Frontiers in Bioengineering and Biotechnology (Apr 2024)
Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces
- 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
Affiliations
- Jeffrey J. Czajka
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Jeffrey J. Czajka
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- Yichao Han
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Yichao Han
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- Joonhoon Kim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Joonhoon Kim
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- Joonhoon Kim
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
- Stephen J. Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Stephen J. Mondo
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Stephen J. Mondo
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beth A. Hofstad
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Beth A. Hofstad
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- AnaLaura Robles
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- AnaLaura Robles
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Juying Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Mei Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Igor V. Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Jon K. Magnuson
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Jon K. Magnuson
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- Jon K. Magnuson
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
- Scott E. Baker
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- Scott E. Baker
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
- Scott E. Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Kyle R. Pomraning
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- DOI
- https://doi.org/10.3389/fbioe.2024.1356551
- Journal volume & issue
-
Vol. 12
Abstract
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.
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