions of greenhouse gases (GHG), arising from fossil fuel combustion and land-use change as a result of human activities, are perturbing the Earth’s climate. Microalgae-derived biofuels have been chased since the 1980s without success but, lately, a new biorefinery concept is receiving increasing attention. Here, we discuss the possible solutions to the many problems that make this process unrealised to date, considering also the possibility of including genetically modified (GM) organisms to improve the productivity and process economics. Currently, unless coupled to a service or higher value product production, biofuels derived from microalgae fail to achieve economic reality. However, provided sufficient development of new technologies, potentially including new or improved organisms to lower both production and processing costs, as well as looking at the utility of distributed versus centralised production models, algae biofuels could achieve an impact, off-setting our heavy reliance on petroleum-based liquid fuels.

Improving lipid production by strain development in microalgae: Strategies, challenges and perspectives

Over the past decade, the number of original articles and reviews presenting microalgae as a promising feedstock for biodiesel has increased tremendously. Many improvements of microalgae have been achieved through selection and strain development for industrial applications. However, the large-scale production of lipids for commercialization is not yet realistic because the production is still much more expensive than that of agricultural products. This review summarizes recent research on the induction of lipid biosynthesis in microalgae and the various strategies of genetic and metabolic engineering for enhancing lipid production. Strain engineering targets are proposed based on these strategies. To address current limitations of strain engineering for lipid production, this review provides insights on recent engineering strategies based on molecular tools and methods, and also discusses further perspectives.

Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane

A selectable marker free, highly expressed single copy locus flanked by insulators was created as landing pad for transgene stacking in sugarcane. These events displayed superior transgene expression compared to single-copy transgenic lines lacking insulators. Excision of the selectable marker gene from transgenic sugarcane lines was supported by FLPe/FRT site-specific recombination. Sugarcane, a tropical C4 grass in the genus Saccharum (Poaceae), accounts for nearly 80% of sugar produced worldwide and is also an important feedstock for biofuel production. Generating transgenic sugarcane with predictable and stable transgene expression is critical for crop improvement. In this study, we generated a highly expressed single copy locus as landing pad for transgene stacking. Transgenic sugarcane lines with stable integration of a single copy nptII expression cassette flanked by insulators supported higher transgene expression along with reduced line to line variation when compared to single copy events without insulators by NPTII ELISA analysis. Subsequently, the nptII selectable marker gene was efficiently excised from the sugarcane genome by the FLPe/FRT site-specific recombination system to create selectable marker free plants. This study provides valuable resources for future gene stacking using site-specific recombination or genome editing tools.

High-efficiency nuclear transformation of the microalgae Nannochloropsis oceanica using Tn5 Transposome for the generation of altered lipid accumulation phenotypes

BACKGROUND

One of the major problems in the production of lipids for biotechnological purposes using microalgae is maintaining a high productivity of these molecules without reducing cellular biomass. High production rates are usually obtained by cultivating microalgae under different stress conditions. However, many of these changes usually result in lower biomass productivity. Therefore, the optimization of the culture conditions and genetic modification techniques in these organisms is needed to generate robust new strains for profitable economic use.

RESULTS

In this work, we describe a new strategy for random mutation of genomic DNA in the microalgae Nannochloropsis oceanica by insertion of a Transposome complex Tn5. This complex contains an antibiotic-resistance cassette commanded by a CMV viral promoter that allows high efficiency of transformation and the generation of mutants. This strategy, complemented with a large-scale identification and selection system for mutants, such as flow cytometry with cell selection, allowed us to obtain clonal cultures of mutants with altered phenotypes in the accumulation of intracellular lipids. The characterization of some of these mutants uncovered new genes that are likely to be involved in the regulation of lipid synthesis, revealing possible cellular responses that influence the intracellular homeostasis of lipids.

CONCLUSION

The strategies proposed here are easy to implement in different types of microalgae and provide a promising scenario for improving biotechnological applications.

