The TOR Signaling Network in the Model Unicellular Green Alga Chlamydomonas reinhardtii

Reactive oxygen species-mediated signal transduction and utilization strategies in microalgae

Reactive oxygen species (ROS) are crucial in stress perception, the integration of environmental signals, and the activation of downstream response networks. This review emphasizes ROS-mediated signaling pathways in microalgae and presents an overview of strategies for leveraging ROS. Eight distinct signaling pathways mediated by ROS in microalgae have been summarized, including the calcium signaling pathway, the target of rapamycin signaling pathway, the mitogen-activated protein kinase signaling pathway, the cyclic adenosine monophosphate/protein kinase A signaling pathway, the ubiquitin/protease pathway, the ROS-regulated transcription factors and enzymes, the endoplasmic reticulum stress, and the retrograde ROS signaling. Moreover, this review outlines three strategies for utilizing ROS: two-stage cultivation, combined stress with phytohormones, and strain engineering. The physicochemical properties of various ROS, together with their redox reactions with downstream targets, have been elucidated to reveal the role of ROS in signal transduction processes while delineating the ROS-mediated signal transduction network within microalgae.

Photoacclimation strategies of Chlamydomonas reinhardtii in response to high-light stress in stationary phase

Under ideal conditions, Chlamydomonas reinhardtii can photoacclimate to excess light through various short- and long-term mechanisms. However, how microalgae handle excess light stress once they exit exponential growth, and especially in stationary phase, is less understood. Our study explored C. reinhardtii's photoprotection capacity and acclimation strategies during high-light stress once batch culture growth reached stationary phase. We monitored cultures of wildtype strain (CC125) over five days once they reached stationary phase under both low-light (LL) and high-light (HL) conditions. Under HL, many photosynthetic proteins were degraded but the stress-related light harvesting complex protein (LHCSR) was rapidly induced and contributed to the rapid activation of nonphotochemical quenching (NPQ). However, the LHCSR3-defective mutant (CC4614, npq4) lacked the rapid induction of quenching typical of post-exponential cultures, indicating that LHCSR3 is required for this response in stationary phase. Collectively, the main strategy for photoacclimation in stationary phase appears to be a dramatic reduction of photosystems while maintaining LHCII-LHCSR antenna complexes that prime the antenna for rapid activation of quenching upon light exposure. Part of this response to HL involves a resumption of cell growth after two days, that we hypothesized is due to the stimulation of growth-regulating pathways due to increased metabolite pools from the HL-induced protein turnover in the cell, something that remains to be tested. These findings demonstrate how C. reinhardtii manages high-light stress during stationary phases to maximize longevity.

NgLst8 Coactivates TOR Signaling to Activate Photosynthetic Growth in Nannochloropsis gaditana

The target of rapamycin (TOR) serves as a central regulator of cell growth, coordinating anabolic and catabolic processes in response to nutrient availability, growth factors, and energy supply. Activation of TOR has been shown to promote photosynthesis, growth, and development in yeast, animals, and plants. In this study, the complete cDNA sequence of the Lst8 gene was obtained from Nannochloropsis gaditana. The structure of N. gaditana LST8 comprises a typical WD40 repeat sequence, exhibiting high sequence similarity to several known LST8 proteins. By overexpressing the Lst8 gene in N. gaditana, we constructed the NgLst8 transgenic algal strain and measured its photosynthetic activity and growth. We observed that an increase in LST8 abundance promotes the expression of TOR-related kinase, thereby enhancing photosynthetic growth. Transcriptome analysis further elucidated the response mechanism of elevated Lst8 abundance in relation to photosynthesis. Our findings indicate that increased Lst8 expression activates ABC transporter proteins and the MAPK signaling pathway, which regulate the transmembrane transport of sugars and other metabolites, integrate photosynthesis, sugar metabolism, and energy signaling, and modulate energy metabolism in algal cells through interactions with the TOR signaling pathway.

Nitrogen starvation leads to TOR kinase-mediated downregulation of fatty acid synthesis in the algae Chlorella sorokiniana and Chlamydomonas reinhardtii

BACKGROUND

When subject to stress conditions such as nutrient limitation microalgae accumulate triacylglycerol (TAG). Fatty acid, a substrate for TAG synthesis is derived from de novo synthesis or by membrane remodeling. The model industrial alga Chlorellasorokiniana accumulates TAG and other storage compounds under nitrogen (N)-limited growth. Molecular mechanisms underlying these processes are still to be elucidated.

RESULT

Previously we used transcriptomics to explore the regulation of TAG synthesis in C. sorokiniana. Surprisingly, our analysis showed that the expression of several key genes encoding enzymes involved in plastidic fatty acid synthesis are significantly repressed. Metabolic labeling with radiolabeled acetate showed that de novo fatty acid synthesis is indeed downregulated under N-limitation. Likewise, inhibition of the Target of Rapamycin kinase (TOR), a key regulator of metabolism and growth, decreased fatty acid synthesis. We compared the changes in proteins and phosphoprotein abundance using a proteomics and phosphoproteomics approach in C. sorokiniana cells under N-limitation or TOR inhibition and found extensive overlap between the N-limited and TOR-inhibited conditions. We also identified changes in the phosphorylation status of TOR complex proteins, TOR-kinase, and RAPTOR, under N-limitation. This indicates that TOR signaling is altered in a nitrogen-dependent manner. We find that TOR-mediated metabolic remodeling of fatty acid synthesis under N-limitation is conserved in the chlorophyte algae Chlorella sorokiniana and Chlamydomonas reinhardtii.

CONCLUSION

Our results indicate that under N-limitation there is significant metabolic remodeling, including fatty acid synthesis, mediated by TOR signaling. This process is conserved across chlorophyte algae. Using proteomic and phosphoproteomic analysis, we show that N-limitation affects TOR signaling and this in-turn affects the metabolic status of the cells. This study presents a link between N-limitation, TOR signaling and fatty acid synthesis in green-lineage.

Regulatory mechanisms of autophagy on DHA and carotenoid accumulation in Crypthecodinium sp. SUN

BACKGROUND

Autophagy is a crucial process of cellular self-destruction and component reutilization that can affect the accumulation of total fatty acids (TFAs) and carotenoids in microalgae. The regulatory effects of autophagy process in a docosahexaenoic acid (DHA) and carotenoids simultaneously producing microalga, Crypthecodinium sp. SUN, has not been studied. Thus, the autophagy inhibitor (3-methyladenine (MA)) and activator (rapamycin) were used to regulate autophagy in Crypthecodinium sp. SUN.

RESULTS

The inhibition of autophagy by 3-MA was verified by transmission electron microscopy, with fewer autophagy vacuoles observed. Besides, 3-MA reduced the glucose absorption and intracellular acetyl-CoA level, which resulting in the decrease of TFA and DHA levels by 15.83 and 26.73% respectively; Surprisingly, 3-MA increased intracellular reactive oxygen species level but decreased the carotenoids level. Comparative transcriptome analysis showed that the downregulation of the glycolysis, pentose phosphate pathway and tricarboxylic acid cycle may underlie the decrease of acetyl-CoA, NADPH and ATP supply for fatty acid biosynthesis; the downregulation of PSY and HMGCR may underlie the decreased carotenoids level. In addition, the class I PI3K-AKT signaling pathway may be crucial for the regulation of carbon and energy metabolism. At last, rapamycin was used to activate autophagy, which significantly enhanced the cell growth and TFA level and eventually resulted in 1.70-fold increase in DHA content.

