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Author: search.filters.author.Hoondee, Patcharaporn

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    Characterization of red pigmented yeasts and genes associated with astaxanthin synthesis in Rhodotorula mucilaginosa HL26-1 and Rhodotorula paludigena LL69-1
    (2026-01-01)
    Hoondee, Patcharaporn
    ;
    Tedsree, Nisachon
    ;
    Phuengjayaem, Sukanya
    ;
    Kingkaew, Engkarat
    ;
    Sritularak, Boonchoo
    Background: Astaxanthin, a red xanthophyll carotenoid, is a powerful antioxidant, anticancer, and glucose and lipid homeostasis regulator. Some pigmented yeasts belonging to the genus Rhodotorula, the well-known yeast for beta-carotene production, have been reported as natural astaxanthin producers. However, the lack of genomic data on astaxanthin-producing strains within these species hinders the identification of biosynthetic routes, molecular characterization of these pathways, and gene editing applications. Methods: This study explored the diversity and astaxanthin production capability of cultivable pigmented yeast in flower samples. The astaxanthin production ability was inspected by three consecutive methods, including thin-layer chromatography (TLC) for the preliminary step, followed by quantitative spectrophotometry and high-performance liquid chromatography (HPLC) for qualitative validation. The draft genome sequence and astaxanthin-producing genes of astaxanthin-producing yeasts were examined. Results: Twelve of 23 yeasts from floral samples exhibited natural pigmentation, with colors ranging from pinkish-orange to red, and exhibited the potential for astaxanthin synthesis. These yeasts were Rhodotorula paludigena (three strains) and Rhodotorula mucilaginosa (nine strains). Among R. mucilaginosa strains, HL26-1 had the greatest astaxanthin content (104.98 ± 0.13 μg/g DCW) and yield (0.9280 ± 0.0012 mg/L). Strain LL69-1 has the greatest astaxanthin content (251.78 ± 0.27 μg/g DCW) and yield (1.8632 ± 0.0023 mg/L) among R. paludigena strains. The 18.78 Mbp R. mucilaginosa HL26-1 genome includes 5,711 protein-coding genes. Conversely, the R. paludigena LL69-1 genome was 20.99 Mbp, encompassing 6,782 predicted genes. A comprehensive investigation of draft genome sequences of these two strains identified CrtE, CrtYB, CrtI, CrtS, and CrtR as potential astaxanthin transcription genes. Conclusion: Here, our results highlight the outstanding potential of two naturally pigmented yeasts, R. mucilaginosa HL26-1 and R. paludigena LL69-1, for astaxanthin production. Furthermore, our findings provide information on the whole genome and protein-encoded genes associated with astaxanthin production, which serve as valuable biological resources for various biotechnological applications.
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    Enhancement of astaxanthin production in novel red yeast Rhodosporidiobolus sp. SP3-3/4 and genomic characterization
    (2025-10-01)
    Phuengjayaem, Sukanya
    ;
    Kingkaew, Engkarat
    ;
    Hoondee, Patcharaporn
    ;
    Tanasupawat, Somboon
    Astaxanthin is a red carotenoid and potent antioxidant with anti-inflammatory, anti-cancer, neuroprotective, and immuno-enhancing benefits. This study focused on enhancing astaxanthin production using a novel red yeast, strain SP3-3/4, through genomic analysis. Strain SP3-3/4 shared 99.66% sequence identity in the D1/D2 domain of the large subunit rRNA gene with Rhodosporidiobolus ruineniae CBS 5001<sup>T</sup>. Whole-genome analysis indicated 82.54% similarity to R. ruineniae JCM 8097<sup>T</sup>, with average nucleotide identity (ANI) values below 80% for other strains. The ANI result, lower than the 95% cutoff, confirms SP3-3/4 as a novel species, Rhodosporidiobolus sp. SP3-3/4. Key astaxanthin synthesis genes, including CrtE, CrtYB, CrtI, CrtS, CrtR, CrtW, CrtO, and CrtZ, were annotated. Astaxanthin production was verified using HPLC and LC-MS. Optimization of medium composition and physical parameters identified optimal conditions as 20 g/L sucrose, 3 g/L yeast extract, and 5 g/L peptone, with an initial medium pH of 6.5. Maximum cell growth and astaxanthin content, reaching 9.615 g/L and 0.46 mg/g DCW, respectively, were achieved after 5 days of cultivation, corresponding to an astaxanthin yield of 6.93 mg/L and a productivity rate of 1.39 mg/L/day. Notably, a maximum productivity of 1.45 mg/L/day occurred in 3 days. These findings elucidated comprehensive optimization of astaxanthin production, incorporating functional genomic assessment and analysis of protein-encoded genes of astaxanthin-producing yeast Rhodosporidiobolus sp. SP3-3/4. Such insights represent valuable biological resources with significant implications for diverse biotechnological and bioinformatics applications.
