Genome Sequencing and Analysis of Thraustochytriidae sp. SZU445 Provides Novel Insights into the Polyunsaturated Fatty Acid Biosynthesis Pathway

Abstract

Thraustochytriidae sp. have broadly gained attention as a prospective resource for the production of omega-3 fatty acids production in significant quantities. In this study, the whole genome of Thraustochytriidae sp. SZU445, which produces high levels of docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA), was sequenced and subjected to protein annotation. The obtained clean reads (63.55 Mb in total) were assembled into 54 contigs and 25 scaffolds, with maximum and minimum lengths of 400 and 0.0054 Mb, respectively. A total of 3513 genes (24.84%) were identified, which could be classified into six pathways and 44 pathway groups, of which 68 genes (1.93%) were involved in lipid metabolism. In the Gene Ontology database, 22,436 genes were annotated as cellular component (8579 genes, 38.24%), molecular function (5236 genes, 23.34%), and biological process (8621 genes, 38.42%). Four enzymes corresponding to the classic fatty acid synthase (FAS) pathway and three enzymes corresponding to the classic polyketide synthase (PKS) pathway were identified in Thraustochytriidae sp. SZU445. Although PKS pathway-associated dehydratase and isomerase enzymes were not detected in Thraustochytriidae sp. SZU445, a putative DHA-and DPA-specific fatty acid pathway was identified.2 of 18 in a number of previous studies, and include the proper development of infant brain and eyes [1,2]; cardiovascular disease prevention [3]; antioxidative, anti-inflammatory [4] as well as anti-cancer properties [5], and the prevention of Alzheimer's disease [6]. Currently, ocean fish are the primary PUFA production source. However, because of the drawbacks of a fishy odor, the accumulation of contaminants, and declining fish stock, it is necessary to identify other sustainable and relatively safer alternative sources of PUFA [7].Thraustochytrids, a single-celled eukaryotic marine protist belonging to the class Labyrinthulomycetes, can accumulate large amounts of DHA, resulting in these organisms having attracted a great deal of scientific and industrial interest. Research has shown that some thraustochytrid strains can be cultivated to yield high biomasses containing substantial quantities of lipids abundant in PUFAs [8]. There is an abundance of research on the optimization of fermentation parameters in terms of salinity [9], pH, temperature [10], and cultivation medium [11] for high DHA production. Besides, 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 [12]. 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 [13][14][15], and delta-5 elongase, delta-6 elongase, and delta-9 elongase have also been successfully identified in some thraustochytrid str...

Temperature Differentially Affects Gene Expression in Antarctic Thraustochytrid Oblongichytrium sp. RT2316-13

“…These are the polyketide synthase (PKS) system found in marine bacteria ( Shewanella sp., [ 30 ]; Vibrio sp., [ 31 ]; Photobacterium profundum , [ 32 ]) and in some thraustochytrids ( Schizochytrium sp., [ 33 ], Thraustochytrium sp. SZU445 [ 34 ]), and the elongase-desaturase system (ω3- and ω6-pathways) (shown in Figure 2 ). Precursors of ω6- and ω3-pathways (i.e.…”

Antarctic Thraustochytrids as Sources of Carotenoids and High-Value Fatty Acids

“…[ 32 ]; Thraustochytrium sp. SZU445 [ 33 ]), the synthesis of long-chain ω-3 PUFA from acetyl-ACP and malonyl-ACP is accomplished by polyketide synthase (PKS) systems, also known as PUFA synthases. Our results implied that the synthesis of long chain ω-3 PUFA in RT2316-16 was not due to a PKS system.…”

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

“…PKS pathway domains are likely involved in the production of DHA, such as AT, DH, MT and ER [75,76]. Genomic and transcriptomic analysis have shown that Thraustochytrids contained some key enzymes of PKS system such as 3-ketoacyl-synthase (KS), ketoreductase (KR), and enoyl reductase (ER) [26]. As a probable source of high-value DHA, the PKS pathway is important in DHA biosynthesis, as genes related to the PKS pathway were mined in the transcriptome study of wild Aurantiochytrium sp.…”

“…Genomic and transcriptomic analysis revealed that both the FAS and PKS pathways of PUFA production were incomplete in Thraustochytrids strains [38]. The dehydratase and isomerase enzymes were not detected in the Thraustochytrids strain SZU445 [26]. Although FAD12, FAD4, and FAD5 have been reported in Thraustochytrids, some Thraustochytrids only contains the desaturase not belonging to the FAS pathway, such as FAD6 [39].…”