Lipid Biosynthesis and its Coordination with Cell Cycle Progression

Combined Effect of Temperature and Different Light Regimes on the Photosynthetic Activity and Lipid Accumulation in the Diatom Phaeodactylum tricornutum

The aim of this study was to investigate the combined effects of temperature and light on the photosynthetic parameters and lipid accumulation in the diatom Phaeodactylum tricornutum, a model organism widely used for studies on diatom physiology, ecology, and biotechnology. Our results highlight the importance of the interaction between temperature and light intensity in influencing growth rates, pigments and active photosystems content, photosynthetic efficiency, lipid production and fatty acid composition in P. tricornutum. Measurements of the maximum electron transport rate (rETRmax) and rETR at maximum PAR (830 µmol m-2 s-1) confirmed that P. tricornutum exhibits significantly higher light sensitivity as growth temperature increases under light/dark cycles at two light intensities (25-60 µmol m-2 s-1). However, this trend was reversed under continuous light (25 µmol m-2 s-1). Moreover, higher rETRmax values (up to double) were observed at higher irradiance, either in intensity or under continuous light regimes, at the two temperatures tested. On the other hand, increasing light intensity amplified the observed effect of temperature on photosystem I (PSI) activity under light/dark regimes, but not under continuous light conditions. This resulted in a greater deficiency in PSI activity, likely due to limitations in electron supply to this photosystem. Furthermore, increasing the culture temperature from 20 °C to 25 °C triggered an increase in the number and size of cytoplasmic lipid droplets under conditions of increased light intensity, with an even more pronounced effect under continuous illumination. Notably, the combination of 25 °C and continuous illumination resulted in a more than twofold increase in triacylglyceride (TAG) content, reaching approximately 17 mg L-1. This condition also caused a substantial rise (up to ≈90%) in the proportions of palmitoleic and palmitic acids in the TAG fatty acid profile.

Multiomics analysis of umbilical cord hematopoietic stem cells from a multiethnic cohort of Hawaii reveals the intergenerational effect of maternal prepregnancy obesity and risks for cancers

BACKGROUND

Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the intergenerational effect of maternal obesity, we hypothesized that the maternal obesity effect is mediated by epigenetic changes in the CD34+/CD38-/Lin- hematopoietic stem cells (uHSCs) in the offspring. To investigate this, we conducted a DNA methylation centric multiomics study. We measured DNA methylation and gene expression of the CD34+/CD38-/Lin- uHSCs and metabolomics of the cord blood, all from a multiethnic cohort from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (n=72, collected between 2016 and 2018).

RESULTS

Differential methylation analysis unveiled a global hypermethylation pattern in the maternal prepregnancy obese group (BH adjusted P < 0.05), after adjusting for major clinical confounders. KEGG pathway enrichment, WGCNA, and PPI analyses revealed that hypermethylated CpG sites were involved in critical biological processes, including cell cycle, protein synthesis, immune signaling, and lipid metabolism. Utilizing Shannon entropy on uHSCs methylation, we discerned notably higher quiescence of uHSCs impacted by maternal obesity. Additionally, the integration of multiomics data-including methylation, gene expression, and metabolomics-provided further evidence of dysfunctions in adipogenesis, erythropoietin production, cell differentiation, and DNA repair, aligning with the findings at the epigenetic level. Furthermore, we trained a random forest classifier using the CpG sites in the genes of the top pathways associated with maternal obesity, and applied it to predict cancer versus adjacent normal sample labels in 14 Cancer Genome Atlas (TCGA) cancer types. Five of 14 cancers showed balanced accuracy of 0.6 or higher: LUSC (0.87), PAAD (0.83), KIRC (0.71), KIRP (0.63) and BRCA (0.60).

CONCLUSIONS

This study revealed the significant correlation between prepregnancy maternal obesity and multiomics-level molecular changes in the uHSCs of offspring, particularly at the DNA methylation level. These maternal-obesity-associated epigenetic markers in uHSCs may contribute to increased risks in certain cancers of the offspring. Larger and multicenter cohort validation studies are warranted to follow up the current single-site study.

Characterizing the extractable proteins from tomato leaves - A proteomics study

The ambition to utilize agricultural by-products has spotlighted tomato leaves as a promising source for plant-based proteins. High-yielding protein extractability is key for its industrial use, but previous studies reported decreased protein extractability at later stages of plant development. This study investigated the underlying factors in protein extractability through a comprehensive proteomics analysis across four plant developmental stages (vegetative, flowering, fruit-forming, mature-fruit). The findings linked reduced yields to a shift in leaf function, from anabolic to catabolic processes and (a)biotic stress responses. This functional shift is accompanied by decreased protein synthesis and increased protein degradation, leading to an overall decrease of the soluble protein fraction. Furthermore, incomplete extraction of soluble proteins from leaves of later developmental stages, suggested the presence of inhibitory molecules hindering the extraction process. These findings indicate that breeding strategies towards increased amounts of soluble proteins and reduced concentration of inhibitory molecules could enhance protein extraction yields.

Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Intergenerational Effect of Maternal Pre-Pregnancy Obesity and Risk Prediction for Cancers

Background

Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the intergenerational effect of maternal obesity, we hypothesized that the maternal obesity effect is mediated by epigenetic changes in the CD34+/CD38-/Lin- hematopoietic stem cells (uHSCs) in the offspring. Towards this, we conducted a DNA methylation centric multi-omics study. We measured the DNA methylation and gene expression in the CD34+/CD38-/Lin- uHSCs and metabolomics of the cord blood, all from a multi-ethnic cohort (n=72) from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (collected between 2016 and 2018).