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    Comparative genomic analysis and optimization of astaxanthin production of Rhodotorula paludigena TL35-5 and Rhodotorula sampaioana PL61-2
    (2024-07-01)
    Hoondee, Patcharaporn
    ;
    Phuengjayaem, Sukanya
    ;
    Kingkaew, Engkarat
    ;
    Rojsitthisak, Pornchai
    ;
    Sritularak, Boonchoo
    Astaxanthin is a powerful antioxidant known to enhance skin, cardiovascular, eye, and brain health. In this study, the genome insights and astaxanthin production of two newly isolated astaxanthin-producing yeasts (TL35-5 and PL61-2) were evaluated and compared. Based on their phenotypic and genotypic characteristics, TL35-5 and PL61-2 were identified as basidiomycetous yeasts belonging to Rhodotorula paludigena and Rhodotorula sampaioana, respectively. To optimize astaxanthin production, the effects of cultural medium composition and cultivation conditions were examined. The optimal conditions for astaxanthin production in R. paludigena TL35-5 involved cultivation in AP medium containing 10 g/L glucose as the sole carbon source, supplemented with 1.92 g/L potassium nitrate, pH 6.5, and incubation at 20C for 3 days with shaking at 200 rpm. For R. sampaioana PL61-2, the optimal medium composition for astaxanthin production consisted of AP medium with 40 g/L glucose, supplemented with 0.67 g/L urea, pH 7.5, and the fermentation was carried out at 20C for 3 days with agitating at 200 rpm. Under their optimal conditions, R. paludigena TL35-5 and R. sampaioana PL61-2 gave the highest astaxanthin yields of 3.689 ± 0.031 and 4.680 ± 0.019 mg/ L, respectively. The genome of TL35-5 was 20,982,417 bp in length, with a GC content of 64.20%. A total of 6,789 protein-encoding genes were predicted. Similarly, the genome of PL61-2 was 21,374,169 bp long, with a GC content of 64.88%. It contained 6,802 predicted protein-encoding genes. Furthermore, all essential genes involved in astaxanthin biosynthesis, including CrtE, CrtYB, CrtI, CrtS, and CrtR, were identified in both R. paludigena TL35-5 and R. sampaioana PL61-2, providing evidence for their ability to produce astaxanthin.
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    Diversity, astaxanthin production, and genomic analysis of Rhodotorula paludigena SP9-15
    (2023-07-01)
    Phuengjayaem, Sukanya
    ;
    Kingkaew, Engkarat
    ;
    Hoondee, Patcharaporn
    ;
    Rojsitthisak, Pornchai
    ;
    Sritularak, Boonchoo
    Astaxanthin is a carotenoid known for its powerful antioxidant properties. This study focused on isolating yeast strains capable of producing astaxanthin from flower and fruit samples collected in Thailand. Out of 115 isolates, 11 strains were identified that produced astaxanthin. Molecular identification techniques revealed that these isolates belonged to two species: Rhodotorula paludigena (5 isolates) and Rhodosporidiobolus ruineniae (6 isolates). Whole-genome analysis of one representative strain, R. paludigena SP9-15, identified putative candidate astaxanthin synthesis-associated genes, such as CrtE, CrtYB, CrtI, CrtS, CrtR, CrtW, CrtO, and CrtZ. High-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) confirmed astaxanthin production. Further optimization of astaxanthin production was carried out by investigating the effects of various factors on the growth rate and astaxanthin production. The optimal conditions were 40 g/L glucose as a carbon source, pH 7.5, and cultivation at 25 °C with 200 rpm for 3 days. Under these conditions, R. paludigena SP9-15 synthesized biomass of 11.771 ± 0.003 g/L, resulting in astaxanthin with a content of 0.558 ± 0.018 mg/g DCW (dry cell weight), an astaxanthin yield of 6.565 ± 0.238 mg/L, and astaxanthin productivity of 2.188 ± 0.069 g/L/day. These findings provide insights into astaxanthin production using red yeast strains from Thailand and highlight the potential of R. paludigena SP9-15 for further application.