De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

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

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

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Transcriptional insights into Chlorella sp. ABC-001: a comparative study of carbon fixation and lipid synthesis under different CO2 conditions

BACKGROUND

Microalgae's low tolerance to high CO2 concentrations presents a significant challenge for its industrial application, especially when considering the utilization of industrial exhaust gas streams with high CO2 content-an economically and environmentally attractive option. Therefore, the objectives of this study were to investigate the metabolic changes in carbon fixation and lipid accumulation of microalgae under ambient air and high CO2 conditions, deepen our understanding of the molecular mechanisms driving these processes, and identify potential target genes for metabolic engineering in microalgae. To accomplish these goals, we conducted a transcriptomic analysis of the high CO2-tolerant strain, Chlorella sp. ABC-001, under two different carbon dioxide levels (ambient air and 10% CO2) and at various growth phases.

RESULTS

Cells cultivated with 10% CO2 exhibited significantly better growth and lipid accumulation rates, achieving up to 2.5-fold higher cell density and twice the lipid content by day 7. To understand the relationship between CO2 concentrations and phenotypes, transcriptomic analysis was conducted across different CO2 conditions and growth phases. According to the analysis of differentially expressed genes and gene ontology, Chlorella sp. ABC-001 exhibited the development of chloroplast organelles during the early exponential phase under high CO2 conditions, resulting in improved CO2 fixation and enhanced photosynthesis. Cobalamin-independent methionine synthase expression was also significantly elevated during the early growth stage, likely contributing to the methionine supply required for various metabolic activities and active proliferation. Conversely, the cells showed sustained repression of carbonic anhydrase and ferredoxin hydrogenase, involved in the carbon concentrating mechanism, throughout the cultivation period under high CO2 conditions. This study also delved into the transcriptomic profiles in the Calvin cycle, nitrogen reductase, and lipid synthesis. Particularly, Chlorella sp. ABC-001 showed high expression levels of genes involved in lipid synthesis, such as glycerol-3-phosphate dehydrogenase and phospholipid-diacylglycerol acyltransferase. These findings suggest potential targets for metabolic engineering aimed at enhancing lipid production in microalgae.

CONCLUSIONS

We expect that our findings will help understand the carbon concentrating mechanism, photosynthesis, nitrogen assimilation, and lipid accumulation metabolisms of green algae according to CO2 concentrations. This study also provides insights into systems metabolic engineering of microalgae for improved performance in the future.

Exploring the Role of Carbon-Based Nanomaterials in Microalgae for the Sustainable Production of Bioactive Compounds and Beyond

An enchanting yet challenging task is the development of higher productivity in plants to meet the ample food demands for the growing global population while harmonizing the ecosystem using front-line technologies. This has kindled the practice of green microalgae cultivation as a driver of key biostimulant products, targeting agronomic needs. To this end, a prodigious and economical strategy for producing bioactive compounds (sources of secondary metabolites) from microalgae using carbon-based nanomaterials (CNMs) as a platform can circumvent these hurdles. Recently, the nanobionics approach of incorporating CNMs with living systems has emerged as a promising technique to develop organelles with new and augmented functions. Herein, we discuss the importance of 2D carbon nanosheets (CNS) as an alternative carbon source for the phototrophic cultivation of microalgae. CNS not only aids in cost reduction for algal cultivation but also confers combinatorial innate or exogenous functions that enhance its programmed biosynthetic metabolism, proliferation, or tolerance to stress. Moreover, the inherent ability of CNS to act as efficient biocatalysts can enhance the rate of photosynthesis. The primary focus of this mini-review is the development of an economic route for enhanced yield of bioactive compounds while simultaneously serving as a heterogeneous platform for enhancing the sustainable production of biostimulants including bioactive compounds from algal biomass for pharmaceutical and nutraceutical applications.

Metabolic pathways for biosynthesis and degradation of starch in Tetraselmis chui during nitrogen deprivation and recovery

Tetraselmis chui is known to accumulate starch when subjected to stress. This phenomenon is widely studied for the purpose of industrial production and process development. Yet, knowledge about the metabolic pathways involved is still immature. Hence, in this study, transcription of 27 starch-related genes was monitored under nitrogen deprivation and resupply in 25 L tubular photobioreactors. T. chui proved to be an efficient starch producer under nitrogen deprivation, accumulating starch up to 56% of relative biomass content. The prolonged absence of nitrogen led to an overall down-regulation of the tested genes, in most instances maintained even after nitrogen replenishment when starch was actively degraded. These gene expression patterns suggest post-transcriptional regulatory mechanisms play a key role in T. chui under nutrient stress. Finally, the high productivity combined with an efficient recovery after nitrogen restitution makes this species a suitable candidate for industrial production of high-starch biomass.

