Transcriptomic and lipidomic analysis reveal the mechanism of phosphorus-induced lipid class remodeling in Nannochloropsis sp. PJ12
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ABSTRACT:
PROVIDER: PRJNA512233 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8380410_1.fastq.gz | Fastqsanger.gz | |||
| SRR8380410_2.fastq.gz | Fastqsanger.gz | |||
| SRR8380411_1.fastq.gz | Fastqsanger.gz | |||
| SRR8380411_2.fastq.gz | Fastqsanger.gz | |||
| SRR8380403_1.fastq.gz | Fastqsanger.gz |
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Project description:Phytoplankton lipids, such as microalgae lipids, are important compounds of increasing interest in bioenergy, food, pharmacy, aquaculture and ecology for their high molecular diversity. There is a taxonomically diverse lipid response under P stress with unresolved questions related to the diversified mechanism behind the lipid responses. A marine microalgae with high EPA content was isolated, named Nannochloropsis sp. PJ12. We reveal a mechanism of phosphorus-induced lipid class remodeling in Nannochloropsis sp. PJ12 based on highly corresponding transcriptome and lipidome data. Phosphorus- deprivation leads to the rapid reduction of phospholipids (PL) and synthesis of the betaine lipids (BL). Phosphorus-complement recovers the content of PL and BL to the original level. The changes are mediated mainly by a glycerophosphoryldiester phosphodiesterases on the transcriptome level. To adapt to low phospholipids, the transcription levels of gene encoding P transporter were upregulated. When Nannochloropsis sp. PJ12 was once again under phosphorus-complement, some of gene encoding P transporter continue to increase on the transcription levels. The novel phospholipid-remodeling scheme opens new avenues for metabolic engineering of lipid composition in algae.
2021-12-20 | GSE124501 | GEO
Project description:In the present study the effect of phosphorus (P) limitation was investigated in the microalgae Nannochloropsis oceanica. Algal cultures were analysed for transcriptomic and lipidomic changes during P-limited growth, with sample time points: 24h, 48h, 53h, 58h and 70h. The transcriptome data identified unique P acquiring genes and the results were also supported by corresponding changes in the lipidome dataset, which showed a lipid class shift from phospholipids to phosphorus-free lipids under P-limitation. During the exponential growth phase a gradual 6-fold reduction of the cellular P level induced RNA transcripts encoding proteins acquiring P from inorganic and organic sources. For this process 6 novel purple acid phosphatases and 5 unique Pi transporters were identified. Additionally, increased gene expression of 2 triose-phosphate transporters (TPTs) indicated the importance of the carbon-to-phosphorus balance for the plastidial anabolic processes. Phospholipid degradation was shown to be an early response to P limitation, by overexpression of sets of 2 novel glycerophosphoryl diester phosphodiesterases (GDPDs), and 3 patatin-like phospholipases of type A. To compensate for phospholipid degradation, the transcriptome and lipidome level showed increased synthesis of sulfoquinovosyl diacylglycerol (SQDG), and diacylglyceroltrimethylhomoserine (DGTS). Phosphorus limitation triggered the lipid class shift in both the exponential growth phase and the triacylglycerol (TAG) accumulation period to release P and increase the organic C:P ratio.
2017-10-31 | GSE95774 | GEO
Project description:Oleaginous microalgae Nannochloropsis spp. are considered to be promissing species for production of biofuels and biomaterials. Nevertheless, its biofuel production remains to be economically unviable. Hence, further improvement of cultivation conditions and genetic traits for high-lipid contents without affecting growth is required. To understand genes involved in neutral lipid accumulation upon nitrogen deprivation (ND) in a novel isolate of Nannochloropsis sp. PJ12, we performed comparative transcriptomic and lipidomic analyses of cells under ND and NR (nitrogen replete) conditions. Transcriptomic profiling indicated that, while enzymes involved in TCA cycle in PJ12 under ND condition were upregulated compared to that under NR condition, those involved in Calvin cycle and glycolysis under ND condition were downregulated, consistent with the observation that quantum yield was reduced under ND condition. Furthermore, we showed that enzymes involved in fatty acid synthesis and glycerolipid synthesis were downregulated but not b-oxidation. Lipidomic profiling indicated that, while the level of neutral lipids in ND cells was increased compared to that of NR cells, level of photosynthetic membrane-lipids DGDG and MGDG was decreased. Taken together, our analysis indicated that TAG accumulation is attributed to the modification of membrane lipids derived primarily from “prokaryotic” pathway and secondarily from “eukaryotic” pathway based on the 16:X or 18:X fatty acid at the sn2 position of the glycerol backbone. We propose that two-phase (NR-ND) growth is ideal for biomass and biofuel production because ND reduces cell growth rate due to the loss of photosynthetic membrane and decreased quantum yield.
