Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

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. toru...

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Published inFrontiers in bioengineering and biotechnology Vol. 8; p. 612832
Main Authors Kim, Joonhoon, Coradetti, Samuel T., Kim, Young-Mo, Gao, Yuqian, Yaegashi, Junko, Zucker, Jeremy D., Munoz, Nathalie, Zink, Erika M., Burnum-Johnson, Kristin E., Baker, Scott E., Simmons, Blake A., Skerker, Jeffrey M., Gladden, John M., Magnuson, Jon K.
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Research Foundation 08.01.2021
Frontiers Media S.A
Subjects
09 BIOMASS FUELS
Bioengineering and Biotechnology
genome-scale models
lignocellulosic biomass
metabolic networks
multi-omics
Rhodosporidium toruloides
lignocellulosic biomass
multi-omics
genome-scale models
metabolic networks
Rhodosporidium toruloides
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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.
AbstractList 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.
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.
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.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.
An oleaginous yeast 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 and reconstructed the genome-scale metabolic network of . 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 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 to date.
Author Burnum-Johnson, Kristin E.
Skerker, Jeffrey M.
Gao, Yuqian
Zink, Erika M.
Gladden, John M.
Kim, Joonhoon
Magnuson, Jon K.
Baker, Scott E.
Kim, Young-Mo
Yaegashi, Junko
Munoz, Nathalie
Simmons, Blake A.
Zucker, Jeremy D.
Coradetti, Samuel T.
AuthorAffiliation 2 Department of Energy, Joint BioEnergy Institute , Emeryville, CA , United States
3 Pacific Northwest National Laboratory , Richland, WA , United States
5 Lawrence Berkeley National Laboratory , Berkeley, CA , United States
6 Department of Bioengineering, University of California, Berkeley , Berkeley, CA , United States
1 Department of Energy, Agile BioFoundry , Emeryville, CA , United States
4 Sandia National Laboratories , Livermore, CA , United States
AuthorAffiliation_xml – name: 4 Sandia National Laboratories , Livermore, CA , United States
– name: 6 Department of Bioengineering, University of California, Berkeley , Berkeley, CA , United States
– name: 5 Lawrence Berkeley National Laboratory , Berkeley, CA , United States
– name: 3 Pacific Northwest National Laboratory , Richland, WA , United States
– name: 2 Department of Energy, Joint BioEnergy Institute , Emeryville, CA , United States
– name: 1 Department of Energy, Agile BioFoundry , Emeryville, CA , United States
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Copyright Copyright © 2021 Kim, Coradetti, Kim, Gao, Yaegashi, Zucker, Munoz, Zink, Burnum-Johnson, Baker, Simmons, Skerker, Gladden and Magnuson.
Copyright © 2021 Kim, Coradetti, Kim, Gao, Yaegashi, Zucker, Munoz, Zink, Burnum-Johnson, Baker, Simmons, Skerker, Gladden and Magnuson. 2021 Kim, Coradetti, Kim, Gao, Yaegashi, Zucker, Munoz, Zink, Burnum-Johnson, Baker, Simmons, Skerker, Gladden and Magnuson
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Keywords lignocellulosic biomass
multi-omics
genome-scale models
metabolic networks
Rhodosporidium toruloides
Language English
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Edited by: Dong-Yup Lee, Sungkyunkwan University, South Korea
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Snippet An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we...
An oleaginous yeast is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of...
An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we...
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SubjectTerms 09 BIOMASS FUELS
Bioengineering and Biotechnology
genome-scale models
lignocellulosic biomass
metabolic networks
multi-omics
Rhodosporidium toruloides
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Title Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides
URI https://www.ncbi.nlm.nih.gov/pubmed/33585414
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