Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum

Remodeling of the terpenoid metabolism during prolonged phosphate depletion in the marine diatom Phaeodactylum tricornutum

Terpenoids are a diverse class of naturally occurring organic compounds, which derive from five-carbon isoprene units and play crucial roles in physiology, ecological interactions such as defense mechanisms, or adaptation to environmental stresses. In Phaeodactylum tricornutum, some of the most important isoprenoids are sterols and pigments, derived from precursors of the cytosolic mevalonate and the plastidial methyl-erythritol 4-phosphate pathway, respectively. However, the regulation of isoprenoid metabolism in P. tricornutum has not yet been characterized, presenting a major gap in our understanding of its ecological functions and adaptations. By leveraging metabolic, photosynthetic, and transcriptomic analyses, we characterized the dynamic remodeling of the isoprenoid pathways during prolonged nutrient stress in wild-type diatoms. We observed the down-regulation of the methylerythritol 4-phosphate and pigment biosynthesis pathways and the upregulation of key genes in the mevalonate and sterol biosynthesis pathways. At the metabolite level, we observed an overall decrease in pigment and no changes in sterol levels. Using a genetically engineered diatom strain to produce a heterologous monoterpenoid to monitor the availability of one of the main terpenoid precursors, geranyl diphosphate (GPP), we suggest that cytosolic GPP pools increase during prolonged phosphate depletion. Our results have demonstrated how the biosynthesis of isoprenoid metabolites and the pools of prenyl phosphate are vastly remodeled during phosphate depletion. We anticipate that the knowledge generated in this study can serve as a foundation for understanding ecological responses and adaptations of diatoms to nutrient stress, contributing to our broader comprehension of marine ecosystem dynamics and design strategies for producing high-value compounds in diatoms.

Monogalactosyldiacylglycerol synthase isoforms play diverse roles inside and outside the diatom plastid

Diatoms derive from a secondary endosymbiosis event, which occurred when a eukaryotic host cell engulfed a red alga. This led to the formation of a complex plastid enclosed by four membranes: two innermost membranes originating from the red alga chloroplast envelope, and two additional peri- and epiplastidial membranes (PPM, EpM). The EpM is linked to the endoplasmic reticulum (ER). The most abundant membrane lipid in diatoms is monogalactosyldiacylglycerol (MGDG), synthesized by galactosyltransferases called MGDG synthases (MGDs), conserved in photosynthetic eukaryotes and considered to be specific to chloroplast membranes. Similar to angiosperms, a multigenic family of MGDs has evolved in diatoms, but through an independent process. We characterized MGDα, MGDβ and MGDγ in Phaeodactylum tricornutum, combining molecular analyses, heterologous expression in Saccharomyces cerevisiae, and studying overexpressing and CRISPR-Cas9-edited lines. MGDα localizes mainly to thylakoids, MGDβ to the PPM, and MGDγ to the ER and EpM. MGDs have distinct specificities for diacylglycerol, consistent with their localization. Results suggest that MGDα is required for thylakoid expansion under optimal conditions, while MGDβ and MGDγ play roles in plastid and non-plastid membranes and in response to environmental stress. Functional compensation among MGDs likely contributes to diatom resilience under adverse conditions and to their ecological success.

Benzophenone-4 inhibition in marine diatoms: Physiological and molecular perspectives

Benzophenone-4 (BP-4), a widely utilized organic ultraviolet (UV) filter, is recognized as a pseudo-persistent contaminant in aquatic environments. To elucidate the effects and mechanisms of BP-4 on marine diatoms, an investigation was conducted on the growth rate, photosynthetic pigment content, photosynthetic parameters, antioxidant enzyme activity, malondialdehyde (MDA) levels, cellular structure, and transcriptome profile of the model species, Phaeodactylum tricornutum. The results showed a pronounced inhibition of algal growth upon exposure to BP-4, with a 144 h-EC50 value of 201 mg·L-1. In addition, BP-4 exposure resulted in a significant reduction in biomass, disruption of cell membrane integrity, and increased MDA accumulation, with levels escalating 3.57-fold at 125 mg·L-1 of BP-4. In the BP-4-treated samples, 1556 differentially expressed genes (DEGs) were identified, of which 985 were upregulated and 571 were downregulated. Gene ontology and KEGG pathway enrichment analysis revealed that the carbon fixation and carbon metabolism processes in P. tricornatum were disrupted in response to BP-4 exposure, along with excessive reactive oxygen species (ROS) production. The upregulation of genes associated with photosynthetic pigment (chlorophyll and carotenoids) synthesis, phospholipid synthesis, ribosome biogenesis, and translation-related pathways may be regarded as a component of P. tricornatum's tolerance mechanism towards BP-4. These results provide preliminary insights into the toxicity and tolerance mechanisms of BP-4 on P. tricornatum. They will contribute to a better understanding of the ecotoxicological impacts of BP-4 on the marine ecosystem and provide valuable information for elimination of BP-4 in aquatic environment by bioremediation.