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Project description:Dataset contains ten whole-cell proteome samples from Nannochloropsis gaditana grown in turbidity-controlled flat plate photobioreactors. Samples analysed with 10-plex TMT labels including four control samples, four nitrogen-deprived samples and two phosphorus-deprived samples. Dataset is part of a study including transcriptomic and lipid analysis of the same samples.
| MSV000085294 | MassIVE
Project description:Phytoplankton are primary producers in the marine ecosystem, where phosphorus is often a limiting factor of their growth. Hence, they have evolved strategies to recycle phosphorus by replacing membrane phospholipids with phosphorus-free lipids. However, mechanisms for replacement of lipid classes remain poorly understood. To improve our understanding, we performed the lipidomic and transcriptomic profiling analyses of an oleaginous marine microalga Nannochloropsis sp. PJ12 in response to phosphorus depletion (PD) and replenishing. In this study, by using (liquid chromatography couple with tandem mass spectrometry) LC-MS/MS-based lipidomic analysis, we show that membrane phospholipid levels are significantly reduced upon PD, while phosphorus-free betaine lipid levels are increased. However, levels of phosphorus-free photosynthetic galactolipid and sulfolipid are not increased upon PD, consistent with the reduced photosynthetic activity. RNA-seq-based transcriptomic analysis indicates that enzymes involved in phospholipid recycling and phosphorus-free lipid synthesis are upregulated, supporting the lipidomic analysis. Furthermore, enzymes involved in FASII (type II fatty acid synthesis) elongation cycle upon PD are transcriptionally downregulated. EPA (eicosapentaenoic acid) level decrease upon PD is revealed by both GC-MS (gas chromatography coupled with mass spectrometry) and LC-MS/MS-based lipidomic analyses. PD-induced alteration is reversed after phosphorus replenishing. Taken together, our results suggest that the alteration of lipid classes upon environmental change of phosphorus is a result of remodeling rather than de novo synthesis in Nannochloropsis sp. PJ12.
| S-EPMC6780086 | biostudies-literature
Project description:Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM), which participates in gene expression and various metabolic processes. Nannochloropsis, a significant oleaginous microalgae of economic significance, demonstrates a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted ChIP-seq and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2,057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions, comprising 853 upregulated genes and 1,204 downregulated genes. Moreover, a total of 5,375 differential Kla peaks were identified, including 5,331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (<= 1 kb) (71.07%), 5’UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research reveals the regulatory functions of lactylation in lipid metabolism and gene expression in Nannochloropsis, offering a new perspective for the investigation of lipid biosynthesis.
2024-06-26 | GSE261019 | GEO
Project description:Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM), which participates in gene expression and various metabolic processes. Nannochloropsis, a significant oleaginous microalgae of economic significance, demonstrates a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted ChIP-seq and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2,057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions, comprising 853 upregulated genes and 1,204 downregulated genes. Moreover, a total of 5,375 differential Kla peaks were identified, including 5,331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (<= 1 kb) (71.07%), 5’UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research reveals the regulatory functions of lactylation in lipid metabolism and gene expression in Nannochloropsis, offering a new perspective for the investigation of lipid biosynthesis.
2024-06-26 | GSE260894 | GEO
Project description:Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the regulation transcriptional control of cell growth and metabolism in Nannochloropsis. Nannochloropsis oceanica CCMP was entrained to 12:12 light:dark cycles and biological replicates collected every 3 hours for a cycle for a total of 16 samples.
2015-08-01 | E-GEOD-69460 | biostudies-arrayexpress
Project description:Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high value lipid products. First success in applying reverse genetics makes Nannochloropsis species attractive models to investigate the cell and molecular biology and biochemistry of this fascinating organism group. (Principle findings) Here we present the assembly of the 28.7 Mb genome of Nannochloropsis oceanica CCMP1779. RNA sequencing data from N-replete and N-depleted growth conditions support a total of 11,973 genes, which in addition to automatic annotation were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors and 109 transcriptional regulators were annotated. In addition, we provide protocols for the transformation of the sequenced strain. (Significance) The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols provides a blueprint for future detailed gene functional analysis and phylogenetic comparison of Nannochloropsis species by a growing academic community focused on this genus. one sample each of nitrogen-replete and nitrogen-depleted conditions
2012-04-04 | E-GEOD-36959 | biostudies-arrayexpress
Project description:Oleaginous microalgae are considered a promising platform for the sustainable production of high-value lipids and biofuel feedstocks. However, current lipid yields are too low to allow for an economically feasible production process. Lipid yields could be enhanced by improving microalgal strains through genetic engineering. Strain improvement strategies for the industrially relevant genus Nannochloropsis have met limited success because most genes of this genus lack a functional annotation, hindering our understanding of lipid metabolism and its regulation. To gain fundamental insights and to provide targets for genetic engineering of lipid metabolism, the aim of this study was to discover novel genes that are associated with higher neutral lipid (NL) content in Nannochloropsis oceanica. Therefore, we constructed a random gene knockout (KO) insertional mutagenesis library of N. oceanica, and we screened it by five rounds of fluorescence-activated cell sorting to select high lipid mutant (HLM) strains. Several strains showed increased NL contents compared to the wild type under favorable growth conditions. By using an adapted cassette PCR strategy involving the type IIS restriction endonuclease MmeI, we traced the responsible genetic KO of the five most promising mutant strains. One particularly promising mutant strain (HLM23) was disrupted in gene NO06G03670, which encodes a putative APETALA2-like transcription factor. HLM23 was not affected in growth rate, had increase d photosynthetic performance and a NL content of 30% dry cell weight^(-1), a 40% increase compared to the wild type. RNA sequencing revealed a transcriptional upregulation of genes related to plastidial fatty acid biosynthesis, glycolysis and the Calvin–Benson–Bassham cycle in this mutant.
2021-05-13 | GSE167058 | GEO