A novel two-stage heterotrophic cultivation for starch-to-protein switch to efficiently enhance protein content of Chlorella sp. MBFJNU-17

This work aimed to firstly establish an efficient and novel two-stage cultivation process to produce microalgal biomass rich in protein using a heterotrophic Chlorella sp. MBFJNU-17 strain. In the first-stage cultivation, to reduce the glucose and urea utilization, microalga achieved a high biomass at 40 g/L glucose and 1 g/L urea; meantime, the expression from starch biosynthesis genes of microalga was up-regulated under nitrogen-starvation conditions for starch accumulation (55.01%). In the second-stage cultivation, based on the over-compensation effect, Chlorella cells after the first-stage cultivation were further treated at 5 g/L glucose and 3 g/L urea to up-regulate starch degradation, central carbon metabolism and urea absorption genes expression to drive intracellular starch-to-protein switch for biosynthetic protein (59.75%). Moreover, microalga performed similar characteristics in a 10-L fermenter by the established process. Taken together, Chlorella sp. MBFJNU-17 was the promising candidate to produce high-value biomass enriched in protein by the established two-stage cultivation.

Transcriptomic survey reveals multiple adaptation mechanisms in response to nitrogen deprivation in marine Porphyridium cruentum

Single-cell red microalga Porphyridium cruentum is potentially considered to be the bioresource for biofuel and pharmaceutical production. Nitrogen is a kind of nutrient component for photosynthetic P. cruentum. Meanwhile, nitrogen stress could induce to accumulate some substances such as lipid and phycoerythrin and affect its growth and physiology. However, how marine microalga Porphyridium cruentum respond and adapt to nitrogen starvation remains elusive. Here, acclimation of the metabolic reprogramming to changes in the nutrient environment was studied by high-throughput mRNA sequencing in the unicellular red alga P. cruentum. Firstly, to reveal transcriptional regulation, de novo transcriptome was assembled and 8,244 unigenes were annotated based on different database. Secondly, under nitrogen deprivation, 2100 unigenes displayed differential expression (1134 upregulation and 966 downregulation, respectively) and some pathways including carbon/nitrogen metabolism, photosynthesis, and lipid metabolism would be reprogrammed in P. cruentum. The result demonstrated that nitrate assimilation (with related unigenes of 8–493 fold upregulation) would be strengthen and photosynthesis (with related unigenes of 6–35 fold downregulation) be impaired under nitrogen deprivation. Importantly, compared to other green algae, red microalga P. cruentum presented a different expression pattern of lipid metabolism in response to nitrogen stress. These observations will also provide novel insight for understanding adaption mechanisms and potential targets for metabolic engineering and synthetic biology in P. cruentum.

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.

Lipid accumulation of Chlorella sp. TLD6B from the Taklimakan Desert under salt stress

Chlorella has become an important raw material for biodiesel production in recent years, and Chlorella sp. TLD6B, a species with high lipid concentrations and high salt and drought tolerance, has been cultivated on a large scale. To explore the lipid accumulation of Chlorella sp. TLD6B and its relationship to external NaCl concentrations, we performed physiological measurements and genome-wide gene expression profiling under different levels of salt stress. Chlorella sp. TLD6B was able to tolerate high levels of salt stress (0.8 M NaCl addition). Lipid concentrations initially increased and then decreased as salt stress increased and were highest under the addition of 0.2 M NaCl. Comparative transcriptomic analysis revealed that salt stress enhanced the expression of genes related to sugar metabolism and fatty acid biosynthesis (the ACCases BC and BCCP, KAS II, and GPDHs involved in TAG synthesis), thereby promoting lipid accumulation under the addition of 0.2 M NaCl. However, high salinity inhibited cell growth. Expression of three SADs, whose encoded products function in unsaturated fatty acid biosynthesis, was up-regulated under high salinity (0.8 M NaCl addition). This research clarifies the relationship between salt tolerance and lipid accumulation and promotes the utilization of Chlorella sp. TLD6B.