Results

Differential methylation (DM) analysis unveiled a global hypermethylation pattern in the maternal pre-pregnancy obese group (BH adjusted p<0.05), after adjusting for major clinical confounders. KEGG pathway enrichment, WGCNA, and PPI analyses revealed hypermethylated CpG sites were involved in critical biological processes, including cell cycle, protein synthesis, immune signaling, and lipid metabolism. . Utilizing Shannon entropy on uHSCs methylation, we discerned notably higher quiescence of uHSCs impacted by maternal obesity. Additionally, the integration of multi-omics data-including methylation, gene expression, and metabolomics-provided further evidence of dysfunctions in adipogenesis, erythropoietin production, cell differentiation, and DNA repair, aligning with the findings at the epigenetic level. Furthermore, we trained a random forest classifier using the CpG sites in the genes of the top pathways associated with maternal obesity, and applied it to predict cancer vs. adjacent normal labels from samples in 14 Cancer Genome Atlas (TCGA) cancer types. Five of 14 cancers showed balanced accuracy of 0.6 or higher: LUSC (0.87), PAAD (0.83), KIRC (0.71), KIRP (0.63) and BRCA (0.60).

Conclusions

This study revealed the significant correlation between pre-pregnancy maternal obesity and multi-omics level molecular changes in the uHSCs of offspring, particularly in DNA methylation. Moreover, these maternal obesity epigenetic markers in uHSCs may predispose offspring to higher risks in certain cancers.

Analysis of the multiparametric cell cycle data

This chapter was originally written in 2011. The idea was to give some history of cell cycle analysis before and after flow cytometry became widely accessible; provide references to educational material for single parameter DNA content analysis, introduce and discuss multiparameter cell cycle analysis in a methodological style, and in a casual style, discuss aspects of the work over the last 40years that we have given thought, performing some experiments, but didn't publish. It feels like there is a linear progression that moves from counting cells for growth curves, to counting labeled mitotic cells by autoradiography, to DNA content analysis, to cell cycle states defined by immunofluorescence plus DNA content analysis, to extraction of cell cycle expression profiles, and finally to probability state modeling, which should be the "right" way to analyze cytometric cell cycle data. This is the sense of this chapter. In 2023, we have updated it, but the exciting, expansive aspects brought about by spectral and mass cytometry are still young and developing, and thus have not been vetted, reviewed, and presented in mature form.

Identification and immune landscape analysis of fatty acid metabolism genes related subtypes of gastric cancer

Fatty acid metabolism (FAM) is associated with prognosis and immune microenvironment remodeling in many tumors. It is currently unknown how FAM affects the immunological microenvironment and prognosis of Gastric cancer (GC). Therefore, the current work aims to categorize GC samples based on the expression status of genes involved in FAM and to identify populations that might benefit from immunotherapy. In total, 50 FAM genes associated with overall survival (OS) were determined through univariate Cox proportional hazard regression analysis by mining the public TCGA and GEO databases. The GSE84437 and TCGA-STAD cohort samples were divided into two clusters using the "NMF" R package. According to the survival curve, patients in Cluster-1 showed considerably longer OS than those in Cluster-2. Patients in Cluster-1 exhibited earlier T stages, more intestinal GCs, and were older. MSI molecular subtypes were mainly distributed in Cluster-1, while GS molecular subtypes were distributed primarily in Cluster-2. There were 227 upregulated and 22 down-regulated genes (logFC > 1 or logFC < - 1, FDR < 0.05) in Cluster-2 compared with Cluster-1. One hub module (edges = 64, nodes = 12) was identified with a module score of 11.636 through Cytoscape plug-in MCODE. KEGG and GO analysis showed that the hub genes were associated with the cell cycle and cell division. Different immune cell infiltrates profile, and immune pathway enrichment existed between the subtypes. In conclusion, the current findings showed that practically all immunological checkpoint and immunoregulatory genes were elevated in patients with Cluster-2 GC, indicating that FAM subtypes may be crucial in GC immunotherapy.

Gut microbiota promote liver regeneration through hepatic membrane phospholipid biosynthesis

BACKGROUND & AIMS

Hepatocyte growth and proliferation depends on membrane phospholipid biosynthesis. Short-chain fatty acids (SCFAs) generated by bacterial fermentation, delivered through the gut-liver axis, significantly contribute to lipid biosynthesis. We therefore hypothesized that dysbiotic insults like antibiotic treatment not only affect gut microbiota, but also impair hepatic lipid synthesis and liver regeneration.

METHODS

Stable isotope labeling and 70% partial hepatectomy (PHx) was carried out in C57Bl/6J wild-type mice, in mice treated with broad-spectrum antibiotics, in germ-free mice and mice colonized with minimal microbiota. The microbiome was analyzed by 16S rRNA gene sequencing and microbial culture. Gut content, liver, blood and primary hepatocyte organoids were tested by mass spectrometry-based lipidomics, quantitative reverse-transcription PCR (qRT-PCR), immunoblot and immunohistochemistry for expression of proliferative and lipogenic markers. Matched biopsies from hyperplastic and hypoplastic liver tissue of patients subjected to surgical intervention to induce hyperplasia were analyzed by qRT-PCR for lipogenic enzymes.

RESULTS

Three days of antibiotic treatment induced persistent dysbiosis with significantly decreased beta-diversity and richness, but a massive increase of Proteobacteria, accompanied by decreased colonic SCFAs. After PHx, antibiotic-treated mice showed delayed liver regeneration, increased mortality, impaired hepatocyte proliferation and decreased hepatic phospholipid synthesis. Expression of the lipogenic enzyme SCD1 was upregulated after PHx but delayed by antibiotic treatment. Germ-free mice essentially recapitulated the phenotype of antibiotic treatment. Phospholipid biosynthesis, hepatocyte proliferation, liver regeneration and survival were rescued in gnotobiotic mice colonized with a minimal SCFA-producing microbial community. SCFAs induced the growth of murine hepatocyte organoids and hepatic SCD1 expression in mice. Further, SCD1 was required for proliferation of human hepatoma cells and was associated with liver regeneration in human patients.

