Transcriptomic Analysis of the Regulation of Lipid Fraction Migration and Fatty Acid Biosynthesis in Schizochytrium sp.

Ren, Lu‐Jing; Hu, Xuechao; Zhao, Xiaoyan; Chen, Shenglan; Wu, Yi Hui; Li, Dan; Yu, Yadong; Geng, Lingjun; Ji, Xiao‐Jun; Huang, He

doi:10.1038/s41598-017-03382-9

Cited by 33 publications

(19 citation statements)

References 45 publications

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“…ATCC20888 without the present of -12 desaturation. Ren et al (2017), detected one elongase and three kinds ( -6, -8, and -12) of desaturase activities in Schizochytrium sp. The missing of some specific enzymes might be the reason of the incomplete genomic information.…”

Section: Discussionmentioning

confidence: 95%

“…ATCC20888 without the present of -12 desaturation. Ren et al (2017), detected one elongase and three kinds ( -6, -8, and -12) of desaturase activities in Schizochytrium sp. PKS pathway of LC-PUFAs synthesis involve the processing of the saturated 16:0 or 18:0 products by repetitive decarboxylative Claisen ester condensations.…”

Section: Introductionmentioning

confidence: 95%

“…In order to uncover the regulatory mechanism of lipid migration and LC-PUFA synthesis, genomics and transcriptomics studies have revealed genes or proteins involved in LC-PUFA biosynthesis (Ren et al, 2017). Scaffolding genome assemblies remain challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies.…”

Section: Introductionmentioning

confidence: 99%

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Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

et al. 2020

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Schizochytrium sp. is the best natural resource for omega-3 long-chain polyunsaturated fatty acids. We report a high-quality genome sequence of Schizochytrium limacinum SR21, which has a 63 Mb genome size, with a contig N50 of 2.67 Mb and 6,838 protein-coding genes. Phylogenomic and comparative genomic analyses revealed that DHA-producing Schizochytrium and Aurantiochytrium strains were highly similar and possessed similar genes. Analysis of the fatty acid synthase (FAS) for LC-PUFAs production results in the annotation of all genes in map00062 and map01212. A gene cluster and 10 ORFs related to PKS pathway were found in the genome. 1,402 differentially expressed genes (DEGs) of the treated groups (0.5 g/L yeast extract) were identified by comparing with the control groups (1.0 g/L yeast extract) at 36 h. A weighted gene coexpression network analysis revealed that 2 of 7 modules correlated highly with the fatty acid and DHA contents. The DEGs and transcription factors were significantly correlated with fatty acid biosynthesis, including MYB, Zinc Finger and ACOX. The results showed that these hub genes are regulated by genes involved in fatty acid biosynthesis pathways. The results providing an important reference for further research on promoting fatty acid and DHA accumulation in S. limacinum SR21.

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Section: Discussionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

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Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

et al. 2020

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“…Moreover, we identified three genes associated with the PKS route of PUFAs biosynthesis—ORFA, ORFB, and ORFC. During the cell growth stage, all genes involved in the PKS pathway showed high expression levels [ 26 ]. Our transcription results showed that PKS genes (ORFA, ORFB, and ORFC), which are directly involved in the DHA biosynthesis, were significantly differentially expressed between normal and high oxygen supply conditions.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome and gene expression analysis of docosahexaenoic acid producer Schizochytrium sp. under different oxygen supply conditions