The molecular mechanisms of Chlorella sp. responding to high CO2: A study based on comparative transcriptome analysis between strains with high- and low-CO2 tolerance

High CO₂ acclimation for microalgae has attracted large research attention owing to the usefulness of microalgae in bio-sequestration of CO₂ from the emission source. In this study, one high CO₂ tolerant (LAMB 31) and non-tolerant (LAMB 122) Chlorella sp. strains were transferred from air to 40% CO₂, during which four time points were chosen for comparative transcriptome analysis. Gene changes started in the lag phase (T1) of population growth with more genes (7889) upregulated in LAMB 31 than in LAMB 122 (1092). Further function enrichments indicated: In LAMB 31, up-regulation of genes in cyclic electron transportation, F-type ATPase and Calvin cycle were associated with the enhancement of carbon fixation abilities; upregulation of genes in phosphorylation together with V-ATPase, which contributed to cytoplasmatic pH stability; Lastly, enhancement of carbon metabolisms including TCA cycle and glycolysis accelerated the consumption of cellular organic carbon. Most of the genes in these pathways and processes showed downregulation in LAMB 122. This study disclosed the most complete transcriptional molecular mechanisms of Chlorella sp. responding to high CO₂ by combining CO₂ fixation, transportation, and metabolic processes. The results provided valuable genetic information for future screening and breeding of microalgae with high-CO₂ tolerance for more efficient CO₂ bio-sequestration.

Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui

Quantitative real-time reverse transcription PCR (RT-qPCR) is a highly sensitive technique that can be applied to analyze how genes are modulated by culture conditions, but identification of appropriate reference genes for normalization is a critical factor to be considered. For this reason, the expression stability of 18 candidate reference genes was evaluated for the green microalgae Tetraselmis chui using the widely employed algorithms geNorm, NormFinder, BestKeeper, the comparative ΔCT method, and RefFinder. Microalgae samples were collected from large scale outdoor photobioreactors during the growing phase (OUT_GP), and during the semi-continuous phase at different times of the day (OUT_DC). Samples from standard indoor cultures under highly controlled conditions (IND) were also collected to complement the other data. Different rankings for the candidate reference genes were obtained depending on the culture conditions and the algorithm employed. After comparison of the achieved ranks with the different methods, the references genes selected for samples from specific culture conditions were ALD and EFL in OUT_GP, RPL32 and UBCE in OUT_DC, and cdkA and UBCE in IND. Moreover, the genes EFL and cdkA or EFL and UBCE appeared as appropriate combinations for pools generated from all samples (ALL). Examination in the OUT_DC cultures of genes encoding the large and small subunits of ADP-glucose pyrophosphorylase (AGPL and AGPS, respectively) confirmed the reliability of the identified reference genes, RPL32 and UBCE. The present study represents a useful contribution for studies of gene expression in T. chui, and also represents the first step to set-up an RT-qPCR platform for quality control of T. chui biomass production in industrial facilities.

De novo transcriptome analysis of Chlorella sorokiniana: effect of glucose assimilation, and moderate light intensity

Chlorella can produce an unusually wide range of metabolites under various nutrient availability, carbon source, and light availability. Glucose, an essential molecule for the growth of microorganisms, also contributes significantly to the metabolism of various metabolic compounds produced by Chlorella. In addition, manipulation of light intensity also induces the formation of secondary metabolites such as pigments, and carotenoids in Chlorella. This study will focus on the effect of glucose addition, and moderate light on the regulation of carotenoid, lipid, starch, and other key metabolic pathways in Chlorella sorokiniana. To gain knowledge about this, we performed transcriptome profiling on C. sorokiniana strain NIES-2168 in response to moderate light stress supplemented with glucose under mixotrophic conditions. A total of 60,982,352 raw paired-end (PE) reads 100 bp in length was obtained from both normal, and mixotrophic samples of C. sorokiniana. After pre-processing, 93.63% high-quality PE reads were obtained, and 18,310 predicted full-length transcripts were assembled. Differential gene expression showed that a total of 937, and 1124 genes were upregulated, and downregulated in mixotrophic samples, respectively. Transcriptome analysis revealed that the mixotrophic condition caused upregulation of genes involved in carotenoids production (specifically lutein biosynthesis), fatty acid biosynthesis, TAG accumulation, and the majority of the carbon fixation pathways. Conversely, starch biosynthesis, sucrose biosynthesis, and isoprenoid biosynthesis were downregulated. Novel insights into the pathways that link the enhanced production of valuable metabolites (such as carotenoids in C. sorokiniana) grown under mixotrophic conditions is presented.