CONCLUSION

Gut microbiota are pivotal for hepatic membrane phospholipid biosynthesis and liver regeneration.

IMPACT AND IMPLICATIONS

Gut microbiota affect hepatic lipid metabolism through the gut-liver axis, but the underlying mechanisms are poorly understood. Perturbations of the gut microbiome, e.g. by antibiotics, impair the production of bacterial metabolites, which normally serve as building blocks for membrane lipids in liver cells. As a consequence, liver regeneration and survival after liver surgery is severely impaired. Even though this study is preclinical, its results might allow physicians in the future to improve patient outcomes after liver surgery, by modulation of gut microbiota or their metabolites.

Oleaginous Heterotrophic Dinoflagellates—Crypthecodiniaceae

The heterotrophic Crypthecodinium cohnii is a major model for dinoflagellate cell biology, and a major industrial producer of docosahexaenoic acid, a key nutraceutical and added pharmaceutical compound. Despite these factors, the family Crypthecodiniaceae is not fully described, which is partly attributable to their degenerative thecal plates, as well as the lack of ribotype-referred morphological description in many taxons. We report here significant genetic distances and phylogenetic cladding that support inter-specific variations within the Crypthecodiniaceae. We describe Crypthecodinium croucheri sp. nov. Kwok, Law and Wong, that have different genome sizes, ribotypes, and amplification fragment length polymorphism profiles when compared to the C. cohnii. The interspecific ribotypes were supported by distinctive truncation-insertion at the ITS regions that were conserved at intraspecific level. The long genetic distances between Crypthecodiniaceae and other dinoflagellate orders support the separation of the group, which includes related taxons with high oil content and degenerative thecal plates, to be ratified to the order level. The current study provides the basis for future specific demarcation-differentiation, which is an important facet in food safety, biosecurity, sustainable agriculture feeds, and biotechnology licensing of new oleaginous models.

Growth conditions inducing G1 cell cycle arrest enhance lipid production in the oleaginous yeast Lipomyces starkeyi

Lipid droplets are cytoplasmic organelles that store lipids for energy and membrane synthesis. The oleaginous yeast Lipomyces starkeyi is one of the most promising lipid producers and has attracted attention as a biofuel source. It is known that the expansion of lipid droplets is enhanced under nutrient-poor conditions. Therefore, we prepared a novel nitrogen-depleted medium (N medium) in which to culture L. starkeyi cells. Lipid accumulation was rapidly induced, and this was reversed by the addition of ammonium. In this condition, cell proliferation stopped and cells with giant lipid droplets were arrested in G1 phase. We investigated whether cell cycle arrest at a specific phase is required for lipid accumulation. Lipid accumulation was repressed in hydroxyurea-synchronized S phase cells and was increased in nocodazole-arrested G2/M phase cells. Moreover, the enrichment of G1 phase cells by rapamycin induced massive lipid accumulation. From these results, we conclude that L. starkeyi cells store lipids from G2/M phase and then arrest cell proliferation in the subsequent G1 phase, where lipid accumulation is enhanced. Cell cycle control is an attractive approach for biofuel production.

Rickettsia conorii survival in THP-1 macrophages involves host lipid droplet alterations and active rickettsial protein production

Rickettsia conorii is a Gram-negative, cytosolic intracellular bacterium that has classically been investigated in terms of endothelial cell infection. However, R. conorii and other human pathogenic Rickettsia species have evolved mechanisms to grow in various cell types, including macrophages, during mammalian infection. During infection of these phagocytes, R. conorii shifts the host cell's overall metabolism towards an anti-inflammatory M2 response, metabolically defined by an increase in host lipid metabolism and oxidative phosphorylation. Lipid metabolism has more recently been identified as a key regulator of host homeostasis through modulation of immune signalling and metabolism. Intracellular pathogens have adapted mechanisms of hijacking host metabolic pathways including host lipid catabolic pathways for various functions required for growth and survival. In the present study, we hypothesised that alterations of host lipid droplets initiated by lipid catabolic pathways during R. conorii infection is important for bacterial survival in macrophages. Herein, we determined that host lipid droplet modulation is initiated early during R. conorii infection, and these alterations rely on active bacteria and lipid catabolic pathways. We also find that these lipid catabolic pathways are essential for efficient bacterial survival. Unlike the mechanisms used by other intracellular pathogens, the catabolism of lipid droplets induced by R. conorii infection is independent of upstream host peroxisome proliferator-activated receptor-alpha (PPARα) signalling. Inhibition of PPARɣ signalling and lipid droplet accumulation in host cells cause a significant decrease in R. conorii survival suggesting a negative correlation with lipid droplet production and R. conorii survival. Together, these results strongly suggest that the modulation of lipid droplets in macrophage cells infected by R. conorii is an important and underappreciated aspect of the infection process. TAKE AWAYS: Host lipid droplets are differentially altered in early and replicative stages of THP-1 macrophage infection with R. conorii. Lipid droplet alterations are initiated in a bacterial-dependent manner and do not require host peroxisome proliferator-activated receptors α or ɣ activation. Pharmacological inhibition of host lipid catabolic processes during R. conorii infection indicates a requirement of lipid catabolism for bacterial survival and initiation of lipid droplet modulation. A significant increase in host lipid droplets during infection has a negative impact on R. conorii survival in THP-1 macrophages.

