DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

; ; ; ; ; ; ; ; ; ;
Publication Date:
Sponsoring Org.:
OSTI Identifier:
Resource Type:
Published Article
Journal Name:
Metabolic Engineering Communications
Additional Journal Information:
Journal Name: Metabolic Engineering Communications Journal Volume: 9 Journal Issue: C; Journal ID: ISSN 2214-0301
Country of Publication:

Citation Formats

Dinh, Hoang V., Suthers, Patrick F., Chan, Siu Hung Joshua, Shen, Yihui, Xiao, Tianxia, Deewan, Anshu, Jagtap, Sujit S., Zhao, Huimin, Rao, Christopher V., Rabinowitz, Joshua D., and Maranas, Costas D. A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. Netherlands: N. p., 2019. Web. doi:10.1016/j.mec.2019.e00101.
Dinh, Hoang V., Suthers, Patrick F., Chan, Siu Hung Joshua, Shen, Yihui, Xiao, Tianxia, Deewan, Anshu, Jagtap, Sujit S., Zhao, Huimin, Rao, Christopher V., Rabinowitz, Joshua D., & Maranas, Costas D. A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. Netherlands.
Dinh, Hoang V., Suthers, Patrick F., Chan, Siu Hung Joshua, Shen, Yihui, Xiao, Tianxia, Deewan, Anshu, Jagtap, Sujit S., Zhao, Huimin, Rao, Christopher V., Rabinowitz, Joshua D., and Maranas, Costas D. Sun . "A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data". Netherlands.
title = {A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data},
author = {Dinh, Hoang V. and Suthers, Patrick F. and Chan, Siu Hung Joshua and Shen, Yihui and Xiao, Tianxia and Deewan, Anshu and Jagtap, Sujit S. and Zhao, Huimin and Rao, Christopher V. and Rabinowitz, Joshua D. and Maranas, Costas D.},
abstractNote = {},
doi = {10.1016/j.mec.2019.e00101},
journal = {Metabolic Engineering Communications},
number = C,
volume = 9,
place = {Netherlands},
year = {2019},
month = {12}

Works referenced in this record:

Metabolic network analysis and experimental study of lipid production in Rhodosporidium toruloides grown on single and mixed substrates
journal, March 2015

  • Bommareddy, Rajesh Reddy; Sabra, Wael; Maheshwari, Garima
  • Microbial Cell Factories, Vol. 14, Issue 1
  • DOI: 10.1186/s12934-015-0217-5

Transcriptional regulation is insufficient to explain substrate‐induced flux changes in Bacillus subtilis
journal, January 2013

  • Chubukov, Victor; Uhr, Markus; Le Chat, Ludovic
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.66

Stabilization of d-amino acid oxidase from Rhodosporidium toruloides by immobilization onto magnetic nanoparticles
journal, December 2008

Compositional profiles of Rhodosporidium toruloides cells under nutrient limitation
journal, February 2017

  • Shen, Hongwei; Zhang, Xibin; Gong, Zhiwei
  • Applied Microbiology and Biotechnology, Vol. 101, Issue 9
  • DOI: 10.1007/s00253-017-8157-0

Engineering Rhodosporidium toruloides with a membrane transporter facilitates production and separation of carotenoids and lipids in a bi-phasic culture
journal, November 2015

  • Lee, Jaslyn J. L.; Chen, Liwei; Cao, Bin
  • Applied Microbiology and Biotechnology, Vol. 100, Issue 2
  • DOI: 10.1007/s00253-015-7102-3

Kinetics of continuous cultivation of the oleaginous yeast Rhodosporidium toruloides
journal, October 2013

Constructing kinetic models of metabolism at genome-scales: A review
journal, September 2015

  • Srinivasan, Shyam; Cluett, William R.; Mahadevan, Radhakrishnan
  • Biotechnology Journal, Vol. 10, Issue 9
  • DOI: 10.1002/biot.201400522

Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica
journal, March 2016

  • Kerkhoven, Eduard J.; Pomraning, Kyle R.; Baker, Scott E.
  • npj Systems Biology and Applications, Vol. 2, Issue 1
  • DOI: 10.1038/npjsba.2016.5

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
journal, October 2015

  • King, Zachary A.; Lu, Justin; Dräger, Andreas
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1049

Connecting extracellular metabolomic measurements to intracellular flux states in yeast
journal, January 2009

  • Mo, Monica L.; Palsson, Bernhard Ø; Herrgård, Markus J.
  • BMC Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1186/1752-0509-3-37

