Frontiers in Bioengineering and Biotechnology (Jan 2021)
Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides
- Joonhoon Kim,
- Joonhoon Kim,
- Joonhoon Kim,
- Samuel T. Coradetti,
- Samuel T. Coradetti,
- Young-Mo Kim,
- Young-Mo Kim,
- Yuqian Gao,
- Yuqian Gao,
- Junko Yaegashi,
- Junko Yaegashi,
- Jeremy D. Zucker,
- Jeremy D. Zucker,
- Nathalie Munoz,
- Nathalie Munoz,
- Erika M. Zink,
- Kristin E. Burnum-Johnson,
- Kristin E. Burnum-Johnson,
- Scott E. Baker,
- Scott E. Baker,
- Scott E. Baker,
- Blake A. Simmons,
- Blake A. Simmons,
- Blake A. Simmons,
- Jeffrey M. Skerker,
- John M. Gladden,
- John M. Gladden,
- John M. Gladden,
- Jon K. Magnuson,
- Jon K. Magnuson,
- Jon K. Magnuson
Affiliations
- Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Joonhoon Kim
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States
- Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
- Samuel T. Coradetti
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Samuel T. Coradetti
- Sandia National Laboratories, Livermore, CA, United States
- Young-Mo Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
- Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, United States
- Junko Yaegashi
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States
- Junko Yaegashi
- Pacific Northwest National Laboratory, Richland, WA, United States
- Jeremy D. Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Jeremy D. Zucker
- Pacific Northwest National Laboratory, Richland, WA, United States
- Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, United States
- Erika M. Zink
- Pacific Northwest National Laboratory, Richland, WA, United States
- Kristin E. Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Kristin E. Burnum-Johnson
- Pacific Northwest National Laboratory, Richland, WA, United States
- Scott E. Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Scott E. Baker
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States
- Scott E. Baker
- Pacific Northwest National Laboratory, Richland, WA, United States
- Blake A. Simmons
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Blake A. Simmons
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States
- Blake A. Simmons
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Jeffrey M. Skerker
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- John M. Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- John M. Gladden
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States
- John M. Gladden
- Sandia National Laboratories, Livermore, CA, United States
- Jon K. Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Jon K. Magnuson
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States
- Jon K. Magnuson
- Pacific Northwest National Laboratory, Richland, WA, United States
- DOI
- https://doi.org/10.3389/fbioe.2020.612832
- Journal volume & issue
-
Vol. 8
Abstract
An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides. High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.
Keywords
- Rhodosporidium toruloides
- multi-omics
- metabolic networks
- genome-scale models
- lignocellulosic biomass