CONCLUSIONS

Our findings indicate the mechanisms of autophagy in Crypthecodinium sp. SUN and highlight a way to manipulate cell metabolism by regulating autophagy. Overall, this study provides valuable insights to guide further research on autophagy-regulated TFA and carotenoids accumulation in Crypthecodinium sp. SUN.

Sugar signals pedal the cell cycle!

Cell cycle involves the sequential and reiterative progression of important events leading to cell division. Progression through a specific phase of the cell cycle is under the control of various factors. Since the cell cycle in multicellular eukaryotes responds to multiple extracellular mitogenic cues, its study in higher forms of life becomes all the more important. One such factor regulating cell cycle progression in plants is sugar signalling. Because the growth of organs depends on both cell growth and proliferation, sugars sensing and signalling are key control points linking sugar perception to regulation of downstream factors which facilitate these key developmental transitions. However, the basis of cell cycle control via sugars is intricate and demands exploration. This review deals with the information on sugar and TOR-SnRK1 signalling and how they manoeuvre various events of the cell cycle to ensure proper growth and development.

TOR in plants: Multidimensional regulators of plant growth and signaling pathways

Target Of Rapamycin (TOR) represents a ubiquitous kinase complex that has emerged as a central regulator of cell growth and metabolism in nearly all eukaryotic organisms. TOR is an evolutionarily conserved protein kinase, functioning as a central signaling hub that integrates diverse internal and external cues to regulate a multitude of biological processes. These processes collectively exert significant influence on plant growth, development, nutrient assimilation, photosynthesis, fruit ripening, and interactions with microorganisms. Within the plant domain, the TOR complex comprises three integral components: TOR, RAPTOR, and LST8. This comprehensive review provides insights into various facets of the TOR protein, encompassing its origin, structure, function, and the regulatory and signaling pathways operative in photosynthetic organisms. Additionally, we explore future perspectives related to this pivotal protein kinase.

Algae communication, conspecific and interspecific: the concepts of phycosphere and algal-bacteria consortia in a photobioreactor (PBR)

Microalgae in the wild often form consortia with other species promoting their own health and resource foraging opportunities. The recent application of microalgae cultivation and deployment in commercial photobioreactors (PBR) so far has focussed on single species of algae, resulting in multi-species consortia being largely unexplored. Reviewing the current status of PBR ecological habitat, this article argues in favor of further investigation into algal communication with conspecifics and interspecifics, including other strains of microalgae and bacteria. These mutualistic species form the 'phycosphere': the microenvironment surrounding microalgal cells, potentiating the production of certain metabolites through biochemical interaction with cohabitating microorganisms. A better understanding of the phycosphere could lead to novel PBR configurations, capable of incorporating algal-microbial consortia, potentially proving more effective than single-species algal systems.

Common environmental stress responses in a model marine diatom

Marine planktonic diatoms are among the most important contributors to phytoplankton blooms and marine net primary production. Their ecological success has been attributed to their ability to rapidly respond to changing environmental conditions. Here, we report common molecular mechanisms used by the model marine diatom Thalassiosira pseudonana to respond to 10 diverse environmental stressors using RNA-Seq analysis. We identify a specific subset of 1076 genes that are differentially expressed in response to stressors that induce an imbalance between energy or resource supply and metabolic capacity, which we termed the diatom environmental stress response (d-ESR). The d-ESR is primarily composed of genes that maintain proteome homeostasis and primary metabolism. Photosynthesis is strongly regulated in response to environmental stressors but chloroplast-encoded genes were predominantly upregulated while the nuclear-encoded genes were mostly downregulated in response to low light and high temperature. In aggregate, these results provide insight into the molecular mechanisms used by diatoms to respond to a range of environmental perturbations and the unique role of the chloroplast in managing environmental stress in diatoms. This study facilitates our understanding of the molecular mechanisms underpinning the ecological success of diatoms in the ocean.

The Arabidopsis Target of Rapamycin (TOR) kinase regulates ammonium assimilation and glutamine metabolism

In eukaryotes, Target of Rapamycin (TOR) is a well conserved kinase that controls cell metabolism and growth in response to nutrients and environmental factors. Nitrogen (N) is an essential element for plants, and TOR functions as a crucial N and amino acid sensor in animals and yeast. However, knowledge on the connections between TOR and the overall N metabolism and assimilation in plants is still limited. In this study, we investigated the regulation of TOR in Arabidopsis (Arabidopsis thaliana) by the N source as well as the impact of TOR deficiency on N metabolism. Inhibition of TOR globally decreased ammonium uptake while triggering a massive accumulation of amino acids, such as Gln, but also of polyamines. Consistently, TOR complex mutants were hypersensitive to Gln. We also showed that the glutamine synthetase inhibitor glufosinate abolishes Gln accumulation resulting from TOR inhibition and improves the growth of TOR complex mutants. These results suggest that a high level of Gln contributes to the reduction in plant growth resulting from TOR inhibition. Glutamine synthetase activity was reduced by TOR inhibition while the enzyme amount increased. In conclusion, our findings show that the TOR pathway is intimately connected to N metabolism and that a decrease in TOR activity results in glutamine synthetase-dependent Gln and amino acid accumulation.

Deciphering the function and evolution of the target of rapamycin signaling pathway in microalgae

Microalgae constitute a highly diverse group of photosynthetic microorganisms that are widely distributed on Earth. The rich diversity of microalgae arose from endosymbiotic events that took place early in the evolution of eukaryotes and gave rise to multiple lineages including green algae, the ancestors of land plants. In addition to their fundamental role as the primary source of marine and freshwater food chains, microalgae are essential producers of oxygen on the planet and a major biotechnological target for sustainable biofuel production and CO2 mitigation. Microalgae integrate light and nutrient signals to regulate cell growth. Recent studies identified the target of rapamycin (TOR) kinase as a central regulator of cell growth and a nutrient sensor in microalgae. TOR promotes protein synthesis and regulates processes that are induced under nutrient stress such as autophagy and the accumulation of triacylglycerol and starch. A detailed analysis of representative genomes from the entire microalgal lineage revealed that the highly conserved central components of the TOR pathway are likely to have been present in the last eukaryotic common ancestor, and the loss of specific TOR signaling elements at an early stage in the evolution of microalgae. Here we examine the evolutionary conservation of TOR signaling components in diverse microalgae and discuss recent progress of this signaling pathway in these organisms.