Carbon fixation gene expression in Skeletonema marinoi in nitrogen-, phosphate-, silicate-starvation, and low-temperature stress exposure

Diatoms are unicellular algae with a set of extraordinary genes, metabolic pathways, and physiological functions acquired by secondary endosymbiosis, especially for their efficient photosynthetic carbon fixation mechanisms, which can be a reason for their successful environmental adaptation and great contribution to primary production. Based on the available genomic information, the expression patterns of carbon fixation genes were analyzed using transcriptomic sequencing and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in Skeletonema marinoi. Meanwhile, suitable reference genes applying to specific experimental treatments were selected. In our results, carbon fixation genes were standardized by actin and TATA box-binding protein-coding genes in growth phase samples and stress conditions, respectively. It was found that a series of carbon fixation genes, such as the pyruvate orthophosphate dikinase (PPDK)-coding gene, had significantly up-regulated expression in nitrogen-starvation, phosphate-starvation, and low-temperature conditions, but consistently down-regulated in silicate-starvation treatment. These carbon fixation genes exhibited variable expression levels in different conditions and will be useful for investigating gene expression mechanisms in S. marinoi and improve our understanding of diatom carbon fixation pathways.

Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalgae

Heterotrophic growth mode is among the most promising strategies put forth to overcome the low biomass and secondary metabolites productivity challenge. To shedding light on the underlying molecular mechanisms, transcriptome meta-analysis was integrated with weighted gene co-expression network analysis (WGCNA), connectivity analysis, functional enrichment, and hubs identification. Meta-analysis and Functional enrichment analysis demonstrated that most of the biological processes are up-regulated at heterotrophic growth condition, which leads to change of genetic architectures and phenotypic outcomes. WGNCA analysis of meta-genes also resulted four significant functional modules across logarithmic (LG), transition (TR), and production peak (PR) phases. The expression pattern and connectivity characteristics of the brown module as a non-preserved module vary across LG, TR, and PR phases. Functional analysis identified Carotenoid biosynthesis, Fatty acid metabolism and Methane metabolism as enriched pathways in the non-preserved module. Our integrated approach was applied here, identified some hubs, such as a serine hydroxymethyltransferase (SHMT1), which is the best candidate for development of metabolites accumulating strains in microalgae. Current study provided a new insight into underlying metabolite accumulation mechanisms and opens new avenue for the future applied studies in the microalgae field.

Exogenous addition of indole acetic acid and kinetin under nitrogen-limited medium enhances lipid yield and expression of glycerol-3-phosphate acyltransferase & diacylglycerol acyltransferase genes in indigenous microalgae: A potential approach for biodiesel production

In the present study, a combination of phytohormones (indole acetic acid and kinetin) was augmented in nitrogen-limited medium to achieve higher biomass and lipid yield in Graesiella emersonii NC-M1 and Chlorophyta sp. NC-M5. This condition was recorded with a 2.3- and 2.5-fold increase in biomass and lipid yield for Graesiella emersonii NC-M1 compared to the nitrogen-limited condition. Also, this condition showed a 1.6- and 1.08-fold increase in lipid yield and neutral lipid compared to the standard condition. Phytohormones addition also reduced oxidative damage caused by nitrogen-limitation and enhanced monounsaturated fatty acid content. Further, a 5.2- and 3.17-fold enhance in expression level of GPAT and DGAT genes were noticed under nitrogen-limited medium supplemented with phytohormones compared to control.

