Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond.
Exophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and meta...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0317796 |
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| author | Hamta Babaei Naeij Zahra Etemadifar John Kilbane Mohammad Hossein Karimi-Jafari Sepideh Mofidifar |
| author_facet | Hamta Babaei Naeij Zahra Etemadifar John Kilbane Mohammad Hossein Karimi-Jafari Sepideh Mofidifar |
| author_sort | Hamta Babaei Naeij |
| collection | DOAJ |
| description | Exophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. Through bioinformatics analysis, we identified genes potentially involved in DBT desulfurization and degradation pathways for hazardous pollutants. We focused on understanding the cost associated with metabolites in sulfur assimilation pathway to assess economic feasibility, optimize resource allocation, and guide metabolic engineering and process design. To overcome knowledge gaps, we developed a genome-scale model for E. spinifera, iEsp1694, enabling a comprehensive investigation into its metabolism. The model was rigorously validated against growth phenotypes and gene essentiality data. Through shadow price analysis, we identified costly metabolites such as 3'-phospho-5'-adenylyl sulfate, 5'-adenylyl sulfate, and choline sulfate when DBT was used as the sulfur source. iEsp1694 encompasses the degradation of aromatic compounds, which serves as a crucial first step in comprehending the pan metabolic capabilities of this strain. |
| format | Article |
| id | doaj-art-58ebec45056443df8b3a7b8ae5872c45 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj-art-58ebec45056443df8b3a7b8ae5872c452025-02-07T05:30:51ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01201e031779610.1371/journal.pone.0317796Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond.Hamta Babaei NaeijZahra EtemadifarJohn KilbaneMohammad Hossein Karimi-JafariSepideh MofidifarExophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. Through bioinformatics analysis, we identified genes potentially involved in DBT desulfurization and degradation pathways for hazardous pollutants. We focused on understanding the cost associated with metabolites in sulfur assimilation pathway to assess economic feasibility, optimize resource allocation, and guide metabolic engineering and process design. To overcome knowledge gaps, we developed a genome-scale model for E. spinifera, iEsp1694, enabling a comprehensive investigation into its metabolism. The model was rigorously validated against growth phenotypes and gene essentiality data. Through shadow price analysis, we identified costly metabolites such as 3'-phospho-5'-adenylyl sulfate, 5'-adenylyl sulfate, and choline sulfate when DBT was used as the sulfur source. iEsp1694 encompasses the degradation of aromatic compounds, which serves as a crucial first step in comprehending the pan metabolic capabilities of this strain.https://doi.org/10.1371/journal.pone.0317796 |
| spellingShingle | Hamta Babaei Naeij Zahra Etemadifar John Kilbane Mohammad Hossein Karimi-Jafari Sepideh Mofidifar Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. PLoS ONE |
| title | Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. |
| title_full | Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. |
| title_fullStr | Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. |
| title_full_unstemmed | Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. |
| title_short | Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. |
| title_sort | unraveling the metabolic landscape of exophiala spinifera strain fm model reconstruction insights into biodesulfurization and beyond |
| url | https://doi.org/10.1371/journal.pone.0317796 |
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