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Time-resolved transcriptome analysis under sulfur starvation stress in the green microalga Chromochloris zofingiensis

ABSTRACT: Chromochloris zofingiensis has been proposed as a potential producer of lipids and the high-value carotenoid astaxanthin. Previous studies have demonstrated that TAG (triacylglycerol) and astaxanthin accumulated in a well-coordinated manner in response to different stresses in C. zofingiensis. The integrated production of lipids with co-products emerges as a new research direction and is proposed to be a promising approach toward offsetting the algal biodiesel production cost. Therefore, it is suggested C. zofingiensis can serve as research models for the integrated production. Sulfur starvation stress simultaneously induced TAG and astaxanthin accumulation in C. zofingiensis. To understand the mechanism underlying TAG and astaxanthin accumulation induced by sulfur starvation stress, we applied time-resolved high-throughput mRNA sequencing in C. zofingiensis.

ORGANISM(S): Chromochloris zofingiensis

PROVIDER: GSE130454 | GEO | 2020/07/27

REPOSITORIES: GEO

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Project description:The oleaginous green microalga Neochloris oleoabundans accumulates both starch and lipids to high levels under stress conditions such as nitrogen starvation. In order to steer the metabolism towards starch or lipids only, it is important to understand the mechanisms behind it. In this study physiological changes and gene expression upon nitrogen starvation were analysed in controlled flat-panel photobioreactors over both short- and long-term time-scales. Starch accumulation is transient and occurs rapidly within 24 hrs upon starvation, while lipid accumulation lasts longer and reaches a maximum after 4 days. The major fraction of accumulated lipids is composed of de novo synthesized neutral lipids - triacylglycerides (TAG) - and is characterized by a decreased composition of the polyunsaturated fatty acids (PUFAs) C18:3 and C16:3 and an increased composition of the mono-unsaturated and saturated fatty acids C18:1/C16:1 and C18:0/C16:0, respectively. RNA-sequencing revealed that genes related to starch biosynthesis and degradation show different temporal expression dynamics compared to those of lipid biosynthesis. An immediate rapid increase in starch synthesis gene expression is followed by an increase in starch degradation and decrease in starch synthesis gene expression. In contrast, increased gene expression for fatty acid and TAG synthesis is initiated later and occurs more gradually. Expression of several fatty acid desaturase (FAD) genes was decreased upon starvation, which corresponds to the observed changes to higher levels of mono-unsaturated and saturated fatty acids. Moreover, several homologs of transcription regulators that were implicated in controlling starch and lipid metabolism in other microalgae showed differential gene expression and might be key regulators of starch and lipid metabolism in N. oleoabundans as well. Promising candidates for future metabolic engineering are a DYRKP homolog that in Chlamydomonas acts as a negative regulator of carbon storage and photosynthetic efficiency under N-starvation, and two bZIP-type regulators that have been implicated to control several steps in microalgal TAG synthesis. Our data for the first time show the temporal dynamics of storage compound accumulation and transcriptional changes on a short- and long-term time-scale during nitrogen starvation in N. oleoabundans, and increases insight into the genetic foundation for starch and lipid metabolism in this microalga. This information and the identified target genes can now be used for metabolic engineering strategies towards tailored N. oleoabundans strains for industrial applications with increased lipid production and altered fatty acid composition.

Project description:We used Chlamydomonas microarray v2.0 to compare the time course expression profiles of two Chlamydomonas reinhardtii strains: wild-type WT and the high hydrogen producing mutant Stm6Glc4 during sulfur starvation induced hydrogen production. Major cellular reorganizations in photosynthetic apparatus, sulfur and carbon metabolism upon H2 production were confirmed as common to both strains. More importantly, our results pointed out factors which lead to the higher hydrogen production in the mutant including higher light sensitivity and lower competitions with hydrogenase by alternative electron sinks. Under S-starvation induced H2 producing conditions the induction of LHCSR3, a chlorophyll binding protein involving in non photochemical quenching, was significantly lower in Stm6Glc4 resulting in significant higher photodamage to photosystem II. Consequently, Stm6Glc4 had a shorter aerobic phase, consumed less starch reserves, and produced H2 earlier at higher rates than WT. We also showed that the loss of mitochondrial DNA-binding protein MOC1 in both knockdown and knockout mutant resulted in higher light sensitivity and improved H2 yield. Furthermore, by comparing our data with previously published ‘omics’ data, we were able to identify genes that responded specifically to either sulfur starvation, anaerobiosis or hydrogen production as well as to provide a more complete picture of S-deprived H2 production in the green alga C. reinhardtii. A total of 33 microarray hydridizations were performed covering samples taken during the course of S deprivation induced H2 producction. The samples included 4 time points in the high hydrogen producing mutant Stm6Glc4 (taken at 16, 28, 52 and 76h) and 6 time points in the wildtype CC-406 (taken at 16, 28, 52, 68, 92, 116h). Samples from each time point were compared directly with the sample taken prior to S starvation from the corresponding strain. Three biological replicates were tested at each time point.

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Time-resolved transcriptome analysis under sulfur starvation stress in the green microalga Chromochloris zofingiensis

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