The Ancient Phosphatidylinositol 3-Kinase Signaling System Is a Master Regulator of Energy and Carbon Metabolism in Algae

Metabolomic, proteomic and lactylated proteomic analyses indicate lactate plays important roles in maintaining energy and C:N homeostasis in Phaeodactylum tricornutum

Background

Phaeodactylum tricornutum accumulates lipids while the growth also increases under high CO₂, shedding light on its potential application in the reduction of CO₂ emissions and at the same time acquiring biodiesel raw materials. However, the sensing and transducing of high C:N signals and the related response mechanism(s) remained unknown.

Results

In this study, a multiple omics analysis was performed with P. tricornutum under low nitrogen (LN) and high CO₂ (HC) conditions. The results indicated that 2-oxoglutarate was significantly increased under both LN and HC. Meanwhile, proteins involved in carbon concentration mechanism decreased, indicated that 2-oxoglutarate might regulate C:N balance through suppressing carbon fixation. Lactate, which acts in energy metabolism, signal transduction and ‘LactoylLys’ modification on proteins, was the most upregulated metabolite under both LN and HC conditions. Meanwhile, proteins involved in carbon, nitrogen and energy metabolisms were significantly regulated. Western blotting analysis suggested that non-histone L-lactylation modification was enhanced under LN and HC. Moreover, lactylated proteins were enriched in photosynthesis, central carbon metabolism, nitrogen metabolism, fatty acid synthesis and oxidative phosphorylation.

Conclusion

It is suggested that lactate might play important roles in energy homeostatic maintenance and C:N balance regulation in P. tricornutum through protein lactylation modification.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02152-8.

Algal biopolymers as sustainable resources for a net-zero carbon bioeconomy

The era for eco-friendly polymers was ushered by the marine plastic menace and with the discovery of emerging pollutants such as micro-, nano-plastics, and plastic leachates from fossil fuel-based polymers. This review investigates algae-derived natural, carbon neutral polysaccharides and polyesters, their structure, biosynthetic mechanisms, biopolymers and biocomposites production process, followed by biodegradability of the polymers. The review proposes acceleration of research in this promising area to address the need for eco-friendly polymers and to increase the cost-effectiveness of algal biorefineries by coupling biofuel, high-value products, and biopolymer production using waste and wastewater-grown algal biomass. Such a strategy improves overall sustainability by lowering costs and carbon emissions in algal biorefineries, eventually contributing towards the much touted circular, net-zero carbon future economies. Finally, this review analyses the evolution of citation networks, which in turn highlight the emergence of a new frontier of sustainable polymers from algae.

Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments

Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in Liriodendron to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between L. chinense and L. tulipifera, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in L. chinense, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in Liriodendron. Our findings reveal ecological adaptive divergence pattern between Liriodendron species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future L. chinense conservation efforts.

Effects of graphene oxide on algal cellular stress response: Evaluating metabolic characters of carbon fixation and nutrient removal

The effects of different concentrations of graphene oxide (GO) on intracellular metabolism in Chlorella vulgaris (C. vulgaris) and removal of nitrogen and phosphorus nutrients by C. vulgaris from synthetic wastewater were studied. The results demonstrated that cell division of Chlorella vulgaris increased at 24 h and decreased at 96 h after exposure to different concentrations of GO. The removal rates of total nitrogen (TN), ammoniacal nitrogen (NH₃-N), phosphate (PO₄^3--P), and chemical oxygen demand (COD) were 24.1%, 70.0%, 37.0%, and 39.6%, respectively, when the concentration of GO was 0.01 mg/L 10 mg/L GO induced severe plasmolysis and cytoplasmic contraction. Furthermore, the protein-like exopolysaccharide (EPS) content of algal cells exposed to 10 mg/L GO decrease to 10.8% of the control group. Simultaneously, the reactive oxygen species (ROS) level was 175.4% of control group. The biological responses to 10 mg/L GO included increase in ROS level, inhibition of saccharide metabolism, and degradation of amino acids. In addition, high concentrations of 10 mg/L GO weakened the carbon fixation process in algal cells. These stress-response behaviors increased cell permeability and oxidative stress. Overall, these findings provide new insights regarding the effects of GO on algal cellular stress responses.

