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Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B

1
GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
2
Institute of Bioinformatics, International Technology Park, Bangalore, 560066 & Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
3
Department of Botany, Kiel University, Olshausenstr. 40, 24098 Kiel, Germany
4
Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
*
Authors to whom correspondence should be addressed.
Equal contribution.
Mar. Drugs 2021, 19(1), 14; https://doi.org/10.3390/md19010014
Received: 20 November 2020 / Revised: 14 December 2020 / Accepted: 24 December 2020 / Published: 30 December 2020
Red yeasts of the genus Rhodotorula are of great interest to the biotechnological industry due to their ability to produce valuable natural products, such as lipids and carotenoids with potential applications as surfactants, food additives, and pharmaceuticals. Herein, we explored the biosynthetic potential of R. mucilaginosa 50-3-19/20B collected from the Mid-Atlantic Ridge using modern genomics and untargeted metabolomics tools. R. mucilaginosa 50-3-19/20B exhibited anticancer activity when grown on PDA medium, while antimicrobial activity was observed when cultured on WSP-30 medium. Applying the bioactive molecular networking approach, the anticancer activity was linked to glycolipids, namely polyol esters of fatty acid (PEFA) derivatives. We purified four PEFAs (14) and the known methyl-2-hydroxy-3-(1H-indol-2-yl)propanoate (5). Their structures were deduced from NMR and HR-MS/MS spectra, but 15 showed no anticancer activity in their pure form. Illumina-based genome sequencing, de novo assembly and standard biosynthetic gene cluster (BGC) analyses were used to illustrate key components of the PEFA biosynthetic pathway. The fatty acid producing BGC3 was identified to be capable of producing precursors of PEFAs. Some Rhodotorula strains are able to convert inulin into high-yielding PEFA and cell lipid using a native exo-inulinase enzyme. The genomic locus for an exo-inulinase enzyme (g1629.t1), which plays an instrumental role in the PEFA production via the mannitol biosynthesis pathway, was identified. This is the first untargeted metabolomics study on R. mucilaginosa providing new genomic insights into PEFA biosynthesis. View Full-Text
Keywords: Rhodotorula; deep-sea sediment; yeast; metabolomics; GNPS molecular networking; dereplication; polyol esters of fatty acids; anticancer; genome sequencing; exo-inulinase enzyme Rhodotorula; deep-sea sediment; yeast; metabolomics; GNPS molecular networking; dereplication; polyol esters of fatty acids; anticancer; genome sequencing; exo-inulinase enzyme
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MDPI and ACS Style

Buedenbender, L.; Kumar, A.; Blümel, M.; Kempken, F.; Tasdemir, D. Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. Mar. Drugs 2021, 19, 14. https://doi.org/10.3390/md19010014

AMA Style

Buedenbender L, Kumar A, Blümel M, Kempken F, Tasdemir D. Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. Marine Drugs. 2021; 19(1):14. https://doi.org/10.3390/md19010014

Chicago/Turabian Style

Buedenbender, Larissa, Abhishek Kumar, Martina Blümel, Frank Kempken, and Deniz Tasdemir. 2021. "Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B" Marine Drugs 19, no. 1: 14. https://doi.org/10.3390/md19010014

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