Delta-5 elongase knockout reduces docosahexaenoic acid and lipid synthesis and increases heat sensitivity in a diatom

Recent global marine lipidomic analysis reveals a strong relationship between ocean temperature and phytoplanktonic abundance of omega-3 long-chain polyunsaturated fatty acids, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which are essential for human nutrition and primarily sourced from phytoplankton in marine food webs. In phytoplanktonic organisms, EPA may play a major role in regulating the phase transition temperature of membranes, while the function of DHA remains unexplored. In the oleaginous diatom Phaeodactylum tricornutum, DHA is distributed mainly on extraplastidial phospholipids, which is very different from the EPA enriched in thylakoid lipids. Here, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9-mediated knockout of delta-5 elongase (ptELO5a), which encodes a delta-5 elongase (ELO5) catalyzing the elongation of EPA to synthesize DHA, led to a substantial interruption of DHA synthesis in P. tricornutum. The ptELO5a mutants showed some alterations in transcriptome and glycerolipidomes, including membrane lipids and triacylglycerols under normal temperature (22 °C), and were more sensitive to elevated temperature (28 °C) than wild type. We conclude that PtELO5a-mediated synthesis of small amounts of DHA has indispensable functions in regulating membrane lipids, indirectly contributing to storage lipid accumulation, and maintaining thermomorphogenesis in P. tricornutum. This study also highlights the significance of DHA synthesis and lipid composition for environmental adaptation of P. tricornutum.

Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid

Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.

A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms

Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.

A key gene, violaxanthin de-epoxidase-like 1, enhances fucoxanthin accumulation in Phaeodactylum tricornutum

BACKGROUND

Fucoxanthin has been widely investigated owing to its beneficial biological properties, and the model diatom Phaeodactylum tricornutum, possessing fucoxanthin (Fux) chlorophyll proteins as light-harvesting systems, is considered to have the potential to become a commercial cell factory for the pigment production.

RESULTS

Here, we compared the pigment contents in 10 different P. tricornutum strains from the globe, and found that strain CCMP631 (Pt6) exhibited the highest Fux content but with a low biomass. Comparison of mRNA levels revealed that higher Fux content in Pt6 was related with the higher expression of gene violaxanthin de-epoxidase-like (VDL) protein 1 (VDL1), which encodes the enzyme catalyzing the tautomerization of violaxanthin to neoxanthin in Fux biosynthesis pathway. Single nucleotide variants of VDL1 gene and allele-specific expression in strains Pt1 (the whole genome sequenced strain CCMP632) and Pt6 were analyzed, and overexpressing of each of the 4 VDL1 alleles, two from Pt1 and two from Pt6, in strain Pt1 leads to an increase in downstream product diadinoxanthin and channels the pigments towards Fux biosynthesis. All the 8 VDL1 overexpression (OE) lines showed significant increases by 8.2 to 41.7% in Fux content without compromising growth, and VDL1 Allele 2 OE lines even exhibited the higher cell density on day 8, with an increase by 24.2-28.7% in two Pt1VDL1-allele 2 OE lines and 7.1-11.1% in two Pt6VDL1-allele 2 OE lines, respectively.

CONCLUSIONS

The results reveal VDL1, localized in the plastid stroma, plays a key role in Fux over-accumulation in P. tricornutum. Overexpressing VDL1, especially allele 2, improved both the Fux content and growth rate, which provides a new strategy for the manipulation of Fux production in the future.