Inferring transcriptomic cell states and transitions only from time series transcriptome data

Cellular stages of biological processes have been characterized using fluorescence-activated cell sorting and genetic perturbations, charting a limited landscape of cellular states. Time series transcriptome data can help define new cellular states at the molecular level since the analysis of transcriptional changes can provide information on cell states and transitions. However, existing methods for inferring cell states from transcriptome data use additional information such as prior knowledge on cell types or cell-type-specific markers to reduce the complexity of data. In this study, we present a novel time series clustering framework to infer TRAnscriptomic Cellular States (TRACS) only from time series transcriptome data by integrating Gaussian process regression, shape-based distance, and ranked pairs algorithm in a single computational framework. TRACS determines patterns that correspond to hidden cellular states by clustering gene expression data. TRACS was used to analyse single-cell and bulk RNA sequencing data and successfully generated cluster networks that reflected the characteristics of key stages of biological processes. Thus, TRACS has a potential to help reveal unknown cellular states and transitions at the molecular level using only time series transcriptome data. TRACS is implemented in Python and available at http://github.com/BML-cbnu/TRACS/ .

Biochemical and Morphological Characterization of Heterotrophic Crypthecodinium cohnii and Chlorella vulgaris Cell Walls

Microalgae are attractive for the food and cosmetic industries because of their nutrient composition. However, the bioaccessibility and extractability of nutrients in microalgae are limited by the rigid and indigestible cell wall. The goal of this study is to explore the cell wall polysaccharides (CWPSs) composition and morphology in heterotrophic Crypthecodinium cohnii and Chlorella vulgaris biomasses during growth. Our results showed that glucose was the major component of CWPSs and exopolysaccharides in C. cohnii. C. vulgaris CWPSs have a similar sugar profile in exponential and stationary phases, essentially composed of rhamnose and galactose. C. vulgaris cell wall thickness increased from 82 nm in the exponential phase to 114 nm in the stationary phase and consisted of two main layers. C. cohnii's cell wall was 133 nm thick and composed of several membranes surrounding thecal plates. Understanding of the microalgae cell wall helps developing a more efficient and targeted biorefinery approach.

Cell Cycle Dependent Modulation of Membrane Dipole Potential and Neurotransmitter Receptor Activity: Role of Membrane Cholesterol

The cell cycle is a sequential multistep process essential for growth and proliferation of cells that make up multicellular organisms. A number of nuclear and cytoplasmic proteins are known to modulate the cell cycle. Yet, the role of lipids, membrane organization, and physical properties in cell cycle progression remains largely elusive. Membrane dipole potential is an important physicochemical property and originates due to the electrostatic potential difference within the membrane because of nonrandom arrangement of amphiphile dipoles and water molecules at the membrane interface. In this work, we explored the modulation of membrane dipole potential in various stages of the cell cycle in CHO-K1 cells. Our results show that membrane dipole potential is highest in the G1 phase relative to S and G2/M phases. This was accompanied by regulation of membrane cholesterol content in the cell cycle. The highest cholesterol content was found in the G1 phase with a considerable reduction in cholesterol in S and G2/M phases. Interestingly, we noted a similarity in the dependence of membrane dipole potential and cholesterol with progress of the cell cycle. In addition, we observed an increase in neutral lipid (which contains esterified cholesterol) content as cells progressed from the G1 to G2/M phase via the S phase of the cell cycle. Importantly, we further observed a cell cycle dependent reduction in ligand binding activity of serotonin_1A receptors expressed in CHO-K1 cells. To the best of our knowledge, these results constitute the first report of cell cycle dependent modulation of membrane dipole potential and activity of a neurotransmitter receptor belonging to the G protein-coupled receptor family. We envision that understanding the basis of cell cycle events from a biophysical perspective would result in a deeper appreciation of the cell cycle and its regulation in relation to cellular function.

Enhanced Efficacy of Combination of Gemcitabine and Phosphatidylserine-Targeted Nanovesicles against Pancreatic Cancer

Phosphatidylserine (PS) is often externalized in viable pancreatic cancer cells and is therapeutically targetable using PS-selective drugs. One of the first-line treatments for advanced pancreatic cancer disease, gemcitabine (GEM), provides only marginal benefit to patients. We therefore investigated the therapeutic benefits of combining GEM and the PS-targeting drug, saposin C-dioleoylphosphatidylserine (SapC-DOPS), for treating pancreatic ductal adenocarcinoma (PDAC). Using cell-cycle analyses and a cell surface PS-based sorting method in vitro, we observed an increase in surface PS as cells progress through the cell cycle from G1 to G2/M. We also observed that GEM treatment preferentially targets G1 phase cells that have low surface PS, resulting in an increased median surface PS level of PDAC cells. Inversely, SapC-DOPS preferentially targets high surface PS cells that are predominantly in the G2/M phase. Finally, combination therapy in subcutaneous and orthotopic PDAC tumors in vivo with SapC-DOPS and GEM or Abraxane (Abr)/GEM (one of the current standards of care) significantly inhibits tumor growth and increases survival compared with individual treatments. Our studies confirm a surface PS and cell cycle-based enhancement of cancer cytotoxicity following SapC-DOPS treatment in combination with GEM or Abr/GEM. Thus, PDAC patients treated with Abr/GEM may benefit from concurrent administration of SapC-DOPS.