Exploring stress tolerance mechanism of evolved freshwater strain Chlorella sp. S30 under 30 g/L salt

Enhancement of stress tolerance to high concentration of salt and CO₂ is beneficial for CO₂ capture by microalgae. Adaptive evolution was performed for improving the tolerance of a freshwater strain, Chlorella sp. AE10, to 30 g/L salt. A resulting strain denoted as Chlorella sp. S30 was obtained after 46 cycles (138 days). The stress tolerance mechanism was analyzed by comparative transcriptomic analysis. Although the evolved strain could tolerate 30 g/L salt, high salinity caused loss to photosynthesis, oxidative phosphorylation, fatty acid biosynthesis and tyrosine metabolism. The related genes of antioxidant enzymes, CO₂ fixation, amino acid biosynthesis, central carbon metabolism and ABC transporter proteins were up-regulated. Besides the up-regulation of several genes in Calvin-Benson cycle, they were also identified in C4 photosynthetic pathway and crassulacean acid metabolism pathway. They were essential for the survival and CO₂ fixation of Chlorella sp. S30 under 30 g/L salt and 10% CO₂.

Genome sequences of Chlorella sorokiniana UTEX 1602 and Micractinium conductrix SAG 241.80: implications to maltose excretion by a green alga

Green algae represent a key segment of the global species capable of photoautotrophic-driven biological carbon fixation. Algae partition fixed-carbon into chemical compounds required for biomass, while diverting excess carbon into internal storage compounds such as starch and lipids or, in certain cases, into targeted extracellular compounds. Two green algae were selected to probe for critical components associated with sugar production and release in a model alga. Chlorella sorokiniana UTEX 1602 - which does not release significant quantities of sugars to the extracellular space - was selected as a control to compare with the maltose-releasing Micractinium conductrix SAG 241.80 - which was originally isolated from an endosymbiotic association with the ciliate Paramecium bursaria. Both strains were subjected to three sequencing approaches to assemble their genomes and annotate their genes. This analysis was further complemented with transcriptional studies during maltose release by M. conductrix SAG 241.80 versus conditions where sugar release is minimal. The annotation revealed that both strains contain homologs for the key components of a putative pathway leading to cytosolic maltose accumulation, while transcriptional studies found few changes in mRNA levels for the genes associated with these established intracellular sugar pathways. A further analysis of potential sugar transporters found multiple homologs for SWEETs and tonoplast sugar transporters. The analysis of transcriptional differences revealed a lesser and more measured global response for M. conductrix SAG 241.80 versus C. sorokiniana UTEX 1602 during conditions resulting in sugar release, providing a catalog of genes that might play a role in extracellular sugar transport.

Molecular characterization of CO2 sequestration and assimilation in microalgae and its biotechnological applications

Microalgae are renewable feedstock for sustainable biofuel production, cell factory for valuable chemicals and promising in alleviation of greenhouse gas CO₂. However, the carbon assimilation capacity is still the bottleneck for higher productivity. Molecular characterization of CO₂ sequestration and assimilation in microalgae has advanced in the past few years and are reviewed here. In some cyanobacteria, genes for 2-oxoglytarate dehydrogenase was replaced by four alternative mechanisms to fulfill TCA cycle. In green algae Coccomyxa subellipsoidea C-169, alternative carbon assimilation pathway was upregulated under high CO₂ conditions. These advances thus provide new insights and new targets for accelerating CO₂ sequestration rate and enhancing bioproduct synthesis in microalgae. When integrated with conventional parameter optimization, molecular approach for microalgae modification targeting at different levels is promising in generating value-added chemicals from green algae and cyanobacteria efficiently in the near future.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Transcriptome-based analysis on carbon metabolism of Haematococcus pluvialis mutant under 15% CO2

To elucidate the mechanism underlying the enhanced growth rate in the Haematococcus pluvialis mutated with ⁶⁰Co-γ rays and domesticated with 15% CO₂, transcriptome sequencing was conducted to clarify the carbon metabolic pathways of mutant cells. The CO₂ fixation rate of mutant cells increased to 2.57gL^-1d^-1 under 15% CO₂ due to the enhanced photosynthesis, carbon fixation, glycolysis pathways. The upregulation of PetH, ATPF0A and PetJ related to photosynthetic electron transport, ATP synthase and NADPH generation promoted the photosynthesis. The upregulation of genes related to Calvin cycle and ppdK promoted carbon fixation in both C3 and C4 photosynthetic pathways. The reallocation of carbon was also enhanced under 15% CO₂. The 19-, 14- and 3.5-fold upregulation of FBA, TPI and PK genes, respectively, remarkably promoted the glycolysis pathways. This accelerated the conversion of photosynthetic carbon to pyruvate, which was an essential precursor for astaxanthin and lipids biosynthesis.