Target of Rapamycin Regulates Photosynthesis and Cell Growth in Auxenochlorella pyrenoidosa

Auxenochlorella pyrenoidosa is an efficient photosynthetic microalga with autotrophic growth and reproduction, which has the advantages of rich nutrition and high protein content. Target of rapamycin (TOR) is a conserved protein kinase in eukaryotes both structurally and functionally, but little is known about the TOR signalling in Auxenochlorella pyrenoidosa. Here, we found a conserved ApTOR protein in Auxenochlorella pyrenoidosa, and the key components of TOR complex 1 (TORC1) were present, while the components RICTOR and SIN1 of the TORC2 were absent in Auxenochlorella pyrenoidosa. Drug sensitivity experiments showed that AZD8055 could effectively inhibit the growth of Auxenochlorella pyrenoidosa, whereas rapamycin, Torin1 and KU0063794 had no obvious effect on the growth of Auxenochlorella pyrenoidosaa. Transcriptome data results indicated that Auxenochlorella pyrenoidosa TOR (ApTOR) regulates various intracellular metabolism and signaling pathways in Auxenochlorella pyrenoidosa. Most genes related to chloroplast development and photosynthesis were significantly down-regulated under ApTOR inhibition by AZD8055. In addition, ApTOR was involved in regulating protein synthesis and catabolism by multiple metabolic pathways in Auxenochlorella pyrenoidosa. Importantly, the inhibition of ApTOR by AZD8055 disrupted the normal carbon and nitrogen metabolism, protein and fatty acid metabolism, and TCA cycle of Auxenochlorella pyrenoidosa cells, thus inhibiting the growth of Auxenochlorella pyrenoidosa. These RNA-seq results indicated that ApTOR plays important roles in photosynthesis, intracellular metabolism and cell growth, and provided some insights into the function of ApTOR in Auxenochlorella pyrenoidosa.

Target of Rapamycin Signaling Involved in the Regulation of Photosynthesis and Cellular Metabolism in Chlorella sorokiniana

Target of rapamycin (TOR) is a serine/threonine protein kinase that plays a central regulating role in cell proliferation, growth, and metabolism, but little is known about the TOR signaling pathway in Chlorella sorokiniana. In this study, a Chlorella sorokiniana DP-1 strain was isolated and identified, and its nutritional compositions were analyzed. Based on homologous sequence analysis, the conserved CsTOR protein was found in the genome of Chlorella sorokiniana. In addition, the key components of TOR complex 1 (TORC1) were present, but the components of TORC2 (RICTOR and SIN1) were absent in Chlorella sorokiniana. Pharmacological assays showed that Chlorella sorokiniana DP-1 was insensitive to rapamycin, Torin1 and KU0063794, whereas AZD8055 could significantly inhibit the growth of Chlorella sorokiniana. RNA-seq analysis showed that CsTOR regulated various metabolic processes and signal transduction pathways in AZD8055-treated Chlorella sorokiniana DP-1. Most genes involved in photosynthesis and carbon fixation in Chlorella sorokiniana DP-1 were significantly downregulated under CsTOR inhibition, indicating that CsTOR positively regulated the photosynthesis in Chlorella sorokiniana. Furthermore, CsTOR controlled protein synthesis and degradation by positively regulating ribosome synthesis and negatively regulating autophagy. These observations suggested that CsTOR plays an important role in photosynthesis and cellular metabolism, and provide new insights into the function of CsTOR in Chlorella sorokiniana.

Gamma-aminobutyric acid coupled with copper ion stress stimulates lipid production of green microalga Monoraphidium sp. QLY-1 through multiple mechanisms

Induction of copper ion (Cu²⁺) stress is a method used to increase lipid accumulation in microalgae, but it decreases cell growth. In this work, the impacts of gamma-aminobutyric acid (GABA) coupled with Cu²⁺ stress on the biomass and oil yield in Monoraphidium sp. QLY-1 were investigated. Results suggested that the combined treatment of GABA and Cu²⁺ resulted in a higher lipid content (55.13%) than Cu²⁺ treatment (48.43%). Furthermore, GABA addition upregulated the levels of lipid-relevant genes, cellular GABA, ethylene (ETH), and antioxidant enzyme activities and alleviated oxidative damage caused by Cu²⁺ stress. The autophagy-relevant gene atg8 was also upregulated by GABA treatment. Further exploration indicated that cell autophagy induced the lipid content up to 58.09% with GABA and Cu²⁺ stress treatment. This investigation demonstrates that the coupling strategy can stimulate lipid production and shed light on the underlying mechanisms in lipid biosynthesis, cell autophagy, and stress response of microalgae.

Role of Autophagy in Haematococcus lacustris Cell Growth under Salinity

The microalga Haematococcus lacustris (formerly H. pluvialis) is able to accumulate high amounts of the carotenoid astaxanthin in the course of adaptation to stresses like salinity. Technologies aimed at production of natural astaxanthin for commercial purposes often involve salinity stress; however, after a switch to stressful conditions, H. lacustris experiences massive cell death which negatively influences astaxanthin yield. This study addressed the possibility to improve cell survival in H. lacustris subjected to salinity via manipulation of the levels of autophagy using AZD8055, a known inhibitor of TOR kinase previously shown to accelerate autophagy in several microalgae. Addition of NaCl in concentrations of 0.2% or 0.8% to the growth medium induced formation of autophagosomes in H. lacustris, while simultaneous addition of AZD8055 up to a final concentration of 0.2 µM further stimulated this process. AZD8055 significantly improved the yield of H. lacustris cells after 5 days of exposure to 0.2% NaCl. Strikingly, this occurred by acceleration of cell growth, and not by acceleration of aplanospore formation. The level of astaxanthin synthesis was not affected by AZD8055. However, cytological data suggested a role of autophagosomes, lysosomes and Golgi cisternae in cell remodeling during high salt stress.

Photosynthetic assimilation of CO2 regulates TOR activity

The target of rapamycin (TOR) kinase is a master regulator that integrates nutrient signals to promote cell growth in all eukaryotes. It is well established that amino acids and glucose are major regulators of TOR signaling in yeast and metazoan, but whether and how TOR responds to carbon availability in photosynthetic organisms is less understood. In this study, we showed that photosynthetic assimilation of CO₂ by the Calvin-Benson-Bassham (CBB) cycle regulates TOR activity in the model single-celled microalga Chlamydomonas reinhardtii Stimulation of CO₂ fixation boosted TOR activity, whereas inhibition of the CBB cycle and photosynthesis down-regulated TOR. We uncovered a tight link between TOR activity and the endogenous level of a set of amino acids including Ala, Glu, Gln, Leu, and Val through the modulation of CO₂ fixation and the use of amino acid synthesis inhibitors. Moreover, the finding that the Chlamydomonas starch-deficient mutant sta6 displayed disproportionate TOR activity and high levels of most amino acids, particularly Gln, further connected carbon assimilation and amino acids to TOR signaling. Thus, our results showed that CO₂ fixation regulates TOR signaling, likely through the synthesis of key amino acids.

