Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces
The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes...
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Bioengineering and Biotechnology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbioe.2024.1356551/full |
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| author | Jeffrey J. Czajka Jeffrey J. Czajka Yichao Han Yichao Han Joonhoon Kim Joonhoon Kim Joonhoon Kim Stephen J. Mondo Stephen J. Mondo Stephen J. Mondo Beth A. Hofstad Beth A. Hofstad AnaLaura Robles AnaLaura Robles Sajeet Haridas Robert Riley Kurt LaButti Jasmyn Pangilinan William Andreopoulos Anna Lipzen Juying Yan Mei Wang Vivian Ng Igor V. Grigoriev Igor V. Grigoriev Joseph W. Spatafora Jon K. Magnuson Jon K. Magnuson Jon K. Magnuson Scott E. Baker Scott E. Baker Scott E. Baker Kyle R. Pomraning Kyle R. Pomraning |
| author_facet | Jeffrey J. Czajka Jeffrey J. Czajka Yichao Han Yichao Han Joonhoon Kim Joonhoon Kim Joonhoon Kim Stephen J. Mondo Stephen J. Mondo Stephen J. Mondo Beth A. Hofstad Beth A. Hofstad AnaLaura Robles AnaLaura Robles Sajeet Haridas Robert Riley Kurt LaButti Jasmyn Pangilinan William Andreopoulos Anna Lipzen Juying Yan Mei Wang Vivian Ng Igor V. Grigoriev Igor V. Grigoriev Joseph W. Spatafora Jon K. Magnuson Jon K. Magnuson Jon K. Magnuson Scott E. Baker Scott E. Baker Scott E. Baker Kyle R. Pomraning Kyle R. Pomraning |
| author_sort | Jeffrey J. Czajka |
| collection | DOAJ |
| description | The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces. |
| first_indexed | 2024-04-24T13:47:38Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2296-4185 |
| language | English |
| last_indexed | 2024-04-24T13:47:38Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
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| spelling | doaj.art-e4235ff99f1948b58b602ca0631e234b2024-04-04T05:07:44ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852024-04-011210.3389/fbioe.2024.13565511356551Genome-scale model development and genomic sequencing of the oleaginous clade LipomycesJeffrey J. Czajka0Jeffrey J. Czajka1Yichao Han2Yichao Han3Joonhoon Kim4Joonhoon Kim5Joonhoon Kim6Stephen J. Mondo7Stephen J. Mondo8Stephen J. Mondo9Beth A. Hofstad10Beth A. Hofstad11AnaLaura Robles12AnaLaura Robles13Sajeet Haridas14Robert Riley15Kurt LaButti16Jasmyn Pangilinan17William Andreopoulos18Anna Lipzen19Juying Yan20Mei Wang21Vivian Ng22Igor V. Grigoriev23Igor V. Grigoriev24Joseph W. Spatafora25Jon K. Magnuson26Jon K. Magnuson27Jon K. Magnuson28Scott E. Baker29Scott E. Baker30Scott E. Baker31Kyle R. Pomraning32Kyle R. Pomraning33Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesUS Department of Energy Joint BioEnergy Institute, Emeryville, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesDepartment of Agricultural Biology, Colorado State University, Fort Collins, CO, United StatesEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesDepartment of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United StatesDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United StatesEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesUS Department of Energy Joint BioEnergy Institute, Emeryville, CA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesUS Department of Energy Joint BioEnergy Institute, Emeryville, CA, United StatesEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United StatesUS Department of Energy Agile BioFoundry, Emeryville, CA, United StatesThe Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.https://www.frontiersin.org/articles/10.3389/fbioe.2024.1356551/fulloleaginous yeastsgenome-scale metabolic modelflux balance analysisLipomycesgenome sequencing |
| spellingShingle | Jeffrey J. Czajka Jeffrey J. Czajka Yichao Han Yichao Han Joonhoon Kim Joonhoon Kim Joonhoon Kim Stephen J. Mondo Stephen J. Mondo Stephen J. Mondo Beth A. Hofstad Beth A. Hofstad AnaLaura Robles AnaLaura Robles Sajeet Haridas Robert Riley Kurt LaButti Jasmyn Pangilinan William Andreopoulos Anna Lipzen Juying Yan Mei Wang Vivian Ng Igor V. Grigoriev Igor V. Grigoriev Joseph W. Spatafora Jon K. Magnuson Jon K. Magnuson Jon K. Magnuson Scott E. Baker Scott E. Baker Scott E. Baker Kyle R. Pomraning Kyle R. Pomraning Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces Frontiers in Bioengineering and Biotechnology oleaginous yeasts genome-scale metabolic model flux balance analysis Lipomyces genome sequencing |
| title | Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces |
| title_full | Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces |
| title_fullStr | Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces |
| title_full_unstemmed | Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces |
| title_short | Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces |
| title_sort | genome scale model development and genomic sequencing of the oleaginous clade lipomyces |
| topic | oleaginous yeasts genome-scale metabolic model flux balance analysis Lipomyces genome sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fbioe.2024.1356551/full |
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