Acidification-induced cellular changes in Symbiodinium isolated from Mussismilia braziliensis

Dinoflagellates from the Symbiodiniaceae family and corals have an ecologically important endosymbiotic relationship. Scleractinian corals cannot survive for long periods without their symbionts. These algae, also known as zooxanthellae, on the other hand, thrives outside the coral cells. The free-living populations of zooxanthellae are essential for the resilience of the coral to environmental stressors such as temperature anomalies and ocean acidification. Yet, little is known about how ocean acidification may affect the free-living zooxanthellae. In this study we aimed to test morphological, physiological and biochemical responses of zooxanthellae from the Symbiodinium genus isolated from the coral Mussismilia braziliensis, endemic to the Brazilian coast, to acidification led by increased atmospheric CO₂. We tested whether photosynthetic yield, cell ultrastructure, cell density and lipid profile would change after up to 16 days of exposure to pH 7.5 in an atmospheric pCO₂ of 1633 μatm. Photosynthetic yield and cell density were negatively affected and chloroplasts showed vesiculated thylakoids, indicating morphological damage. Moreover, Symbiodinium fatty acid profile drastically changed in acidified condition, showing lower polyunsaturated fatty acids and higher saturated fatty acids contents, when compared to the control, non-acidified condition. These results show that seawater acidification as an only stressor causes significant changes in the physiology, biochemistry and ultrastructure of free-living Symbiodinium.

Quantitative proteomics reveals the key molecular events occurring at different cell cycle phases of the in situ blooming dinoflagellate cells

Dinoflagellate blooms are the results of rapid cell proliferation governed by cell cycle, a highly-ordered series of events that culminates in cell division. However, little is known about cell cycle progression of the in situ bloom cells. Here, we compared proteomes of the in situ blooming cells of a dinoflagellate Prorocentrum donghaiense collected at different cell cycle phases. The blooming P. donghaiense cells completed a cell cycle within 24 h with a high synchronization rate of 82.7%. Proteins associated with photosynthesis, porphyrin and chlorophyll synthesis, carbon, nitrogen and amino acid metabolisms exhibited high expressions at the G₁ phase; DNA replication and mismatch repair related proteins were more abundant at the S phase; while protein synthesis and oxidative phosphorylation were highly enriched at the G₂/M phase. Cell cycle proteins presented similar periodic diel patterns to other eukaryotic cells, and higher expressions of proliferating cell nuclear antigen and cyclin dependent kinase 2 at the S phase ensured the smooth S-G₂/M transition. Strikingly, four histones were first identified in P. donghaiense and highly expressed at the G₂/M phase, indicating their potential roles in regulating cell cycle. This study presents the first quantitative survey, to our knowledge, of proteome changes at different cell cycle phases of the in situ blooming cells in natural environment and provides insights into cell cycle regulation of the blooming dinoflagellate cells.

Plastidial and Mitochondrial Malonyl CoA-ACP Malonyltransferase is Essential for Cell Division and Its Overexpression Increases Storage Oil Content

Malonyl-acyl carrier protein (ACP) is a key building block for the synthesis of fatty acids, which are important components of cell membranes, storage oils and lipid-signaling molecules. Malonyl CoA-ACP malonyltransferase (MCAMT) catalyzes the production of malonyl-ACP and CoA from malonyl-CoA and ACP. Here, we report that MCAMT plays a critical role in cell division and has the potential to increase the storage oil content in Arabidopsis. The quantitative real-time PCR and MCAMT promoter:GUS analyses showed that MCAMT is predominantly expressed in shoot and root apical meristems, leaf hydathodes and developing embryos. The fluorescent signals of MCAMT:eYFP were observed in both chloroplasts and mitochondria of tobacco leaf protoplasts. In particular, the N-terminal region (amino acid residues 1-30) of MCAMT was required for mitochondrial targeting. The Arabidopsis mcamt-1 and -2 mutants exhibited an embryo-lethal phenotype because of the arrest of embryo development at the globular stage. The transgenic Arabidopsis expressing antisense MCAMT RNA showed growth retardation caused by the defects in cell division. The overexpression of MCAMT driven by the promoter of the senescence-associated 1 (SEN1) gene, which is predominantly expressed in developing seeds, increased the seed yield and storage oil content of Arabidopsis. Taken together, the plastidial and mitochondrial MCAMT is essential for Arabidopsis cell division and is a novel genetic resource useful for enhancing storage oil content in oilseed crops.

Organellar carbon metabolism is coordinated with distinct developmental phases of secondary xylem

Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers. In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series. The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of carbon metabolism during xylem secondary growth. We show that the central processes of organellar carbon metabolism are distinctly coordinated across the developmental stages of wood formation and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that, during xylogenesis, plastid-targeted carbon metabolism is partially regulated by the central clock for carbon allocation towards primary and secondary xylem growth, and we discuss these networks in the context of previously established associations with wood-related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid- and mitochondrial-localized carbon metabolism during xylogenesis.

Do lipids shape the eukaryotic cell cycle?

Successful passage through the cell cycle presents a number of structural challenges to the cell. Inceptive studies carried out in the last five years have produced clear evidence of modulations in the lipid profile (sometimes referred to as the lipidome) of eukaryotes as a function of the cell cycle. This mounting body of evidence indicates that lipids play key roles in the structural transformations seen across the cycle. The accumulation of this evidence coincides with a revolution in our understanding of how lipid composition regulates a plethora of biological processes ranging from protein activity through to cellular signalling and membrane compartmentalisation. In this review, we discuss evidence from biological, chemical and physical studies of the lipid fraction across the cell cycle that demonstrate that lipids are well-developed cellular components at the heart of the biological machinery responsible for managing progress through the cell cycle. Furthermore, we discuss the mechanisms by which this careful control is exercised.