Inositol polyphosphates and target of rapamycin kinase signalling govern photosystem II protein phosphorylation and photosynthetic function under light stress in Chlamydomonas

Stress and nutrient availability influence cell proliferation through complex intracellular signalling networks. In a previous study it was found that pyro-inositol polyphosphates (InsP₇ and InsP₈ ) produced by VIP1 kinase, and target of rapamycin (TOR) kinase signalling interacted synergistically to control cell growth and lipid metabolism in the green alga Chlamydomonas reinhardtii. However, the relationship between InsPs and TOR was not completely elucidated. We used an in vivo assay for TOR activity together with global proteomic and phosphoproteomic analyses to assess differences between wild-type and vip1-1 in the presence and absence of rapamycin. We found that TOR signalling is more severely affected by the inhibitor rapamycin in a vip1-1 mutant compared with wild-type, indicating that InsP₇ and InsP₈ produced by VIP1 act independently but also coordinately with TOR. Additionally, among hundreds of differentially phosphorylated peptides detected, an enrichment for photosynthesis-related proteins was observed, particularly photosystem II proteins. The significance of these results was underscored by the finding that vip1-1 strains show multiple defects in photosynthetic physiology that were exacerbated under high light conditions. These results suggest a novel role for inositol pyrophosphates and TOR signalling in coordinating photosystem phosphorylation patterns in Chlamydomonas cells in response to light stress and possibly other stresses.

Crosslinking mass spectrometry unveils novel interactions and structural distinctions in the model green alga Chlamydomonas reinhardtii

Interactomics is an emerging field that seeks to identify both transient and complex-bound protein interactions that are essential for metabolic functions. Crosslinking mass spectrometry (XL-MS) has enabled untargeted global analysis of these protein networks, permitting largescale simultaneous analysis of protein structure and interactions. Increased commercial availability of highly specific, cell permeable crosslinkers has propelled the study of these critical interactions forward, with the development of MS-cleavable crosslinkers further increasing confidence in identifications. Herein, the global interactome of the unicellular alga Chlamydomonas reinhardtii was analyzed via XL-MS by implementing the MS-cleavable disuccinimidyl sulfoxide (DSSO) crosslinker and enriching for crosslinks using strong cation exchange chromatography. Gentle lysis via repeated freeze-thaw cycles facilitated in vitro analysis of 157 protein-protein crosslinks (interlinks) and 612 peptides linked to peptides of the same protein (intralinks) at 1% FDR throughout the C. reinhardtii proteome. The interlinks confirmed known protein relationships across the cytosol and chloroplast, including coverage on 42% and 38% of the small and large ribosomal subunits, respectively. Of the 157 identified interlinks, 92% represent the first empirical evidence of interaction observed in C. reinhardtii. Several of these crosslinks point to novel associations between proteins, including the identification of a previously uncharacterized Mg-chelatase associated protein (Cre11.g477733.t1.2) bound to seven distinct lysines on Mg-chelatase (Cre06.g306300.t1.2). Additionally, the observed intralinks facilitated characterization of novel protein structures across the C. reinhardtii proteome. Together, these data establish a framework of protein-protein interactions that can be further explored to facilitate understanding of the dynamic protein landscape in C. reinhardtii.

Transcriptomic and Physiological Responses of the Tropical Reef Calcified Macroalga Amphiroa fragilissima to Elevated Temperature1

Calcareous macroalgae are of particular ecological importance as primary producers, carbonate sediment builders, and habitat providers in coral reef ecosystems. Ocean warming is a major threat to calcareous algae, but it remains unclear exactly how these algae will respond to it. In this study, the potential physiological impacts of ocean warming on the calcareous alga Amphiroa fragilissima were evaluated in laboratory experiments. Increasing temperature from 26 to 28°C had positive effects on algal growth rate and chlorophyll a content, but these parameters decreased significantly at 32°C, which is 5°C above the annual mean temperature in the study region. Algal bleaching occurred at 34°C. There were no significant differences in CaCO₃ content of thalli among different temperatures; however, calcification rate was inhibited significantly at 32 and 34°C. Transcriptome analyses using the Illumina RNA-seq platform showed that differentially expressed genes were annotated mainly in the categories of steroid biosynthesis, gap junction, ribosome, and mTOR signaling pathway. The expression levels of PsbA and PsbP were suppressed at 32°C, implying that inactivation of photosystem II could be a main reason for the decreased photosynthetic rate. Down-regulation of the genes encoding carbonic anhydrase and nitrate reductase was observed at 32°C, which could inhibit growth rate. Additionally, several genes that might be related to calcification were identified, including CAMK, CDPK, and CAM and genes encoding alpha-catenin and carbonic anhydrase. This study contributes to our understanding of the effects of temperature on algal calcification and provides a theoretical basis to protect ecological diversity of coral reef ecosystems.

A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites

Protein phosphorylation, which is one of the most important post-translational modifications (PTMs), is involved in regulating myriad cellular processes. Herein, we present a novel deep learning based approach for organism-specific protein phosphorylation site prediction in Chlamydomonas reinhardtii, a model algal phototroph. An ensemble model combining convolutional neural networks and long short-term memory (LSTM) achieves the best performance in predicting phosphorylation sites in C. reinhardtii. Deemed Chlamy-EnPhosSite, the measured best AUC and MCC are 0.90 and 0.64 respectively for a combined dataset of serine (S) and threonine (T) in independent testing higher than those measures for other predictors. When applied to the entire C. reinhardtii proteome (totaling 1,809,304 S and T sites), Chlamy-EnPhosSite yielded 499,411 phosphorylated sites with a cut-off value of 0.5 and 237,949 phosphorylated sites with a cut-off value of 0.7. These predictions were compared to an experimental dataset of phosphosites identified by liquid chromatography-tandem mass spectrometry (LC–MS/MS) in a blinded study and approximately 89.69% of 2,663 C. reinhardtii S and T phosphorylation sites were successfully predicted by Chlamy-EnPhosSite at a probability cut-off of 0.5 and 76.83% of sites were successfully identified at a more stringent 0.7 cut-off. Interestingly, Chlamy-EnPhosSite also successfully predicted experimentally confirmed phosphorylation sites in a protein sequence (e.g., RPS6 S245) which did not appear in the training dataset, highlighting prediction accuracy and the power of leveraging predictions to identify biologically relevant PTM sites. These results demonstrate that our method represents a robust and complementary technique for high-throughput phosphorylation site prediction in C. reinhardtii. It has potential to serve as a useful tool to the community. Chlamy-EnPhosSite will contribute to the understanding of how protein phosphorylation influences various biological processes in this important model microalga.

Outer membrane protein a in Acinetobacter baumannii induces autophagy through mTOR signalling pathways in the lung of SD rats

Outer membrane protein A (OmpA) of Acinetobacter baumannii (A. baumannii) is associated with autophagy, which plays an important role in its pathogenicity. However, its exact pathophysiological role in the process of lung tissue cell autophagy remains unclear. In this study, animal and cell infection models were established by wild A. baumannii strain and An OmpA knockout mutant (OmpA-/- A. baumannii) strain. The expression levels of markers autophagy, histological change, cell viability and protein expression levels of inflammatory cytokines were examined. OmpA-/-A. baumannii was successfully constructed. The capacities of bacterial adhesion and invasion to host cells increased more obviously in the AB group and the AB + Rapa group than in the OmpA-/- AB group and AB + CQ group. The AB group and AB + Rapa group could produce double membrane vacuoles, endoplasmic reticulum dilation, mitochondrial ridge rupture, and mitochondrial vacuoles. OmpA could lead to increased LC3, AMPK, and PAMPK protein release, and decreased levels of P62, mTOR and pmTOR proteins in vivo and in vitro. OmpA caused lung pathology and the release of inflammatory cytokines. A. baumannii OmpA promotes autophagy in lung cells through the mTOR signalling pathway, which increases the bacterial colonization ability in the double-layer membrane autophagosome formed by the autophagy reaction to escape the clearance of bacteria by the host, promote the release of inflammatory mediators and aggravate the damage to the host.

