Owing to the importance of cell membrane function and numerous cellular processes for maintaining health, long-chain polyunsaturated fatty acids (LC-PUFAs) have attracted much attention. LC-PUFAs can be classified into two principal families, namely, omega-3 (n-3) and omega-6 (n-6) fatty acids (FAs) [1]. The typical n-3 LC-PUFAs are docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), which can strongly influence monocyte physiology. Previous studies have reported that DHA could potently inhibit platelet aggregation [2] and reduce haemoglobin formation [3] and can be used to treat cardiovascular diseases [4] and prevent osteoporosis [5]. Currently, the primary commercial source of DHA is floating fish [6]; however, the industry is severely limited by the low original levels and the instability of n-3 LC-PUFAs due to differences among fish, the climate and high concentrations of cholesterol [7]. Microalgae, such as Thraustochytrium and Schizochytrium, with abundant FA content, have emerged as promising producers of n-3 LC-PUFAs [8]. The fermentation process of the Schizochytrium sp. SR 21 was optimized with bioreactor cultivation, with the DHA content doubled up to 66.72 ± 0.31% w/w total lipids [9]. The FA content required in the industry is currently 40–45 g l− 1, and the biomass required is 200 g l− 1 [10]. Nevertheless, it is difficult for the general wild-type (WT) strain to meet the requirements of industrial production due to the low biomass and n-3 LC-PUFA content, which account for the high cost of the downstream process [11].
To obtain high-yield DHA-producing strains for microbial industrial fermentation, artificial mutagenesis has been applied. Ultraviolet (UV) radiation, a kind of non-ionizing radiation, causes gene mutation via maximum absorption by purines and pyrimidines present in DNA [12]. With UV irradiation, the DHA percentage of the total fatty acids up to 56.22% was achieved using the mutant, which was 38.88% higher than the parent strain [13]. Therefore, UV radiation was used as method for mutagenesis to obtain a Schizochytrium strain with a high yield of DHA. De novo assembly of RNA-seq data serves as an important tool for studying the transcriptomes of “non-model” organisms without existing genome sequences [14]. Recently, transcriptome analysis has emerged as an essential method for the genes identification involved in the secondary metabolites biosynthesis [15], such as those involved in fatty acids accumulation in the microalgae Nannochloropsis sp. [16], Schizochytrium mangrovei PQ6 [17], Neochloris oleoabundans [18], Euglena gracilis [19], and Rhodomonas sp. [20]. There is an abundance of research on the optimization of fermentation parameters in terms of salinity, pH, temperature, and cultivation medium for high DHA production [21]. In addition, metabolic engineering is also used as a promising approach to promote DHA productivity. Recent research has indicated that DHA is synthesized by two distinct pathways in thraustochytrid: the fatty acid synthase (FAS) pathway and the polyketide synthase (PKS) pathway [22]. The standard FAS pathway synthesizes fatty acids through a series of elongase- and desaturase-catalyzed reactions. Delta-4 desaturase, delta-5 desaturase, and delta-12 desaturase have been reported in Thraustochytrium aureum ATCC 34304 [23], and delta-5 elongase, delta-6 elongase, and delta-9 elongase have also been successfully identified in some thraustochytrid strains [24]. Fatty acids are synthesized through the PKS pathway via highly repetitive cycles of four reactions, including condensation by ketoacyl synthase (KS), ketoreduction (KR), dehydration, and enoyl reduction (ER). Nevertheless, to date, the exact biosynthetic mechanism of DHA in Thraustochytrid species remains unknown.
In this study, UV mutagenesis was utilized to obtain competitive Thraustochytriidae sp. strain with enhanced biomass and DHA production. By comparing the transcriptome between the mutant and the parent strain, the key genes related to the increasing DHA accumulation were explored.