Whole Transcriptomic Analysis Provides Insights into Molecular Mechanisms for Toxin Biosynthesis in a Toxic Dinoflagellate Alexandrium catenella (ACHK-T)

Paralytic shellfish toxins (PSTs), a group of neurotoxic alkaloids, are the most potent biotoxins for aquatic ecosystems and human health. Marine dinoflagellates and freshwater cyanobacteria are two producers of PSTs. The biosynthesis mechanism of PSTs has been well elucidated in cyanobacteria; however, it remains ambiguous in dinoflagellates. Here, we compared the transcriptome profiles of a toxin-producing dinoflagellate Alexandrium catenella (ACHK-T) at different toxin biosynthesis stages within the cell cycle using RNA-seq. The intracellular toxin content increased gradually in the middle G1 phase and rapidly in the late G1 phase, and then remained relatively stable in other phases. Samples from four toxin biosynthesis stages were selected for sequencing, and finally yielded 110,370 unigenes, of which 66,141 were successfully annotated in the known databases. An analysis of differentially expressed genes revealed that 2866 genes altered significantly and 297 were co-expressed throughout the four stages. These genes participated mainly in protein metabolism, carbohydrate metabolism, and the oxidation-reduction process. A total of 138 homologues of toxin genes were identified, but they altered insignificantly among different stages, indicating that toxin biosynthesis might be regulated translationally or post-translationally. Our results will serve as an important transcriptomic resource to characterize key molecular processes underlying dinoflagellate toxin biosynthesis.

Cyclin-dependent kinase activity enhances phosphatidylcholine biosynthesis in Arabidopsis by repressing phosphatidic acid phosphohydrolase activity

Coordination of endomembrane biogenesis with cell cycle progression is considered to be important in maintaining cell function during growth and development. We previously showed that the disruption of PHOSPHATIDIC ACID PHOSPHOHYDROLASE (PAH) activity in Arabidopsis thaliana stimulates biosynthesis of the major phospholipid phosphatidylcholine (PC) and causes expansion of the endoplasmic reticulum. Here we show that PC biosynthesis is repressed by disruption of the core cell cycle regulator CYCLIN-DEPENDENT KINASE A;1 (CDKA;1) and that this repression is reliant on PAH. Furthermore, we show that cyclin-dependent kinases (CDKs) phosphorylate PAH1 at serine 162, which reduces both its activity and membrane association. Expression of a CDK-insensitive version of PAH1 with a serine 162 to alanine substitution represses PC biosynthesis and also reduces the rate of cell division in early leaf development. Together our findings reveal a physiologically important mechanism that couples the rate of phospholipid biosynthesis and endomembrane biogenesis to cell cycle progression in Arabidopsis.

The fatty acid synthase inhibitor triclosan: repurposing an anti-microbial agent for targeting prostate cancer

Inhibition of FASN has emerged as a promising therapeutic target in cancer, and numerous inhibitors have been investigated. However, severe pharmacological limitations have challenged their clinical testing. The synthetic FASN inhibitor triclosan, which was initially developed as a topical antibacterial agent, is merely affected by these pharmacological limitations. Yet, little is known about its mechanism in inhibiting the growth of cancer cells. Here we compared the cellular and molecular effects of triclosan in a panel of eight malignant and non-malignant prostate cell lines to the well-known FASN inhibitors C75 and orlistat, which target different partial catalytic activities of FASN. Triclosan displayed a superior cytotoxic profile with a several-fold lower IC50 than C75 or orlistat. Structure-function analysis revealed that alcohol functionality of the parent phenol is critical for inhibitory action. Rescue experiments confirmed that end product starvation was a major cause of cytotoxicity. Importantly, triclosan, C75 and orlistat induced distinct changes to morphology, cell cycle, lipid content and the expression of key enzymes of lipid metabolism, demonstrating that inhibition of different partial catalytic activities of FASN activates different metabolic pathways. These finding combined with its well-documented pharmacological safety profile make triclosan a promising drug candidate for the treatment of prostate cancer.

Design and Synthesis of a Screening Library Using the Natural Product Scaffold 3-Chloro-4-hydroxyphenylacetic Acid

The fungal metabolite 3-chloro-4-hydroxyphenylacetic acid (1) was utilized in the generation of a unique drug-like screening library using parallel solution-phase synthesis. A 20-membered amide library (3-22) was generated by first converting 1 to methyl (3-chloro-4-hydroxyphenyl)acetate (2), then reacting this scaffold with a diverse series of primary amines via a solvent-free aminolysis procedure. The structures of the synthetic analogues (3-22) were elucidated by spectroscopic data analysis. The structures of compounds 8, 12, and 22 were confirmed by single X-ray crystallographic analysis. All compounds were evaluated for cytotoxicity against a human prostate cancer cell line (LNCaP) and for antiparasitic activity toward Trypanosoma brucei brucei and Plasmodium falciparum and showed no significant activity at 10 μM. The library was also tested for effects on the lipid content of LNCaP and PC-3 prostate cancer cells, and it was demonstrated that the fluorobenzyl analogues (12-14) significantly reduced cellular phospholipid and neutral lipid levels.

Denhaminols A-H, dihydro-β-agarofurans from the endemic Australian rainforest plant Denhamia celastroides

Eight new dihydro-β-agarofurans, denhaminols A-H (1-8), were isolated from the leaves of the Australian rainforest tree Denhamia celastroides. The chemical structures of 1-8 were elucidated following analysis of 1D/2D NMR and MS data. The absolute configuration of denhaminol A (1) was determined by single-crystal X-ray crystallography. All compounds were evaluated for cytotoxic activity against the human prostate cancer cell line LNCaP, using live-cell imaging and metabolic assays. Denhaminols A (1) and G (7) were also tested for their effects on the lipid content of LNCaP cells. This is the first report of secondary metabolites from D. celastroides.