Lipid accumulation patterns and role of different fatty acid types towards mitigating salinity fluctuations in Chlorella vulgaris

Mangrove-dwelling microalgae are well adapted to frequent encounters of salinity fluctuations across their various growth phases but are lesser studied. The current study explored the adaptive changes (in terms of biomass, oil content and fatty acid composition) of mangrove-isolated C. vulgaris UMT-M1 cultured under different salinity levels (5, 10, 15, 20, 30 ppt). The highest total oil content was recorded in cultures at 15 ppt salinity (63.5% of dry weight) with uncompromised biomass productivity, thus highlighting the ‘trigger-threshold’ for oil accumulation in C. vulgaris UMT-M1. Subsequently, C. vulgaris UMT-M1 was further assessed across different growth phases under 15 ppt. The various short, medium and long-chain fatty acids (particularly C20:0), coupled with a high level of C18:3n3 PUFA reported at early exponential phase represents their physiological importance during rapid cell growth. Accumulation of C18:1 and C18:2 at stationary growth phase across all salinities was seen as cells accumulating substrate for C18:3n3 should the cells anticipate a move from stationary phase into new growth phase. This study sheds some light on the possibility of ‘triggered’ oil accumulation with uninterrupted growth and the participation of various fatty acid types upon salinity mitigation in a mangrove-dwelling microalgae.

Enteromorpha compressa extract induces anticancer activity through apoptosis and autophagy in oral cancer

Marine algae are an auspicious source of innovative bioactive compounds containing possible therapeutic agents against mammalian cancers. However, the mechanism by which bioactive algal compounds exhibit anticancer activity against oral squamous cell carcinoma (OSCC) is scant. The main objective of the current study was to explore the properties of the Enteromorpha compressa solvent extracts that induced autophagy and apoptosis with reference to their potent phytochemical and antioxidant properties. The presence of bioactive compounds were confirmed by UV and FT-IR spectroscopy. The free radical scavenging activity were analyzed by evaluating H₂O₂, DPPH, superoxide and hydroxyl activity. The anticancer activities of the extracts were investigated by employing clonogenic and scratch assay. The apoptosis potential was evaluated by DAPI and MMP by Rh123 fluorescence assay. Moreover, the CAT, SOD, GPX, APX, and GR activities were measured. The autophagy potential was evaluated by LC3 puncta formation, acridine orange in addition to LysoTracker staining. The present investigation revealed that the methanolic extract of E. compressa elicited robust free radical scavenging activity that discerns its antiproliferative potency. Moreover, the methanolic algal extract boosted intrinsic apoptosis against OSCC by downregulating protective antioxidant enzymes. Furthermore, it also revealed induction of autophagy to promote cell death in oral cancer cells. The presence of novel bioactive compounds in E. compressa has uncovered possible therapeutic value against OSCC by modulating antioxidant defense system, apoptosis and autophagy that could be used to explore very competent algal candidates for the development of potential alternative anticancer drugs.

The Plant Target of Rapamycin: A Conduc TOR of Nutrition and Metabolism in Photosynthetic Organisms

Living organisms possess many mechanisms to sense nutrients and favorable conditions, which allow them to grow and develop. Photosynthetic organisms are very diverse, from green unicellular algae to multicellular flowering plants, but most of them are sessile and thus unable to escape from the biotic and abiotic stresses they experience. The Target of Rapamycin (TOR) signaling pathway is conserved in all eukaryotes and acts as a central regulatory hub between growth and extrinsic factors, such as nutrients or stress. However, relatively little is known about the regulations and roles of this pathway in plants and algae. Although some features of the TOR pathway seem to have been highly conserved throughout evolution, others clearly differ in plants, perhaps reflecting adaptations to different lifestyles and the rewiring of this primordial signaling module to adapt to specific requirements. Indeed, TOR is involved in plant responses to a vast array of signals including nutrients, hormones, light, stresses or pathogens. In this review, we will summarize recent studies that address the regulations of TOR by nutrients in photosynthetic organisms, and the roles of TOR in controlling important metabolic pathways, highlighting similarities and differences with the other eukaryotes.

Adaptation to Aquatic and Terrestrial Environments in Chlorella vulgaris (Chlorophyta)

The globally distributed green microalga Chlorella vulgaris (Chlorophyta) colonizes aquatic and terrestrial habitats, but the molecular mechanisms underpinning survival in these two contrasting environments are far from understood. Here, we compared the authentic strain of C. vulgaris from an aquatic habitat with a strain from a terrestrial high alpine habitat previously determined as Chlorella mirabilis. Molecular phylogeny of SSU rDNA (823 bp) showed that the two strains differed by one nucleotide only. Sequencing of the ITS2 region confirmed that both strains belong to the same species, but to distinct ribotypes. Therefore, the terrestrial strain was re-assessed as C. vulgaris. To study the response to environmental conditions experienced on land, we assessed the effects of irradiance and temperature on growth, of temperature on photosynthesis and respiration, and of desiccation and rehydration on photosynthetic performance. In contrast to the aquatic strain, the terrestrial strain tolerated higher temperatures and light conditions, had a higher photosynthesis-to-respiration ratio at 25°C, still grew at 30°C and was able to fully recover photosynthetic performance after desiccation at 84% relative humidity. The two strains differed most in their response to the dehydration/rehydration treatment, which was further investigated by untargeted GC–MS-based metabolite profiling to gain insights into metabolic traits differentiating the two strains. The two strains differed in their allocation of carbon and nitrogen into their primary metabolites. Overall, the terrestrial strain had higher contents of readily available nitrogen-based metabolites, especially amino acids and the polyamine putrescine. Dehydration and rehydration led to differential regulation of the amino acid metabolism, the tricarboxylic acid cycle and sucrose metabolism. The data are discussed with a view to differences in phenotypic plasticity of the two strains, and we suggest that the two genetically almost identical C. vulgaris strains are attractive models to study mechanisms that protect from abiotic stress factors, which are more frequent in terrestrial than aquatic habitats, such as desiccation and irradiation.

TOR kinase activity in Chlamydomonas reinhardtii is modulated by cellular metabolic states

Target of rapamycin (TOR) kinase is a sensor and a central integrator of internal and external metabolic cues. However, in algae and in higher plants, the components of TOR kinase signaling are yet to be characterized. Here, we establish an assay system to study TOR kinase activity in Chlamydomonas reinhardtii using the phosphorylation status of its putative downstream target, CrS6K. Using this assay, we probe the modulation of cellular TOR kinase activity under various physiological states such as photoautotrophy, heterotrophy, mixotrophy, and nitrogen (N) starvation. Importantly, we uncover that excess acetate in the medium leads to high cellular reactive oxygen species levels, triggering autophagy and a concomitant drop in TOR kinase activity in a dose-dependent manner, thus leading to a N-starvation-like cellular phenotype, even when nitrogen is present.