Interplay Between Lipid Metabolism and Autophagy

Autophagy is a self-eating process of using lysosomes to degrade macromolecular substances (e.g., proteins and organelles) that are damaged, degenerated, or aging. Lipid metabolism is the synthesis and degradation of lipids (e.g., triglycerides, steroids, and phospholipids) to generate energy or produce the structural components of cell membranes. There is a complex interplay between lipid metabolism (e.g., digestion, absorption, catabolism, biosynthesis, and peroxidation) and autophagy machinery, leading to the modulation of cell homeostasis, including cell survival and death. In particular, lipid metabolism is involved in the formation of autophagic membrane structures (e.g., phagophores and autophagosomes) during stress. Moreover, autophagy, especially selective autophagy (e.g., lipophagy, ferritinophagy, clockophagy, and mitophagy), promotes lipid catabolism or lipid peroxidation-induced ferroptosis through the degradation of various substances within the cell. A better understanding of the mechanisms of autophagy and possible links to lipid metabolism will undoubtedly promote potential treatments for a variety of diseases.

The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability

The marine microalgae Nannochloropsis oceanica (CCMP1779) is a prolific producer of oil and is considered a viable and sustainable resource for biofuel feedstocks. Nitrogen (N) availability has a strong impact on the physiological status and metabolism of microalgal cells, but the exact nature of this response is poorly understood. To fill this gap we performed transcriptomic profiling combined with cellular and molecular analyses of N. oceanica CCMP1779 during the transition from quiescence to autotrophy. N deprivation-induced quiescence was accompanied by a strong reorganization of the photosynthetic apparatus and changes in the lipid homeostasis, leading to accumulation of triacylglycerol. Cell cycle activation and re-establishment of photosynthetic activity observed in response to resupply of the growth medium with N were accompanied by a rapid degradation of triacylglycerol stored in lipid droplets (LDs). Besides observing LD translocation into vacuoles, we also provide evidence for direct interaction between the LD surface protein (NoLDSP) and AUTOPHAGY-RELATED8 (NoATG8) protein and show a role of microlipophagy in LD turnover in N. oceanica CCMP1779. This knowledge is crucial not only for understanding the fundamental mechanisms controlling the cellular energy homeostasis in microalgal cells but also for development of efficient strategies to achieve higher algal biomass and better microalgal lipid productivity.

Lipidome Remodeling and Autophagic Respose in the Arachidonic-Acid-Rich Microalga Lobosphaera incisa Under Nitrogen and Phosphorous Deprivation

The green microalga Lobosphaera incisa accumulates triacylglycerols (TAGs) with exceptionally high levels of long-chain polyunsaturated fatty acid (LC-PUFA) arachidonic acid (ARA) under nitrogen (N) deprivation. Phosphorous (P) deprivation induces milder changes in fatty acid composition, cell ultrastructure, and growth performance. We hypothesized that the resource-demanding biosynthesis and sequestration of ARA-rich TAG in lipid droplets (LDs) are associated with the enhancement of catabolic processes, including membrane lipid turnover and autophagic activity. Although this work focuses mainly on N deprivation, a comparative analysis of N and P deprivation responses is included. The results of lipidomic profiling showed a differential impact of N and P deprivation on the reorganization of glycerolipids. The formation of TAG under N deprivation was associated with the enhanced breakdown of chloroplast glycerolipids and the formation of lyso-lipids. N-deprived cells displayed a profound reorganization of cell ultrastructure, including internalization of cellular material into autophagic vacuoles, concomitant with the formation of LDs, while P-deprived cells showed better cellular ultrastructural integrity. The expression of the hallmark autophagy protein ATG8 and the major lipid droplet protein (MLDP) genes were coordinately upregulated, but to different extents under either N or P deprivation. The expression of the Δ5-desaturase gene, involved in the final step of ARA biosynthesis, was coordinated with ATG8 and MLDP, exclusively under N deprivation. Concanamycin A, the inhibitor of vacuolar proteolysis and autophagic flux, suppressed growth and enhanced levels of ATG8 and TAG in N-replete cells. The proportions of ARA in TAG decreased with a concomitant increase in oleic acid under both N-replete and N-deprived conditions. The photosynthetic apparatus's recovery from N deprivation was impaired in the presence of the inhibitor, along with the delayed LD degradation. The GFP-ATG8 processing assay showed the release of free GFP in N-replete and N-deprived cells, supporting the existence of autophagic flux. This study provides the first insight into the homeostatic role of autophagy in L. incisa and points to a possible metabolic link between autophagy and ARA-rich TAG biosynthesis.