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts
journal, September 2012

STAR: ultrafast universal RNA-seq aligner
journal, October 2012

High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

  • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1672

Oleaginous yeast: a value-added platform for renewable oils
journal, July 2015

  • Probst, Kyle V.; Schulte, Leslie R.; Durrett, Timothy P.
  • Critical Reviews in Biotechnology, Vol. 36, Issue 5
  • DOI: 10.3109/07388551.2015.1064855

Genome-scale modeling of yeast: chronology, applications and critical perspectives
journal, July 2017

Lipid production in batch and fed-batch cultures of Rhodosporidium toruloidesfrom 5 and 6 carbon carbohydrates
journal, May 2012

  • Wiebe, Marilyn G.; Koivuranta, Kari; Penttilä, Merja
  • BMC Biotechnology, Vol. 12, Issue 1
  • DOI: 10.1186/1472-6750-12-26

Architecture and Biosynthesis of the Saccharomyces cerevisiae Cell Wall
journal, November 2012

Bilevel optimization techniques in computational strain design
journal, January 2015

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation
journal, September 2016

  • Zhang, Shuyan; Ito, Masakazu; Skerker, Jeffrey M.
  • Applied Microbiology and Biotechnology, Vol. 100, Issue 21
  • DOI: 10.1007/s00253-016-7815-y

Possible regulatory roles of ATP:citrate lyase, malic enzyme, and AMP deaminase in lipid accumulation by Rhodosporidium toruloides CBS 14
journal, November 1985

  • Evans, Christopher Thomas; Ratledge, Colin
  • Canadian Journal of Microbiology, Vol. 31, Issue 11
  • DOI: 10.1139/m85-189

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
journal, March 2018

  • Coradetti, Samuel T.; Pinel, Dominic; Geiselman, Gina M.
  • eLife, Vol. 7
  • DOI: 10.7554/eLife.32110

Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
journal, December 2016

  • Khodayari, Ali; Maranas, Costas D.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13806

Dihydroxyacetone Kinases in Saccharomyces cerevisiae Are Involved in Detoxification of Dihydroxyacetone
journal, October 2002

  • Molin, Mikael; Norbeck, Joakim; Blomberg, Anders
  • Journal of Biological Chemistry, Vol. 278, Issue 3
  • DOI: 10.1074/jbc.M203030200

Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol
journal, December 2017

Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models
journal, July 2017

The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications
journal, March 2018

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
journal, October 2003

Diversity and origin of alternative NADH:ubiquinone oxidoreductases
journal, August 2000

Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes
journal, June 2012

  • Tamano, Koichi; Bruno, Kenneth S.; Karagiosis, Sue A.
  • Applied Microbiology and Biotechnology, Vol. 97, Issue 1
  • DOI: 10.1007/s00253-012-4193-y

Characterizing the metabolic phenotype: A phenotype phase plane analysis
journal, December 2001

  • Edwards, Jeremy S.; Ramakrishna, Ramprasad; Palsson, Bernhard O.
  • Biotechnology and Bioengineering, Vol. 77, Issue 1, p. 27-36
  • DOI: 10.1002/bit.10047

Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production
journal, January 2013

Production of d-arabitol from d-xylose by the oleaginous yeast Rhodosporidium toruloides IFO0880
journal, November 2017

  • Jagtap, Sujit Sadashiv; Rao, Christopher V.
  • Applied Microbiology and Biotechnology, Vol. 102, Issue 1
  • DOI: 10.1007/s00253-017-8581-1

Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
journal, January 2013

  • Mueller, Thomas J.; Berla, Bertram M.; Pakrasi, Himadri B.
  • BMC Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1752-0509-7-142

Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models
journal, September 2015

  • Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas
  • Metabolites, Vol. 5, Issue 4
  • DOI: 10.3390/metabo5040536

Eighteen new oleaginous yeast species
journal, April 2016

  • Garay, Luis A.; Sitepu, Irnayuli R.; Cajka, Tomas
  • Journal of Industrial Microbiology & Biotechnology, Vol. 43, Issue 7
  • DOI: 10.1007/s10295-016-1765-3

The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica
journal, July 2015

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
journal, January 2004

  • Koonin, Eugene V.; Fedorova, Natalie D.; Jackson, John D.
  • Genome Biology, Vol. 5, Issue 2
  • DOI: 10.1186/gb-2004-5-2-r7

Microbial lipid production by Rhodosporidium toruloides under sulfate-limited conditions
journal, January 2011

Cell Wall-Related Bionumbers and Bioestimates of Saccharomyces cerevisiae and Candida albicans
journal, November 2013