Microalgal Target of Rapamycin (TOR): A Central Regulatory Hub for Growth, Stress Response and Biomass Production

Target of rapamycin (TOR) is an evolutionarily conserved protein kinase that plays an important role in the regulation of cell growth and the sensing of nutrient and energy status in eukaryotes. In yeasts and mammals, the roles of TOR have been very well described and various functions of TOR signaling in plant lineages have also been revealed over the past 20 years. In the case of microalgae, the functions of TOR have been primarily studied in the model green alga Chlamydomonas reinhardtii and were summarized in an earlier single review article. However, the recent development of tools for the functional analysis of TOR has helped to reveal the involvement of TOR in various functions, including autophagy, transcription, translation, accumulation of energy storage molecules, etc., in microalgae. In the present review, we discuss recent novel findings relating to TOR signaling and its roles in microalgae along with relevant information on land plants and also provide details of topics that must be addressed in future studies to reveal how TOR regulates various physiological functions in microalgae.

Algal Autophagy Is Necessary for the Regulation of Carbon Metabolism Under Nutrient Deficiency

Autophagy is a mechanism to recycle intracellular constituents such as amino acids and other carbon- and nitrogen (N)-containing compounds. Although autophagy-related (ATG) genes required for autophagy are encoded by many algal genomes, their functional importance in microalgae in nutrient-deficiency has not been appraised using ATG-defective mutants. Recently, by characterization of an insertional mutant of the ATG8 encoding a ubiquitin-like protein indispensable for autophagosome formation in a green alga Chlamydomonas reinhardtii, we have provided evidence that supports the following notions. ATG8 protein is required for the degradation of lipid droplets and triacylglycerol (TAG) triggered by resupply of N to cell culture in N-deficient conditions. ATG8 protein is also necessary for starch accumulation under phosphorus-deficient conditions. Algal autophagy is not necessary for inheritance of chloroplast and mitochondrial genomes. In this review, we discuss the physiological roles of algal autophagy associated with nutrient deficiency revealed by the genetic and biochemical analyses using disruption mutants and reagents that inhibit the fatty acid biosynthesis and vacuolar H⁺-ATPase.

Phosphorus Availability Regulates TORC1 Signaling via LST8 in Chlamydomonas

Target of rapamycin complex 1 (TORC1) is a central regulator of cell growth. It balances anabolic and catabolic processes in response to nutrients, growth factors, and energy availability. Nitrogen- and carbon-containing metabolites have been shown to activate TORC1 in yeast, animals, and plants. Here, we show that phosphorus (P) regulates TORC1 signaling in the model green alga Chlamydomonas (Chlamydomonas reinhardtii) via LST8, a conserved TORC1 subunit that interacts with the kinase domain of TOR. P starvation results in a sharp decrease in LST8 abundance and downregulation of TORC1 activity. A hypomorphic lst8 mutation resulted in decreased LST8 abundance, and it both reduced TORC1 signaling and altered the cellular response to P starvation. Additionally, we found that LST8 levels and TORC1 activity were not properly regulated in a mutant defective in the transcription factor PSR1, which is the major mediator of P deprivation responses in Chlamydomonas. Unlike wild-type cells, the psr1 mutant failed to downregulate LST8 abundance and TORC1 activity when under P limitation. These results identify PSR1 as an upstream regulator of TORC1 and demonstrate that TORC1 is a key component in P signaling in Chlamydomonas.

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.

Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii

While the role of TOR kinase in the chloroplast biogenesis and transcriptional regulation of photosynthesis is well documented in Arabidopsis, the functional relevance of this metabolic sensor kinase in chloroplast-mitochondria cross talk is unknown. Using Chlamydomonas reinhardtii as the model system, we demonstrate the role of TOR kinase in the regulation of chloroplast and mitochondrial functions: We show that TOR kinase inhibition impairs the maintenance of high ETR associated with PSII and low NPQ and inhibits efficient state transitions between PSII and PSI. While compromised photosynthetic functions are observed in TOR kinase inhibited cells, same conditions lead to augmentation in mitochondrial basal respiration rate by twofold and concomitantly a rise in ATP production. Interestingly, such upregulated mitochondrial functions in TOR-inhibited cells are mediated by fragmented mitochondria via upregulating COXIIb and downregulating Hxk1 and AOX1 protein levels. We propose that TOR kinase may act as a sensor that counter-regulates chloroplast versus mitochondrial functions in a normal C. reinhardtii cell.

Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes

The target of rapamycin (TOR) kinase is a master metabolic regulator with roles in nutritional sensing, protein translation, and autophagy. In Chlamydomonas reinhardtii, a unicellular green alga, TOR has been linked to the regulation of increased triacylglycerol (TAG) accumulation, suggesting that TOR or a downstream target(s) is responsible for the elusive “lipid switch” in control of increasing TAG accumulation under nutrient limitation. However, while TOR has been well characterized in mammalian systems, it is still poorly understood in photosynthetic systems, and little work has been done to show the role of oxidative signaling in TOR regulation. In this study, the TOR inhibitor AZD8055 was used to relate reversible thiol oxidation to the physiological changes seen under TOR inhibition, including increased TAG content. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 401 proteins were determined to have significant changes in oxidation following TOR inhibition. These oxidative changes mirrored characterized physiological modifications, supporting the role of reversible thiol oxidation in TOR regulation of TAG production, protein translation, carbohydrate catabolism, and photosynthesis through the use of reversible thiol oxidation. The delineation of redox-controlled proteins under TOR inhibition provides a framework for further characterization of the TOR pathway in photosynthetic eukaryotes.

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.

Targeting TOR signaling for enhanced lipid productivity in algae

Microalgae can produce large quantities of triacylglycerols (TAGs) and other neutral lipids that are suitable for making biofuels and as feedstocks for green chemistry. However, TAGs accumulate under stress conditions that also stop growth, leading to a trade-off between biomass production and TAG yield. Recently, in the model marine diatom Phaeodactylum tricornutum it was shown that inhibition of the target of rapamycin (TOR) kinase boosts lipid productivity by promoting TAG production without stopping growth. We believe that basic knowledge in this emerging field is required to develop innovative strategies to improve neutral lipid accumulation in oleaginous microalgae. In this minireview, we discuss current research on the TOR signaling pathway with a focus on its control on lipid homeostasis. We first provide an overview of the well characterized roles of TOR in mammalian lipogenesis, adipogenesis and lipolysis. We then present evidence of a role for TOR in controlling TAG accumulation in microalgae, and draw parallels between the situation in animals, plants and microalgae to propose a model of TOR signaling for TAG accumulation in microalgae.

