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

Abstract

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...

Mechanism study on the enhanced DHA synthesis in the mutant Thraustochytriidae sp. through comparative transcriptomic analysis

“…X2 (Table 4). The mutation led to the formation of ORFC, which contains two DH domains and one ER domain, with up-regulation similar to that observed by Zhi-Qian Bi (2018) [45]. The mutation also improved the expression of DH and ER in Thraustochytriu, which suggests increased production of DHA.…”

Comparative Transcriptomic Analysis Uncovers Genes Responsible for the DHA Enhancement in the Mutant Aurantiochytrium sp.

“…X2 ( Table 4). The mutation led to the formation of ORFC (open reading frame control), which contains two DH domains and one ER domain, with up-regulation similar to that observed by Zhi-Qian Bi (2018) [81]. The mutation also improved the expression of DH and ER in Thraustochytriu, which suggests increased production of DHA.…”

Effects of Methanol on Carotenoids as Well as Biomass and Fatty Acid Biosynthesis in Schizochytrium limacinum B4D1

“…Furthermore, Bi et al have reported that the expression of ME genes under a high oxygen supply is significantly upregulated in Schizochytrium sp. strain HX-308 (24). However, our results showed that the expression of two genes encoding ME (ME-1, ME-2) was downregulated under the H condition.…”

“…The central carbon metabolism pathway is the main route for generating NADH and ATP, two important factors for cell growth (24). In most microorganisms, EMP and the TCA cycle are principally responsible for generating ATP and NADH.…”