Transcriptome sequencing and comparative analysis of Schizochytrium mangrovei PQ6 at different cultivation times

Hoang, Minh Hien; Nguyen, Charlene; Pham, Huy Quang; Nguyen, Lam Van; Duc, Le Hoang; Sơn, Lê Văn; Hải, Trương Nam; Chu, Ha Hoang; Nhan, Lam Dai; Anh, Hoàng Thị Lan; Thom, Le Thi; Quynh, Hoang Thi; Ha, Nguyen Cam; Nhat, Pham Van; Hồng, Đặng Diễm

doi:10.1007/s10529-016-2165-5

Cited by 18 publications

(13 citation statements)

References 18 publications

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“…SZU445 was not observed to contain delta-12, delta-15, or delta-6 desaturases by whole-genome sequencing and protein annotation; however, it could synthesize PUFAs. A similar phenomenon has also been reported in a number of other studies, where Arthrospira platensis was observed to only have 15-cis-phytoene desaturase and zeta-carotene desaturase, and Strongylocentrotus nudus was observed to only have delta-5, delta-6, and delta-9 desaturases [41][42][43][44]. This result may indicate that the FAS pathway is not the primary pathway responsible for PUFA synthesis.…”

Section: Fatty Acid Synthesis By the Fas Pathwaysupporting

confidence: 84%

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

Zhu

Liu

et al. 2020

Marine Drugs

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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...

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Section: Fatty Acid Synthesis By the Fas Pathwaysupporting

confidence: 84%

“…SZU445, but an isomerase and a DH were not identified; however, Thraustochytrium sp. SZU445 can also generate PUFAs such as DHA (C22:5) [42][43][44].…”

Section: Fatty Acid Synthesis By the Pks Pathwaymentioning

confidence: 99%

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

Zhu

Liu

et al. 2020

Marine Drugs

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“…Minh Hien et al . 35 identified only two unigenes encoding elongase protein and one unigene encoding D6 desaturase. The missing of some specific enzymes might be the reason of the incomplete desaturation-elongation pathway.…”

Section: Discussionmentioning

confidence: 99%

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

Ren

Zhao

et al. 2017

Sci Rep

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Schizochytrium sp. is the main source of docosahexaenoic acid-rich oil, which is widely used in food additive and pharmaceutical industry. In this study, using RNA-seq, comparative transcriptomic analyses were performed at four stages of DHA fermentation by Schizochytrium sp to get potential genes related to cell transition from cell growth to lipid accumulation and then to lipid turnover. 1406, 385, 1384 differently expressed genes were identified by comparisons in pairs of S2 vs S1, S3 vs S2 and S4 vs S3. Functional analysis revealed that binding and single-organism process might be involve in the cell transition from cell growth to lipid accumulation while oxidation-reduction process played an important role in the transition from lipid accumulation to lipid turnover. pfaC in the PKS pathway showed higher sensitivity to the environmental change, which might be the key regulator for enhancing PUFA biosynthesis in the future. Some other genes in signal transduction and cell transport were revealed to be related to lipid turnover, which would enrich the current knowledge regarding lipid metabolism and help to enhance the DHA production and enrich different lipid fractions by Schizochytrium in the future.

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“…Schizochytrium mangrovei cells were stained with 15-mM Nile Red (9-[Diethylamino]-5H-benzo[a]phenoxazin-5-one) prior to visualization by fluorescence microscopy as described by Hoang et al (2014). TEM analysis was performed as described by Hoang et al (2016).…”

Section: Methodsmentioning

confidence: 99%

Different fermentation strategies by Schizochytrium mangrovei strain pq6 to produce feedstock for exploitation of squalene and omega‐3 fatty acids

Hoang

Nguyen

et al. 2018

Journal of Phycology

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Schizochytrium mangrovei strain PQ6 was investigated for coproduction of docosahexaenoic acid (C22: 6ω-3, DHA) and squalene using a 30-L bioreactor with a working volume of 15 L under various batch and fed-batch fermentation process regimes. The fed-batch process was a more efficient cultivation strategy for achieving higher biomass production rich in DHA and squalene. The final biomass, total lipid, unsaponifiable lipid content, and DHA productivity were 105.25 g · L , 43.40% of dry cell weight, 8.58% total lipid, and 61.66 mg · g · L , respectively, after a 96 h fed-batch fermentation. The squalene content was highest at 48 h after feeding glucose (98.07 mg · g of lipid). Differences in lipid accumulation during fermentation were correlated with changes in ultrastructure using transmission electron microscopy and Nile Red staining of cells. The results may be of relevance to industrial-scale coproduction of DHA and squalene in heterotrophic marine microalgae such as Schizochytrium.

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Transcriptome sequencing and comparative analysis of Schizochytrium mangrovei PQ6 at different cultivation times

Abstract: The possible roles of PUFAs pathways, such as those mediated by fatty acid synthase, polyketide synthase, and desaturase/elongase, co-exist in S. mangrovei PQ6.

Cited by 18 publications

References 18 publications

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

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

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

Different fermentation strategies by Schizochytrium mangrovei strain pq6 to produce feedstock for exploitation of squalene and omega‐3 fatty acids

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