Cell cycle control by the target of rapamycin signalling pathway in plants

Cells need to ensure a sufficient nutrient and energy supply before committing to proliferate. In response to positive mitogenic signals, such as light, sugar availability, and hormones, the target of rapamycin (TOR) signalling pathway promotes cell growth that connects to the entry and passage through the cell division cycle via multiple signalling mechanisms. Here, we summarize current understanding of cell cycle regulation by the RBR-E2F regulatory hub and the DREAM-like complexes, and highlight possible functional relationships between these regulators and TOR signalling. A genetic screen recently uncovered a downstream signalling component to TOR that regulates cell proliferation, YAK1, a member of the dual specificity tyrosine phosphorylation-regulated kinase (DYRK) family. YAK1 activates the plant-specific SIAMESE-RELATED (SMR) cyclin-dependent kinase inhibitors and therefore could be important to regulate both the CDKA-RBR-E2F pathway to control the G1/S transition and the mitotic CDKB1;1 to control the G2/M transition. TOR, as a master regulator of both protein synthesis-driven cell growth and cell proliferation is also central for cell size homeostasis. We conclude the review by briefly highlighting the potential applications of combining TOR and cell cycle knowledge in the context of ensuring future food security.

TOR inhibitors: from mammalian outcomes to pharmacogenetics in plants and algae

Target of rapamycin (TOR) is a conserved eukaryotic phosphatidylinositol 3-kinase-related kinase that regulates growth and metabolism in response to environment in plants and algae. The study of the plant and algal TOR pathway has largely depended on TOR inhibitors first developed for non-photosynthetic eukaryotes. In animals and yeast, fundamental work on the TOR pathway has benefited from the allosteric TOR inhibitor rapamycin and more recently from ATP-competitive TOR inhibitors (asTORis) that circumvent the limitations of rapamycin. The asTORis, developed for medical application, inhibit TOR complex 1 (TORC1) more efficiently than rapamycin and also inhibit rapamycin-resistant TORCs. This review presents knowledge on TOR inhibitors from the mammalian field and underlines important considerations for plant and algal biologists. It discusses the use of rapamycin and asTORis in plants and algae and concludes with guidelines for physiological studies and genetic screens with TOR inhibitors.

Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets

Target of rapamycin (TOR) kinase is a conserved regulator of cell growth whose activity is modulated in response to nutrients, energy and stress. Key proteins involved in the pathway are conserved in the model photosynthetic microalga Chlamydomonas reinhardtii, but the substrates of TOR kinase and downstream signaling network have not been elucidated. Our study provides a new resource for investigating the phosphorylation networks governed by the TOR kinase pathway in Chlamydomonas. We used quantitative phosphoproteomics to investigate the effects of inhibiting Chlamydomonas TOR kinase on dynamic protein phosphorylation. Wild-type and AZD-insensitive Chlamydomonas strains were treated with TOR-specific chemical inhibitors (rapamycin, AZD8055 and Torin1), after which differentially affected phosphosites were identified. Our quantitative phosphoproteomic dataset comprised 2547 unique phosphosites from 1432 different proteins. Inhibition of TOR kinase caused significant quantitative changes in phosphorylation at 258 phosphosites, from 219 unique phosphopeptides. Our results include Chlamydomonas homologs of TOR signaling-related proteins, including a site on RPS6 with a decrease in phosphorylation. Additionally, phosphosites on proteins involved in translation and carotenoid biosynthesis were identified. Follow-up experiments guided by these phosphoproteomic findings in lycopene beta/epsilon cyclase showed that carotenoid levels are affected by TORC1 inhibition and carotenoid production is under TOR control in algae.

Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas

Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii, to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.

Target of Rapamycin Inhibition in Chlamydomonas reinhardtii Triggers de Novo Amino Acid Synthesis by Enhancing Nitrogen Assimilation

The Target of Rapamycin (TOR) kinase is a central regulator of growth and metabolism in all eukaryotic organisms, including animals, fungi, and plants. Even though the inputs and outputs of TOR signaling are well characterized for animals and fungi, our understanding of the upstream regulators of TOR and its downstream targets is still fragmentary in photosynthetic organisms. In this study, we employed the rapamycin-sensitive green alga Chlamydomonas reinhardtii to elucidate the molecular cause of the amino acid accumulation that occurs after rapamycin-induced inhibition of TOR. Using different growth conditions and stable ¹³C- and ¹⁵N-isotope labeling, we show that this phenotype is accompanied by increased nitrogen (N) uptake, which is induced within minutes of TOR inhibition. Interestingly, this increased N influx is accompanied by increased activities of glutamine synthetase and glutamine oxoglutarate aminotransferase, the main N-assimilating enzymes, which are responsible for the rise in levels of several amino acids, which occurs within a few minutes. Accordingly, we conclude that even though translation initiation and autophagy have been reported to be the main downstream targets of TOR, the upregulation of de novo amino acid synthesis seems to be one of the earliest responses induced after the inhibition of TOR in Chlamydomonas.

The target of rapamycin kinase affects biomass accumulation and cell cycle progression by altering carbon/nitrogen balance in synchronized Chlamydomonas reinhardtii cells

Several metabolic processes tightly regulate growth and biomass accumulation. A highly conserved protein complex containing the target of rapamycin (TOR) kinase is known to integrate intra- and extracellular stimuli controlling nutrient allocation and hence cellular growth. Although several functions of TOR have been described in various heterotrophic eukaryotes, our understanding lags far behind in photosynthetic organisms. In the present investigation, we used the model alga Chlamydomonas reinhardtii to conduct a time-resolved analysis of molecular and physiological features throughout the diurnal cycle after TOR inhibition. Detailed examination of the cell cycle phases revealed that growth is not only repressed by 50%, but also that significant, non-linear delays in the progression can be observed. By using metabolomics analysis, we elucidated that the growth repression was mainly driven by differential carbon partitioning between anabolic and catabolic processes. Accordingly, the time-resolved analysis illustrated that metabolic processes including amino acid-, starch- and triacylglycerol synthesis, as well RNA degradation, were redirected within minutes of TOR inhibition. Here especially the high accumulation of nitrogen-containing compounds indicated that an active TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression.

AC-202, a highly effective fluorophore for the visualization of lipid droplets in green algae and diatoms

BACKGROUND

Lipid-specific live cell dyes are an important tool for the study of algal lipid metabolism, the monitoring of lipid production, and the identification of algal strains with high lipid yields. Nile Red and BODIPY have emerged as the principal dyes for these purposes. However, they suffer from a number of shortcomings including for specificity, penetration, interference from chlorophyll autofluorescence, and incompatibility with widely used genetically encoded reporters in the green and blue regions of the spectrum such as the green fluorescent protein and the red fluorescent protein.

RESULTS

We tested a new blue fluorescent dye, AC-202, in both the green algae Chlamydomonas reinhardtii and the pennate diatom Phaeodactylum tricornutum. We show that AC-202 is effective in both algae and that after minimal sample preparation, it can label lipid droplets induced by nitrogen starvation or by inhibitors of the TOR (target of rapamycin) kinase. We found that AC-202 benefits from a low background signal and is therefore more sensitive than BODIPY for semiquantitative in vivo fluorescence measurements. Finally, a co-staining experiment indicated that AC-202 can be used for multicolor imaging in combination with both red and green fluorophores.