Integration of a Galdieria plasma membrane sugar transporter enables heterotrophic growth of the obligate photoautotrophic red alga Cynanidioschyzon merolae

The unicellular thermoacidophilic red alga Cyanidioschyzon merolae is an emerging model organism of photosynthetic eukaryotes. Its relatively simple genome (16.5 Mbp) with very low-genetic redundancy and its cellular structure possessing one chloroplast, mitochondrion, peroxisome, and other organelles have facilitated studies. In addition, this alga is genetically tractable, and the nuclear and chloroplast genomes can be modified by integration of transgenes via homologous recombination. Recent studies have attempted to clarify the structure and function of the photosystems of this alga. However, it is difficult to obtain photosynthesis-defective mutants for molecular genetic studies because this organism is an obligate autotroph. To overcome this issue in C. merolae, we expressed a plasma membrane sugar transporter, GsSPT1, from Galdieria sulphuraria, which is an evolutionary relative of C. merolae and capable of heterotrophic growth. The heterologously expressed GsSPT1 localized at the plasma membrane. GsSPT1 enabled C. merolae to grow mixotrophically and heterotrophically, in which cells grew in the dark with glucose or in the light with a photosynthetic inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and glucose. When the GsSPT1 transgene multiplied on the C. merolae chromosome via the URA Cm-Gs selection marker, which can multiply itself and its flanking transgene, GsSPT1 protein level increased and the heterotrophic and mixotrophic growth of the transformant accelerated. We also found that GsSPT1 overexpressing C. merolae efficiently formed colonies on solidified medium under light with glucose and DCMU. Thus, GsSPT1 overexpresser will facilitate single colony isolation and analyses of photosynthesis-deficient mutants produced either by random or site-directed mutagenesis. In addition, our results yielded evidence supporting that the presence or absence of plasma membrane sugar transporters is a major cause of difference in trophic properties between C. merolae and G. sulphuraria.

miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii

MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.

Evaluation of strategies for improving the transgene expression in an oleaginous microalga Scenedesmus acutus

Background

Genetic transformation of microalgae has been hampered by inefficient transgene expression, limiting the progress of microalgal biotechnology. Many vector tools and strategies have been developed in recent years to improve transgene expression in the model microalga Chlamydomonas, but these were hardly applied to other microalgae. In this work, naturally-isolated oleaginous microalgae were accessed for genetic transformation, and various expression systems were evaluated in a selected microalga to circumvent inefficient transgene expression.

Results

Initially, a strain of Scenedesmus acutus was selected from the oleaginous microalgal collection based on its highest transformation rate and transgene stability. This strain, which had very low or no GFP reporter expression, was first tested to improve transgene expression by using intron-containing constructs and the transcript fusion using ble::E2A. The intron-containing constructs yielded 2.5–7.5% of transformants with 2–4-fold fluorescence signals, while the majority of the transformants of the transcript fusion had the fluorescence signals up to 10-fold. Subsequently, three UV-induced S. acutus mutants were isolated with moderate increases in the level and frequency of transgene expression (2–3-fold and 10–12%, respectively). Finally, a transcript fusion system was developed using psy white mutants with an expression vector containing PSY::E2A for complementation and light selection. Transformants with green colonies were selected under light exposure, and the transgene expression was detected at protein levels. Although the improvement using PSY::E2A was only minor (1–2-fold increase and ~ 7% of transformants), this system provides an alternative selectable marker that is compatible with large-scale culture.

Conclusions

Here, the overall improvement of transgene expression using the Chlamydomonas tools was moderate. The most effective tool so far is the transcript fusion using ble::E2A system. This work demonstrates that, so far, genetic engineering of non-model microalgae is still a challenging task. Further development of tools and strategies for transgene expression in microalgae are critically needed.

Electronic supplementary material

The online version of this article (10.1186/s12896-018-0497-z) contains supplementary material, which is available to authorized users.

Visualizing Filamentous Actin Using Phalloidin in Chlamydomonas reinhardtii

This protocol aims to visualize the filamentous actin network in Chlamydomonas reinhardtii. We improved fixed-cell labeling conditions using the F-actin probe, phalloidin. We created a Chlamydomonas-optimized protocol by halving the phalloidin incubation time, electing for optimal fixation conditions, and selecting for a healthy cell population. This phalloidin protocol is quick, effective, and is the only labeling method to date that allows for reliable actin filament detection in fixed vegetative Chlamydomonas cells. This method reveals previously unidentified actin structures in Chlamydomonas and novel insights into cytoskeletal dynamics.

