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Title: Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides

Abstract

Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. The red basidiomycete yeast Rhodosporidium toruloides is a promising and robust host for lipid- and terpene-derived chemicals. Previous studies demonstrated assimilation of a range of substrates, from C 5/C 6 sugars to aromatic molecules similar to lignin monomers. In the current study, we analyzed the potential of R. toruloides to assimilate d-galacturonic acid, a major sugar in many pectin-rich agricultural waste streams, including sugar beet pulp and citrus peels. d-Galacturonic acid is not a preferred substrate for many fungi, but its metabolism was found to be on par with those of d-glucose and d-xylose in R. toruloides. A genomewide analysis by combined transcriptome sequencing (RNA-seq) and RB-TDNA-seq revealed those genes with high relevance for fitness on d-galacturonic acid. While R. toruloides was found to utilize the nonphosphorylative catabolic pathway known from ascomycetes, the maximal velocities of several enzymes exceeded those previously reported. Inmore » addition, an efficient downstream glycerol catabolism and a novel transcription factor were found to be important for d-galacturonic acid utilization. These results set the basis for use of R. toruloides as a potential host for pectin-rich waste conversions and demonstrate its suitability as a model for metabolic studies with basidiomycetes. The switch from the traditional fossil-based industry to a green and sustainable bioeconomy demands the complete utilization of renewable feedstocks. Many currently used bioconversion hosts are unable to utilize major components of plant biomass, warranting the identification of microorganisms with broader catabolic capacity and characterization of their unique biochemical pathways. d-Galacturonic acid is a plant component of bioconversion interest and is the major backbone sugar of pectin, a plant cell wall polysaccharide abundant in soft and young plant tissues. The red basidiomycete and oleaginous yeast Rhodosporidium toruloides has been previously shown to utilize a range of sugars and aromatic molecules. Using state-of-the-art functional genomic methods and physiological and biochemical assays, we elucidated the molecular basis underlying the efficient metabolism of d-galacturonic acid. This study identified an efficient pathway for uronic acid conversion to guide future engineering efforts and represents the first detailed metabolic analysis of pectin metabolism in a basidiomycete fungus.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3];  [2];  [2]; ORCiD logo [2];  [3]; ORCiD logo [4]; ORCiD logo [4]; ORCiD logo [4]; ORCiD logo [2];  [5]
  1. Univ. of California, Berkeley, CA (United States); Energy Biosciences Inst., Berkeley, CA (United States)
  2. Technische Univ. München, Freising (Germany)
  3. Energy Biosciences Inst., Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Energy Biosciences Inst., Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. Univ. of Queensland, Brisbane, QLD (Australia)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF)
OSTI Identifier:
1591856
Grant/Contract Number:  
AC02-05CH11231; 1330914; OO1605; OO6J01
Resource Type:
Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 4; Journal Issue: 6; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Rhodosporidium toruloides; aerobic catabolism; carbon metabolism; galacturonic acid; yeasts

Citation Formats

Protzko, Ryan J., Hach, Christina A., Coradetti, Samuel T., Hackhofer, Magdalena A., Magosch, Sonja, Thieme, Nils, Geiselman, Gina M., Arkin, Adam P., Skerker, Jeffrey M., Dueber, John E., Benz, J. Philipp, and Vickers, Claudia. Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides. United States: N. p., 2019. Web. doi:10.1128/mSystems.00389-19.
Protzko, Ryan J., Hach, Christina A., Coradetti, Samuel T., Hackhofer, Magdalena A., Magosch, Sonja, Thieme, Nils, Geiselman, Gina M., Arkin, Adam P., Skerker, Jeffrey M., Dueber, John E., Benz, J. Philipp, & Vickers, Claudia. Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides. United States. doi:10.1128/mSystems.00389-19.
Protzko, Ryan J., Hach, Christina A., Coradetti, Samuel T., Hackhofer, Magdalena A., Magosch, Sonja, Thieme, Nils, Geiselman, Gina M., Arkin, Adam P., Skerker, Jeffrey M., Dueber, John E., Benz, J. Philipp, and Vickers, Claudia. Tue . "Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides". United States. doi:10.1128/mSystems.00389-19. https://www.osti.gov/servlets/purl/1591856.
@article{osti_1591856,
title = {Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides},
author = {Protzko, Ryan J. and Hach, Christina A. and Coradetti, Samuel T. and Hackhofer, Magdalena A. and Magosch, Sonja and Thieme, Nils and Geiselman, Gina M. and Arkin, Adam P. and Skerker, Jeffrey M. and Dueber, John E. and Benz, J. Philipp and Vickers, Claudia},
abstractNote = {Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. The red basidiomycete yeast Rhodosporidium toruloides is a promising and robust host for lipid- and terpene-derived chemicals. Previous studies demonstrated assimilation of a range of substrates, from C5/C6 sugars to aromatic molecules similar to lignin monomers. In the current study, we analyzed the potential of R. toruloides to assimilate d-galacturonic acid, a major sugar in many pectin-rich agricultural waste streams, including sugar beet pulp and citrus peels. d-Galacturonic acid is not a preferred substrate for many fungi, but its metabolism was found to be on par with those of d-glucose and d-xylose in R. toruloides. A genomewide analysis by combined transcriptome sequencing (RNA-seq) and RB-TDNA-seq revealed those genes with high relevance for fitness on d-galacturonic acid. While R. toruloides was found to utilize the nonphosphorylative catabolic pathway known from ascomycetes, the maximal velocities of several enzymes exceeded those previously reported. In addition, an efficient downstream glycerol catabolism and a novel transcription factor were found to be important for d-galacturonic acid utilization. These results set the basis for use of R. toruloides as a potential host for pectin-rich waste conversions and demonstrate its suitability as a model for metabolic studies with basidiomycetes. The switch from the traditional fossil-based industry to a green and sustainable bioeconomy demands the complete utilization of renewable feedstocks. Many currently used bioconversion hosts are unable to utilize major components of plant biomass, warranting the identification of microorganisms with broader catabolic capacity and characterization of their unique biochemical pathways. d-Galacturonic acid is a plant component of bioconversion interest and is the major backbone sugar of pectin, a plant cell wall polysaccharide abundant in soft and young plant tissues. The red basidiomycete and oleaginous yeast Rhodosporidium toruloides has been previously shown to utilize a range of sugars and aromatic molecules. Using state-of-the-art functional genomic methods and physiological and biochemical assays, we elucidated the molecular basis underlying the efficient metabolism of d-galacturonic acid. This study identified an efficient pathway for uronic acid conversion to guide future engineering efforts and represents the first detailed metabolic analysis of pectin metabolism in a basidiomycete fungus.},
doi = {10.1128/mSystems.00389-19},
journal = {mSystems},
number = 6,
volume = 4,
place = {United States},
year = {2019},
month = {12}
}

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