CONCLUSIONS

AC-202 is an alternative and highly effective fluorophore for algal research that resolves drawbacks encountered with other neutral lipid dyes. AC-202 can be used to rapidly and sensitively visualize lipid droplets, and will contribute to the identification of metabolic and signaling pathways involved in lipid droplet formation, monitoring lipid production, and in the development of screens for algal strains suitable for biofuel production.

Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii

Rapamycin is an inhibitor of the evolutionary conserved Target of Rapamycin (TOR) kinase which promotes and coordinates translation with cell growth and division. In heterotrophic organisms, TOR regulation is based on intra- and extracellular stimuli such as amino acids level and insulin perception. However, how plant TOR pathways have evolved to integrate plastid endosymbiosis is a remaining question. Despite the close association of the TOR signaling with the coordination between protein turn-over and growth, proteome and phosphoproteome acclimation to a rapamycin treatment have not yet been thoroughly investigated in Chlamydomonas reinhardtii. In this study, we have used in vivo label-free phospho-proteomic analysis to profile both protein and phosphorylation changes at 0, 24, and 48 h in Chlamydomonas cells treated with rapamycin. Using multivariate statistics we highlight the impact of TOR inhibition on both the proteome and the phosphoproteome. Two-way ANOVA distinguished differential levels of proteins and phosphoproteins in response either to culture duration and rapamycin treatment or combined effects. Finally, protein-protein interaction networks and functional enrichment analysis underlined the relation between plastid and mitochondrial metabolism. Prominent changes of proteins involved in sulfur, cysteine, and methionine as well as nucleotide metabolism on the one hand, and changes in the TCA cycle on the other highlight the interplay of chloroplast and mitochondria metabolism. Furthermore, TOR inhibition revealed changes in the endomembrane trafficking system. Phosphoproteomics data, on the other hand, highlighted specific differentially regulated phosphorylation sites for calcium-regulated protein kinases as well as ATG7, S6K, and PP2C. To conclude we provide a first combined Chlamydomonas proteomics and phosphoproteomics dataset in response to TOR inhibition, which will support further investigations.

Evolutionary Conservation of the Components in the TOR Signaling Pathways

Target of rapamycin (TOR) is an evolutionarily conserved protein kinase that controls multiple cellular processes upon various intracellular and extracellular stimuli. Since its first discovery, extensive studies have been conducted both in yeast and animal species including humans. Those studies have revealed that TOR forms two structurally and physiologically distinct protein complexes; TOR complex 1 (TORC1) is ubiquitous among eukaryotes including animals, yeast, protozoa, and plants, while TOR complex 2 (TORC2) is conserved in diverse eukaryotic species other than plants. The studies have also identified two crucial regulators of mammalian TORC1 (mTORC1), Ras homolog enriched in brain (RHEB) and RAG GTPases. Of these, RAG regulates TORC1 in yeast as well and is conserved among eukaryotes with the green algae and land plants as apparent exceptions. RHEB is present in various eukaryotes but sporadically missing in multiple taxa. RHEB, in the budding yeast Saccharomyces cerevisiae, appears to be extremely divergent with concomitant loss of its function as a TORC1 regulator. In this review, we summarize the evolutionarily conserved functions of the key regulatory subunits of TORC1 and TORC2, namely RAPTOR, RICTOR, and SIN1. We also delve into the evolutionary conservation of RHEB and RAG and discuss the conserved roles of these GTPases in regulating TORC1.

The TORC2-Dependent Signaling Network in the Yeast Saccharomyces cerevisiae

To grow, eukaryotic cells must expand by inserting glycerolipids, sphingolipids, sterols, and proteins into their plasma membrane, and maintain the proper levels and bilayer distribution. A fungal cell must coordinate growth with enlargement of its cell wall. In Saccharomyces cerevisiae, a plasma membrane-localized protein kinase complex, Target of Rapamicin (TOR) complex-2 (TORC2) (mammalian ortholog is mTORC2), serves as a sensor and master regulator of these plasma membrane- and cell wall-associated events by directly phosphorylating and thereby stimulating the activity of two types of effector protein kinases: Ypk1 (mammalian ortholog is SGK1), along with a paralog (Ypk2); and, Pkc1 (mammalian ortholog is PKN2/PRK2). Ypk1 is a central regulator of pathways and processes required for plasma membrane lipid and protein homeostasis, and requires phosphorylation on its T-loop by eisosome-associated protein kinase Pkh1 (mammalian ortholog is PDK1) and a paralog (Pkh2). For cell survival under various stresses, Ypk1 function requires TORC2-mediated phosphorylation at multiple sites near its C terminus. Pkc1 controls diverse processes, especially cell wall synthesis and integrity. Pkc1 is also regulated by Pkh1- and TORC2-dependent phosphorylation, but, in addition, by interaction with Rho1-GTP and lipids phosphatidylserine (PtdSer) and diacylglycerol (DAG). We also describe here what is currently known about the downstream substrates modulated by Ypk1-mediated and Pkc1-mediated phosphorylation.

Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organism Chlamydomonas reinhardtii

BACKGROUND

Nitrogen deprivation and replenishment induces massive changes at the physiological and molecular level in the green alga Chlamydomonas reinhardtii, including reversible starch and lipid accumulation. Stress signal perception and acclimation involves transient protein phosphorylation. This study aims to provide the first experimental phosphoprotein dataset for the adaptation of C. reinhardtii during nitrogen depletion and recovery growth phases and its impact on lipid accumulation.

RESULTS

To decipher the signaling pathways involved in this dynamic process, we applied a label-free in vivo shotgun phosphoproteomics analysis on nitrogen-depleted and recovered samples. 1227 phosphopeptides belonging to 732 phosphoproteins were identified and quantified. 470 phosphopeptides showed a significant change across the experimental set-up. Multivariate statistics revealed the reversible phosphorylation process and the time/condition-dependent dynamic rearrangement of the phosphoproteome. Protein-protein interaction analysis of differentially regulated phosphoproteins identified protein kinases and phosphatases, such as DYRKP and an AtGRIK1 orthologue, called CDPKK2, as central players in the coordination of translational, photosynthetic, proteomic and metabolomic activity. Phosphorylation of RPS6, ATG13, and NNK1 proteins points toward a specific regulation of the TOR pathway under nitrogen deprivation. Differential phosphorylation pattern of several eukaryotic initiation factor proteins (EIF) suggests a major control on protein translation and turnover.

CONCLUSION

This work provides the first phosphoproteomics dataset obtained for Chlamydomonas responses to nitrogen availability, revealing multifactorial signaling pathways and their regulatory function for biofuel production. The reproducibility of the experimental set-up allows direct comparison with proteomics and metabolomics datasets and refines therefore the current model of Chlamydomonas acclimation to various nitrogen levels. Integration of physiological, proteomics, metabolomics, and phosphoproteomics data reveals three phases of acclimation to N availability: (i) a rapid response triggering starch accumulation as well as energy metabolism while chloroplast structure is conserved followed by (ii) chloroplast degradation combined with cell autophagy and lipid accumulation and finally (iii) chloroplast regeneration and cell growth activation after nitrogen replenishment. Plastid development seems to be further interconnected with primary metabolism and energy stress signaling in order to coordinate cellular mechanism to nitrogen availability stress.