Engineering the unicellular alga Phaeodactylum tricornutum for high-value plant triterpenoid production

Plant triterpenoids constitute a diverse class of organic compounds that play a major role in development, plant defence and environmental interaction. Several triterpenes have demonstrated potential as pharmaceuticals. One example is betulin, which has shown promise as a pharmaceutical precursor for the treatment of certain cancers and HIV. Major challenges for triterpenoid commercialization include their low production levels and their cost-effective purification from the complex mixtures present in their natural hosts. Therefore, attempts to produce these compounds in industrially relevant microbial systems such as bacteria and yeasts have attracted great interest. Here, we report the production of the triterpenes betulin and its precursor lupeol in the photosynthetic diatom Phaeodactylum tricornutum, a unicellular eukaryotic alga. This was achieved by introducing three plant enzymes in the microalga: a Lotus japonicus oxidosqualene cyclase and a Medicago truncatula cytochrome P450 along with its native reductase. The introduction of the L. japonicus oxidosqualene cyclase perturbed the mRNA expression levels of the native mevalonate and sterol biosynthesis pathway. The best performing strains were selected and grown in a 550-L pilot-scale photobioreactor facility. To our knowledge, this is the most extensive pathway engineering undertaken in a diatom and the first time that a sapogenin has been artificially produced in a microalga, demonstrating the feasibility of the photo-bio-production of more complex high-value, metabolites in microalgae.

Intron-containing algal transgenes mediate efficient recombinant gene expression in the green microalga Chlamydomonas reinhardtii

Among green freshwater microalgae, Chlamydomonas reinhardtii has the most comprehensive and developed molecular toolkit, however, advanced genetic and metabolic engineering driven from the nuclear genome is generally hindered by inherently low transgene expression levels. Progressive strain development and synthetic promoters have improved the capacity of transgene expression; however, the responsible regulatory mechanisms are still not fully understood. Here, we elucidate the sequence specific dynamics of native regulatory element insertion into nuclear transgenes. Systematic insertions of the first intron of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit 2 (rbcS2i1) throughout codon-optimized coding sequences (CDS) generates optimized algal transgenes which express reliably in C. reinhardtii. The optimal rbcS2i1 insertion site for efficient splicing was systematically determined and improved gene expression rates were shown using a codon-optimized sesquiterpene synthase CDS. Sequential insertions of rbcS2i1 were found to have a step-wise additive effect on all levels of transgene expression, which is likely correlated to a synergy of transcriptional machinery recruitment and mimicking the short average exon lengths natively found in the C. reinhardtii genome. We further demonstrate the value of this optimization with five representative transgene examples and provide guidelines for the design of any desired sequence with this strategy.

Gene expression and promoter characterization of heat-shock protein 90B gene (HSP90B) in the model unicellular green alga Chlamydomonas reinhardtii

Molecular chaperones or heat shock proteins are a large protein family with important functions in every cellular organism. Among all types of the heat shock proteins, information on the ER-localized HSP90 protein (HSP90B) and its encoding gene is relatively scarce in the literature, especially in photosynthetic organisms. In this study, expression profiles as well as promoter sequence of the HSP90B gene were investigated in the model green alga Chlamydomonas reinhardtii. We have found that HSP90B is strongly induced by heat and ER stresses, while other short-term exposure to abiotic stresses, such as salinity, dark-to-light transition or light stress does not appear to affect the expression. Promoter truncation analysis as well as chromatin immunoprecipitation using the antibodies recognizing histone H3 and acetylated histone H3, revealed a putative core constitutive promoter sequence between -1 to -253 bp from the transcription start site. Our results also suggested that the nucleotides upstream of the core promoter may contain repressive elements such as putative repressor binding site(s).

Enhancing heterologous expression in Chlamydomonas reinhardtii by transcript sequence optimization

Various species of microalgae have recently emerged as promising host-organisms for use in biotechnology industries due to their unique properties. These include efficient conversion of sunlight into organic compounds, the ability to grow in extreme conditions and the occurrence of numerous post-translational modification pathways. However, the inability to obtain high levels of nuclear heterologous gene expression in microalgae hinders the development of the entire field. To overcome this limitation, we analyzed different sequence optimization algorithms while studying the effect of transcript sequence features on heterologous expression in the model microalga Chlamydomonas reinhardtii, whose genome consists of rare features such as a high GC content. Based on the analysis of genomic data, we created eight unique sequences coding for a synthetic ferredoxin-hydrogenase enzyme, used here as a reporter gene. Following in silico design, these synthetic genes were transformed into the C. reinhardtii nucleus, after which gene expression levels were measured. The empirical data, measured in vivo show a discrepancy of up to 65-fold between the different constructs. In this work we demonstrate how the combination of computational methods and our empirical results enable us to learn about the way gene expression is encoded in the C. reinhardtii transcripts. We describe the deleterious effect on overall expression of codons encoding for splicing signals. Subsequently, our analysis shows that utilization of a frequent subset of preferred codons results in elevated transcript levels, and that mRNA folding energy in the vicinity of translation initiation significantly affects gene expression.