Ren

et al. 2018

Biotechnol Biofuels

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BackgroundSchizochytrium sp. is a promising strain for the production of docosahexaenoic acid (DHA)-rich oil and biodiesel, and has been widely used in the food additive and bioenergy industries. Oxygen is a particularly important environmental factor for cell growth and DHA synthesis. In general, higher oxygen supply favors lipid accumulation, but could lead to a reduction of the DHA percentage in total fatty acids in Schizochytrium sp. To tackle this problem, it is essential to understand the mechanisms regulating the response of Schizochytrium sp. to oxygen. In this study, we aimed to explore the acclimatization of this DHA producer to different oxygen supply conditions by examining the transcriptome changes.ResultsTwo different fermentation processes, namely normal oxygen supply condition (shift agitation speeds from 400 rpm to 300 rpm) and high oxygen supply condition (constant agitation speeds: 400 rpm), were designed to study how the fermentation characteristics of Schizochytrium sp. HX-308 were affected by different oxygen supply conditions. The results indicated that high oxygen supply condition resulted in 49% and 37.5% improvement in the maximum cell dry weight (CDW) and total lipid concentration, respectively. However, the DHA percentage in total fatty acids decreased to 35%, which was 31.4% lower than that produced by normal oxygen supply condition. Moreover, transcriptome analysis was performed to explore the effect of the oxygen supply condition on genetic expression and metabolism. The results showed that glycolysis and pentose phosphate pathway metabolism-associated genes (hexokinase, phosphofructokinase, fructose-bisphosphate aldolase, glucose-6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase) were substantially upregulated in response to high oxygen supply, resulting in more NADPH was available for Schizochytrium. Specially, high oxygen supply condition also led to genes (Δ6 desaturase, Δ12 desaturase, FAS, ORFA, ORFB, and ORFC) involved in fatty acid biosynthesis upregulation. In addition, a transcriptional upregulation of catalase (CAT) became apparent under high oxygen supply condition, while superoxide dismutase (SOD) and ascorbate peroxidase (APX) were found to be down-regulated.ConclusionsThis study is the first to investigate the differences of gene expression at different levels of oxygen availability in the DHA producer Schizochytrium. The results of transcriptome analyses indicated that high oxygen supply condition resulting in more NADPH and acetyl-CoA production for cell growth and lipid synthesis in Schizochytrium. Δ12 desaturase and ORFC showed higher expression levels at high oxygen supply condition, which might be the key regulators for enhancing fatty acid biosynthesis in the future. These results enrich the current knowledge regarding genetic expression and provide important information to enhance DHA production in Schizochytrium sp.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1250-5) contains supplementary material, whi...

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“…Among the three genes encoding PKS enzymes, ORFC expression was increased the most, and was 4.12- and 3.34-fold higher than that of the parental strain at 60 and 180 h, respectively. ORFC contains two DH (dehydrase) domains and one ER (enoyl-ACP reductase) domain, which showed higher sensitivity to the changes of environmental factors [ 61 ]. DH catalyzes the conversion of ketoacyl-ACP to enoyl-ACP, and the ER domain catalyzes the final step of fatty acid chain extension in which it reduces the double bond.…”

Section: Discussionmentioning

confidence: 99%

Development of a cooperative two-factor adaptive-evolution method to enhance lipid production and prevent lipid peroxidation in Schizochytrium sp.

Sun

Ren

et al. 2018

Biotechnol Biofuels

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BackgroundSchizochytrium sp. is a marine microalga with great potential as a promising sustainable source of lipids rich in docosahexaenoic acid (DHA). This organism’s lipid accumulation machinery can be induced by various stress conditions, but this stress induction usually comes at the expense of lower biomass in industrial fermentations. Moreover, oxidative damage induced by various environmental stresses can result in the peroxidation of lipids, and especially polyunsaturated fatty acids, which causes unstable DHA production, but is often ignored in fermentation processes. Therefore, it is urgent to develop new production strains that not only have a high DHA production capacity, but also possess strong antioxidant defenses.ResultsAdaptive laboratory evolution (ALE) is an effective method for the development of beneficial phenotypes in industrial microorganisms. Here, a novel cooperative two-factor ALE strategy based on concomitant low temperature and high salinity was applied to improve the production capacity of Schizochytrium sp. Low-temperature conditions were used to improve the DHA content, and high salinity was applied to stimulate lipid accumulation and enhance the antioxidative defense systems of Schizochytrium sp. After 30 adaptation cycles, a maximal cell dry weight of 126.4 g/L and DHA yield of 38.12 g/L were obtained in the endpoint strain ALE-TF30, which was 27.42 and 57.52% higher than parental strain, respectively. Moreover, the fact that ALE-TF30 had the lowest concentrations of reactive oxygen species and malondialdehyde among all strains indicated that lipid peroxidation was greatly suppressed by the evolutionary process. Accordingly, the ALE-TF30 strain exhibited an overall increase of gene expression levels of antioxidant enzymes and polyketide synthases compared to the parental strain.ConclusionThis study provides important clues on how to overcome the negative effects of lipid peroxidation on DHA production in Schizochytrium sp. Taken together, the cooperative two-factor ALE process can not only increase the accumulation of lipids rich in DHA, but also prevent the loss of produced lipid caused by lipid peroxidation. The strategy proposed here may provide a new and alternative direction for the industrial cultivation of oil-producing microalgae.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1065-4) contains supplementary material, which is available to authorized users.

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Transcriptomic Analysis of the Regulation of Lipid Fraction Migration and Fatty Acid Biosynthesis in Schizochytrium sp.

Cited by 33 publications

References 45 publications

Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

Transcriptome and gene expression analysis of docosahexaenoic acid producer Schizochytrium sp. under different oxygen supply conditions

Development of a cooperative two-factor adaptive-evolution method to enhance lipid production and prevent lipid peroxidation in Schizochytrium sp.

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