  • Klis, Frans M.; de Koster, Chris G.; Brul, Stanley
  • Eukaryotic Cell, Vol. 13, Issue 1
  • DOI: 10.1128/EC.00250-13

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
journal, April 2010

  • Ranganathan, Sridhar; Suthers, Patrick F.; Maranas, Costas D.
  • PLoS Computational Biology, Vol. 6, Issue 4
  • DOI: 10.1371/journal.pcbi.1000744

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes
journal, January 2017

Atg22 Recycles Amino Acids to Link the Degradative and Recycling Functions of Autophagy
journal, December 2006

  • Yang, Zhifen; Huang, Ju; Geng, Jiefei
  • Molecular Biology of the Cell, Vol. 17, Issue 12
  • DOI: 10.1091/mbc.e06-06-0479

Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols
journal, June 2018

  • Ferreira, Raphael; Teixeira, Paulo Gonçalves; Gossing, Michael
  • Metabolic Engineering Communications, Vol. 6
  • DOI: 10.1016/j.meteno.2018.01.002

Improving prediction fidelity of cellular metabolism with kinetic descriptions
journal, December 2015

COBRApy: COnstraints-Based Reconstruction and Analysis for Python
journal, January 2013

  • Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard O.
  • BMC Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1752-0509-7-74

The biomass objective function
journal, June 2010

The proteome analysis of oleaginous yeast Lipomyces starkeyi: Comparative proteomic analysis of Lipomyces starkeyi
journal, October 2010

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories
journal, November 2015

  • Maia, Paulo; Rocha, Miguel; Rocha, Isabel
  • Microbiology and Molecular Biology Reviews, Vol. 80, Issue 1
  • DOI: 10.1128/MMBR.00014-15

CDD: NCBI's conserved domain database
journal, November 2014

  • Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1221

A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010

The biochemistry of peroxisomal β-oxidation in the yeast Saccharomyces cerevisiae
journal, April 2003

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

  • Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
  • Nature Biotechnology, Vol. 36, Issue 7
  • DOI: 10.1038/nbt.4163 and MIRIAM Registry: community resources to provide persistent identification
journal, December 2011

  • Juty, N.; Le Novere, N.; Laibe, C.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1097

An overview of lipid metabolism in yeasts and its impact on biotechnological processes
journal, March 2011

  • Beopoulos, Athanasios; Nicaud, Jean-Marc; Gaillardin, Claude
  • Applied Microbiology and Biotechnology, Vol. 90, Issue 4, p. 1193-1206
  • DOI: 10.1007/s00253-011-3212-8

Statistical reconciliation of the elemental and molecular biomass composition ofSaccharomyces cerevisiae
journal, January 2001

  • Lange, H. C.; Heijnen, J. J.
  • Biotechnology and Bioengineering, Vol. 75, Issue 3
  • DOI: 10.1002/bit.10054

Using Genome-scale Models to Predict Biological Capabilities
journal, May 2015

Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides
journal, May 2018

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
journal, February 2016

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 11, Issue 1
  • DOI: 10.1186/s40793-016-0138-x

The ethanol-inducible YAT1 gene from yeast encodes a presumptive mitochondrial outer carnitine acetyltransferase.
journal, December 1993

A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
journal, January 2007

  • Feist, Adam M.; Henry, Christopher S.; Reed, Jennifer L.
  • Molecular Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1038/msb4100155

Protein O -Glycosylation in Fungi: Diverse Structures and Multiple Functions
journal, June 2007

  • Goto, Masatoshi
  • Bioscience, Biotechnology, and Biochemistry, Vol. 71, Issue 6
  • DOI: 10.1271/bbb.70080

Rhodosporidium toruloides cultivated in NaCl-enriched glucose-based media: Adaptation dynamics and lipid production
journal, May 2016

  • Tchakouteu, Sidoine Sadjeu; Kopsahelis, Nikolaos; Chatzifragkou, Afroditi
  • Engineering in Life Sciences, Vol. 17, Issue 3
  • DOI: 10.1002/elsc.201500125

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
journal, February 2015

  • Brettin, Thomas; Davis, James J.; Disz, Terry
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep08365

Engineering Rhodosporidium toruloides for increased lipid production : Engineering
journal, November 2015

  • Zhang, Shuyan; Skerker, Jeffrey M.; Rutter, Charles D.
  • Biotechnology and Bioengineering, Vol. 113, Issue 5
  • DOI: 10.1002/bit.25864