Human Intrinsic Factor Expression for Bioavailable Vitamin B12 Enrichment in Microalgae

Dietary supplements and functional foods are becoming increasingly popular complements to regular diets. A recurring ingredient is the essential cofactor vitamin B₁₂ (B₁₂). Microalgae are making their way into the dietary supplement and functional food market but do not produce B₁₂, and their B₁₂ content is very variable. In this study, the suitability of using the human B₁₂-binding protein intrinsic factor (IF) to enrich bioavailable B₁₂ using microalgae was tested. The IF protein was successfully expressed from the nuclear genome of the model microalga Chlamydomonasreinhardtii and the addition of an N-terminal ARS2 signal peptide resulted in efficient IF secretion to the medium. Co-abundance of B₁₂ and the secreted IF suggests the algal produced IF protein is functional and B₁₂-binding. Utilizing IF expression could be an efficient tool to generate B₁₂-enriched microalgae in a controlled manner that is suitable for vegetarians and, potentially, more bioavailable for humans.

High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates

Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205-kbp circular chloroplast genome and ~15.8-kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. Forty-six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3'-end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.

Using YFP as a Reporter of Gene Expression in the Green Alga Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii is a valuable experimental system in plant biology for studying metal homeostasis. Analyzing transcriptional regulation with promoter-fusion constructs in C. reinhardtii is a powerful method for connecting metal-responsive regulation with cis-regulatory elements, but overcoming expression-level variability between transformants and optimizing experimental conditions can be laborious. Here, we provide detailed protocols for the high-throughput cultivation of C. reinhardtii and assaying Venus fluorescence as a reporter for promoter activity. We also describe procedural considerations for relating metal supply to transcriptional activity.

Current status and perspectives of genome editing technology for microalgae

Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.

Genetic engineering of medium-chain-length fatty acid synthesis in Dunaliella tertiolecta for improved biodiesel production

Genetic engineering of microalgae to accumulate high levels of medium-chain-length fatty acids (MCFAs) represents an attractive strategy to improve the quality of microalgae-based biodiesel, but it has thus far been least successful. We demonstrate that one limitation is the availability of fatty acyl-acyl carrier protein (ACP) substrate pool for acyl-ACP thioesterase (TE). A combinational expression platform that involved plant lauric acid-biased TE (C12TE) and MCFA-specific ketoacyl-ACP synthase (KASIV) increased lauric acid (C12:0) and myristic acid (C14:0) accumulation by almost sevenfold and fourfold, respectively, compared with native strain. These findings suggest a platform for further investigation into the enlargement of MCFA acyl-ACP substrate pool as an approach to sustainably improve quality of microalgae-based biodiesel with regard to MCFA production.

Expression of the heterologous Dunaliella tertiolecta fatty acyl-ACP thioesterase leads to increased lipid production in Chlamydomonas reinhardtii

Biofuel production from genetically-engineered microalgae is currently among the most widely studied strategies in generating renewable energy. However, microalgae currently suffer from low oil yields which limit the commercial feasibility of industrial-scale production. A major bottleneck in cost-efficient biofuel production from microalgae is the dilemma between biomass productivity and lipid accumulation. When grown under stressful culture conditions such as nitrogen depletion, microalgae accumulate large amounts of neutral lipids, but it comes at the expense of growth which negatively impacts overall lipid productivity. Overexpression of acyl-ACP thioesterases (TE) had been successful in increasing the production of fatty acids (FA) in prokaryotes such as E. coli and cyanobacteria, but has not been effectively tested in microalgae. In this study, we introduced a TE from D. tertiolecta (DtTE) into C. reinhardtii to investigate its effects on FA production without compromising growth. The results indicate that C. reinhardtii transformants were able to produce 63 and 94% more neutral lipids than the wild-type, which translates to an approximately 56% improvement in total lipids, without compromising growth. These findings demonstrate the cross-species functionality of TE, and provide a platform for further studies into using TE as a strategy to increase biofuel production from microalgae.