Recycling of food waste as nutrients in Chlorella vulgaris cultivation

Heterotrophic cultivation of Chlorella vulgaris was investigated in food waste hydrolysate. The highest exponential growth rate in terms of biomass of 0.8day(-1) was obtained in a hydrolysate consisting of 17.9gL(-1) glucose, 0.1gL(-1) free amino nitrogen, 0.3gL(-1) phosphate and 4.8mgL(-1) nitrate, while the growth rate was reduced in higher concentrated hydrolysates. C. vulgaris utilized the nutrients recovered from food waste for the formation of biomass and 0.9g biomass was produced per gram glucose consumed. The microalgal biomass produced in nutrient sufficient batch cultures consisted of around 400mgg(-1) carbohydrates, 200mgg(-1) proteins and 200mgg(-1) lipids. The conversion of nutrients derived from food waste and the balanced biomass composition make C. vulgaris a promising strain for the recycling of food waste in food, feed and fuel productions.

Fatty acid and phospholipid syntheses are prerequisites for the cell cycle of Symbiodinium and their endosymbiosis within sea anemones

Lipids are a source of metabolic energy, as well as essential components of cellular membranes. Although they have been shown to be key players in the regulation of cell proliferation in various eukaryotes, including microalgae, their role in the cell cycle of cnidarian-dinoflagellate (genus Symbiodinium) endosymbioses remains to be elucidated. The present study examined the effects of a lipid synthesis inhibitor, cerulenin, on the cell cycle of both cultured Symbiodinium (clade B) and those engaged in an endosymbiotic association with the sea anemone Aiptasia pulchella. In the former, cerulenin exposure was found to inhibit free fatty acid (FFA) synthesis, as it does in other organisms. Additionally, while it also significantly inhibited the synthesis of phosphatidylethanolamine (PE), it did not affect the production of sterol ester (SE) or phosphatidylcholine (PC). Interestingly, cerulenin also significantly retarded cell division by arresting the cell cycles at the G₀/G₁ phase. Cerulenin-treated Symbiodinium were found to be taken up by anemone hosts at a significantly depressed quantity in comparison with control Symbiodinium. Furthermore, the uptake of cerulenin-treated Symbiodinium in host tentacles occurred much more slowly than in untreated controls. These results indicate that FFA and PE may play critical roles in the recognition, proliferation, and ultimately the success of endosymbiosis with anemones.

New insights on cytological and metabolic features of Ostreopsis cf. ovata Fukuyo (Dinophyceae): a multidisciplinary approach

The harmful dinoflagellate Ostreopsis cf. ovata has been causing toxic events along the Mediterranean coasts and other temperate and tropical areas, with increasing frequency during the last decade. Despite many studies, important biological features of this species are still poorly known. An integrated study, using different microscopy and molecular techniques, Raman microspectroscopy and high resolution liquid chromatography-mass spectrometry (HR LC-MS), was undertaken to elucidate cytological aspects, and identify main metabolites including toxins. The species was genetically identified as O. cf. ovata, Atlantic-Mediterranean clade. The ultrastructural results show unique features of the mucilage network abundantly produced by this species to colonize benthic substrates, with a new role of trichocysts, never described before. The amorphous polysaccharidic component of mucilage appears to derive from pusule fibrous material and mucocysts. In all stages of growth, the cells show an abundant production of lipids. Different developmental stages of chloroplasts are found in the peripheral cytoplasm and in the centre of cell. In vivo Raman microspectroscopy confirms the presence of the carotenoid peridinin in O. cf. ovata, and detects in several specimen the abundant presence of unsaturated lipids structurally related to docosahexaenoic acid. The HR LC-MS analysis reveals that ovatoxin-a is the predominant toxin, together with decreasing amounts of ovatoxin-b, -d/e, -c and putative palytoxin. Toxins concentration on a per cell basis increases from exponential to senescent phase. The results suggest that benthic blooms of this species are probably related to features such as the ability to create a unique mucilaginous sheath covering the sea bottom, associated with the production of potent toxins as palytoxin-like compounds. In this way, O. cf. ovata may be able to rapidly colonize benthic substrates outcompeting other species.

Comparative responses of two species of marine phytoplankton to metolachlor exposure

Metolachlor, a chloroacetanilide herbicide, has been frequently detected in coastal waters. This study examined the growth, photosynthesis, and detoxification responses of chlorophyte Dunaliella tertiolecta (DT) and brown tide alga Aureococcus anophagefferens (AA) upon 5-day exposure to 0.5-5 mg L(-1) metolachlor. Growth was assessed with exponential growth rate, and 5th day in vivo chlorophyll fluorescence, chlorophyll a, b or c, cell density and cell size. The photosynthesis function was assessed with photochemical parameters of photosystem II (PSII) during the mid-exponential growth phase (i.e. 2-4 day metolachlor exposure). The biochemical detoxification was analyzed with glutathione production and metolachlor degradation. Results show that metolachlor caused up to ∼9% inhibition in growth rate in both species and an expected ∼35% and 25% inhibition in chlorophyll based endpoints in DT and AA respectively. DT had an up to 70% inhibition in cell density, but AA a 35% hormesis at 1 mg L(-1) metolachlor and no significant inhibition, as compared to the controls. Both DT and AA's cell sizes were enlarged by metolachlor exposure, but greater in DT (1.2% per mg L(-1)) than in AA (0.68% per mg L(-1)). On PSII photochemistry, maximum quantum yield was not affected in both species; PSII optical cross section and connectivity factor increased in DT but decreased in AA, suggesting species specific impact on PSII function. On detoxification responses, glutathione production, when normalized to total chlorophyll a, was not affected by metolachlor in both species; further, despite of heterotrophic capacity of A. anophagefferens metolachlor was not significantly degraded by this alga during the 5-day incubation. The species specific effects on algal growth have ecological implications of potential selective inhibition of chlorophytes by metolachlor herbicide.