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
journal, May 2010

  • Feist, Adam M.; Zielinski, Daniel C.; Orth, Jeffrey D.
  • Metabolic Engineering, Vol. 12, Issue 3, p. 173-186
  • DOI: 10.1016/j.ymben.2009.10.003

DeepLoc: prediction of protein subcellular localization using deep learning
journal, July 2017

  • Almagro Armenteros, José Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae
  • Bioinformatics, Vol. 33, Issue 21
  • DOI: 10.1093/bioinformatics/btx431

Fatty acids from oleaginous yeasts and yeast-like fungi and their potential applications
journal, February 2018

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
journal, August 2015

Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals
journal, November 2017

Torulene and torularhodin: “new” fungal carotenoids for industry?
journal, March 2018

  • Kot, Anna M.; Błażejak, Stanisław; Gientka, Iwona
  • Microbial Cell Factories, Vol. 17, Issue 1
  • DOI: 10.1186/s12934-018-0893-z

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models
journal, February 2011

  • Schellenberger, Jan; Lewis, Nathan E.; Palsson, Bernhard Ø.
  • Biophysical Journal, Vol. 100, Issue 3
  • DOI: 10.1016/j.bpj.2010.12.3707

Systems strategies for developing industrial microbial strains
journal, October 2015

  • Lee, Sang Yup; Kim, Hyun Uk
  • Nature Biotechnology, Vol. 33, Issue 10
  • DOI: 10.1038/nbt.3365

Optimizing genome-scale network reconstructions
journal, May 2014

  • Monk, Jonathan; Nogales, Juan; Palsson, Bernhard O.
  • Nature Biotechnology, Vol. 32, Issue 5
  • DOI: 10.1038/nbt.2870

Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations
journal, September 2015

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
journal, April 2017

  • Fritzemeier, Claus Jonathan; Hartleb, Daniel; Szappanos, Balázs
  • PLOS Computational Biology, Vol. 13, Issue 4
  • DOI: 10.1371/journal.pcbi.1005494

The MetaCyc database of metabolic pathways and enzymes
journal, October 2017

  • Caspi, Ron; Billington, Richard; Fulcher, Carol A.
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx935

Advancing oleaginous microorganisms to produce lipid via metabolic engineering technology
journal, October 2013

What is flux balance analysis?
journal, March 2010

  • Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
  • Nature Biotechnology, Vol. 28, Issue 3
  • DOI: 10.1038/nbt.1614

A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides
journal, January 2012

  • Zhu, Zhiwei; Zhang, Sufang; Liu, Hongwei
  • Nature Communications, Vol. 3, Issue 1
  • DOI: 10.1038/ncomms2112

Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism
journal, August 2013

  • Aung, Hnin W.; Henry, Susan A.; Walker, Larry P.
  • Industrial Biotechnology, Vol. 9, Issue 4
  • DOI: 10.1089/ind.2013.0013

High-density cultivation of oleaginous yeast Rhodosporidium toruloides Y4 in fed-batch culture
journal, August 2007

Optimization of lipid production with a genome-scale model of Yarrowia lipolytica
journal, October 2015

Comprehensive analysis of a metabolic model for lipid production in Rhodosporidium toruloides
journal, August 2018

Effects of biomass hydrolysis by-products on oleaginous yeast Rhodosporidium toruloides
journal, October 2009

Control of Lipid Accumulation in the Yeast Yarrowia lipolytica
journal, October 2008

  • Beopoulos, A.; Mrozova, Z.; Thevenieau, F.
  • Applied and Environmental Microbiology, Vol. 74, Issue 24, p. 7779-7789
  • DOI: 10.1128/AEM.01412-08

Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production
journal, January 2014

  • Blazeck, John; Hill, Andrew; Liu, Leqian
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4131

Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals
journal, February 2014

Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes
journal, December 2014

  • Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih; Leong, Susanna Su Jan
  • Frontiers in Bioengineering and Biotechnology, Vol. 2
  • DOI: 10.3389/fbioe.2014.00078

Next-generation genome-scale models for metabolic engineering
journal, December 2015

Dna base Composition of some Species of Yeasts and Yeast-Like Fungi
journal, January 1971

  • Nakase, Takashi; Komagata, Kazuo
  • The Journal of General and Applied Microbiology, Vol. 17, Issue 5
  • DOI: 10.2323/jgam.17.363

Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica
journal, February 2016

  • Silverman, Andrew M.; Qiao, Kangjian; Xu, Peng
  • Applied Microbiology and Biotechnology, Vol. 100, Issue 8
  • DOI: 10.1007/s00253-016-7376-0