Enhancement of β-carotene production by regulating the autophagy-carotenoid biosynthesis seesaw in Chlamydomonas reinhardtii

This work aimed to demonstrate a new strategy for enhancing the production of carotenoids through the regulation of seesaw cross-talk between autophagy and carotenoid biosynthesis pathways in Chlamydomonas reinhardtii. Autophagy-related ATG1 and ATG8 genes were first silenced using artificial microRNA, which in turn reduced the mRNA expression of ATG1 and ATG8 by 84.4% and 74.3%, respectively. While ATG1 kinase controls early step in autophagy induction and ATG8 is an essential factor for the downstream formation of autophagosome membranes, the decreased expression of these genes led to a 2.34-fold increase in the amount of β-carotene content (i.e., 23.75 mg/g DCW). Furthermore, all mutants seemed to exhibit greater biodiesel properties than that of wild-type due to increased accumulation of saturated and monounsaturated fatty acids. These results support the role of autophagy in regulating the production of valuable metabolites, which could contribute to uplifting the economic outlook of nascent algal biorefinery.

Dynamic Interactions between Autophagosomes and Lipid Droplets in Chlamydomonas reinhardtii

Autophagy is a highly conserved catabolic process in eukaryotic cells by which waste cellular components are recycled to maintain growth in both favorable and stress conditions. Autophagy has been linked to lipid metabolism in microalgae; however, the mechanism underlying this interaction remains unclear. In this study, transgenic Chlamydomonas reinhardtii cells that stably express the red fluorescent protein (mCherry) tagged-ATG8 as an autophagy marker were established. By using this tool, we were able to follow the autophagy process in live microalgal cells under various conditions. Live-cell and transmission electron microscopy (TEM) imaging revealed physical contacts between lipid droplets and autophagic structures during the early stage of nitrogen starvation, while fusion of these two organelles was observed in prolonged nutritional deficiency, suggesting that an autophagy-related pathway might be involved in lipid droplet turnover in this alga. Our results thus shed light on the interplay between autophagy and lipid metabolism in C. reinhardtii, and this autophagy marker would be a valuable asset for further investigations on autophagic processes in microalgae.

Nitrogen modulation under chemostat cultivation mode induces biomass and lipid production by Chlorella vulgaris and reduces antenna pigment accumulation

Algal growth limitation in large-scale cultivation mostly results from high level synthesis of photosynthetic pigments, owing to self-shading effects and attenuation of light distribution. To overcome this problem, here we investigated the influence of nitrogen modulation on changes in antenna pigments as well as biomass and lipid production by Chlorella vulgaris under a chemostat continuous cultivation mode. The production of algal antenna pigments, including chlorophylls and carotenoids, was promoted in a total nitrogen (TN) concentration-dependent manner. Maximum algal biomass and lipid production were obtained from 70 mg/L of TN concentration along with a significant increase in light transmittance and reduction in antenna pigments. Furthermore, the composition of polyunsaturated fatty acids remarkably augmented at low TN concentrations. These results suggest that the reduction in algal antenna pigment synthesis via modulation of nitrogen concentration may serve as an effective strategy to enhance algal biomass and lipid production.