Neutral lipid accumulation at elevated temperature in conditional mutants of two microalgae species

Triacylglycerols, an energy storage compound in microalgae, are known to be accumulated after nitrogen starvation of microalgae cells. Microalgae could be of importance for future biodiesel production due to their fast growth rate and high oil content. In collections of temperature sensitive mutants of Chlamydomonas reinhardtii and Chlorella vulgaris, nine out of fourty-one mutants in C. reinhardtii and eleven out of fifty-three mutants in C. vulgaris contained increased amounts of neutral lipids, predominantly as triacylglycerols. Upon temperature induced cell-cycle arrest, these mutants showed enlarged cellular volume compared with the wild type. The C. reinhardtii mutants were analyzed further and one type of mutants displayed a shift in lipid composition from polar membrane lipids to neutral lipids after a temperature up-shift, while the second type of mutants accumulated more total lipid per cell, predominantly as neutral lipids as compared with the wild type. Three C. reinhardtii mutants were analyzed further and found to be arrested after DNA synthesis but prior to cell division in the cell cycle. These mutants will be useful in order to further understand neutral lipid accumulation in microalgae and suggest possibilities for biodiesel production by specific induction of lipid accumulation in miroalgal cultures by cell-cycle inhibition.

Flow cytometry for the development of biotechnological processes with microalgae

The current interest in microalgae as a sustainable source of next generation biofuels and other valuable substances is driving exploration of their use as unique biotechnological production systems. To design and optimise appropriate production strategies, the behaviour of particular microalgal species should be well characterised under different culture conditions. Thus, flow cytometric (FCM) methods, which are already well established in environmental and toxicological studies of microalgae, are also useful for analysing the physiological state of microalgae, and have the potential to contribute to the rapid development of feasible bioprocesses. These methods are commonly based on the examination of intrinsic features of individual cells within a population (such as autofluorescence or size). Cells possessing the desired physiological or morphological features, which are detectable with or without fluorescent staining, are counted or isolated (sorted) using an FCM device. The options for implementation of FCM in the development of biotechnological processes detailed in this review are (i) analysing the chemical composition of biomass, (ii) monitoring cellular enzyme activity and cell viability, and (iii) sorting cells to isolate those overproducing the target compound or for the preparation of axenic cultures.

Lipid droplet de novo formation and fission are linked to the cell cycle in fission yeast

Cells sequester neutral lipids in bodies called lipid droplets. Thus, the formation and breakdown of the droplets are important for cellular metabolism; unfortunately, these processes are difficult to quantify. Here, we used time-lapse confocal microscopy to track the formation, movement and size changes of lipid droplets throughout the cell cycle in fission yeast Schizosaccharomyces pombe. In theory, the number of lipid droplets in these cells must increase for daughter cells to have the same number of droplets as the parent at a reference point in the cell cycle. We observed stable droplet formation events in G2 phase that were divided evenly between de novo formation of nascent droplets and fission of preexisting droplets. The observations that lipid droplet number is linked to the cell cycle and that droplets can form via fission were both new discoveries. Thus, we scrutinized each fission event for multiple signatures to eliminate possible artifacts from our microscopy. We augmented our time-lapse confocal microscopy with electron microscopy, which showed lipid droplet 'intermediates': droplets shaped like dumbbells that are potentially in transition states between two spherical droplets. Using these complementary microscopy techniques and also dynamic simulations, we show that lipid droplets can form by fission.

An unusual S-adenosylmethionine synthetase gene from dinoflagellate is methylated

Background

S-Adenosylmethionine synthetase (AdoMetS) catalyzes the formation of S-Adenosylmethionine (AdoMet), the major methyl group donor in cells. AdoMet-mediated methylation of DNA is known to have regulatory effects on DNA transcription and chromosome structure. Transcription of environmental-responsive genes was demonstrated to be mediated via DNA methylation in dinoflagellates.

Results

A full-length cDNA encoding AdoMetS was cloned from the dinoflagellate Crypthecodinium cohnii. Phylogenetic analysis suggests that the CcAdoMetS gene, is associated with the clade of higher plant orthrologues, and not to the clade of the animal orthrologues. Surprisingly, three extra stretches of residues (8 to 19 amino acids) were found on CcAdoMetS, when compared to other members of this usually conserved protein family. Modeled on the bacterial AdeMetS, two of the extra loops are located close to the methionine binding site. Despite this, the CcAdoMetS was able to rescue the corresponding mutant of budding yeast. Southern analysis, coupled with methylation-sensitive and insensitive enzyme digestion of C. cohnii genomic DNA, demonstrated that the AdoMetS gene is itself methylated. The increase in digestibility of methylation-sensitive enzymes on AdoMet synthetase gene observed following the addition of DNA methylation inhibitors L-ethionine and 5-azacytidine suggests the presence of cytosine methylation sites within CcAdoMetS gene. During the cell cycle, both the transcript and protein levels of CcAdoMetS peaked at the G1 phase. L-ethionine was able to delay the cell cycle at the entry of S phase. A cell cycle delay at the exit of G2/M phase was induced by 5-azacytidine.

Conclusion

The present study demonstrates a major role of AdoMet-mediated DNA methylation in the regulation of cell proliferation and that the CcAdoMetS gene is itself methylated.