Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts

Coradetti, Samuel T.; Adamczyk, Paul A.; Liu, Di; Gao, Yuqian; Otoupal, Peter B.; Geiselman, Gina M.; Webb-Robertson, Bobbie-Jo M.; Burnet, Meagan C.; Kim, Young-Mo; Burnum-Johnson, Kristin E.; Magnuson, Jon; Gladden, John M.

doi:10.1186/s12934-023-02148-5

Title: Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts

Journal Article · 03 August 2023 · Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-023-02148-5 · OSTI ID:1993646

Coradetti, Samuel T.; Adamczyk, Paul A.; Liu, Di; Gao, Yuqian; Otoupal, Peter B.; Geiselman, Gina M.; Webb-Robertson, Bobbie-Jo M.; Burnet, Meagan C.; Kim, Young-Mo; Burnum-Johnson, Kristin E.; Magnuson, Jon; Gladden, John M.

Abstract Efficient conversion of pentose sugars remains a significant barrier to the replacement of petroleum-derived chemicals with plant biomass-derived bioproducts. While the oleaginous yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides ) has a relatively robust native metabolism of pentose sugars compared to other wild yeasts, faster assimilation of those sugars will be required for industrial utilization of pentoses. To increase the rate of pentose assimilation in R. toruloides, we leveraged previously reported high-throughput fitness data to identify potential regulators of pentose catabolism. Two genes were selected for further investigation, a putative transcription factor (RTO4_12978, Pnt1) and a homolog of a glucose transceptor involved in carbon catabolite repression (RTO4_11990). Overexpression of Pnt1 increased the specific growth rate approximately twofold early in cultures on xylose and increased the maximum specific growth by 18% while decreasing accumulation of arabitol and xylitol in fast-growing cultures. Improved growth dynamics on xylose translated to a 120% increase in the overall rate of xylose conversion to fatty alcohols in batch culture. Proteomic analysis confirmed that Pnt1 is a major regulator of pentose catabolism in R. toruloides. Deletion of RTO4_11990 increased the growth rate on xylose, but did not relieve carbon catabolite repression in the presence of glucose. Carbon catabolite repression signaling networks remain poorly characterized in R. toruloides and likely comprise a different set of proteins than those mainly characterized in ascomycete fungi.

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Research Organization:: Environmental Molecular Sciences Laboratory (EMSL), Richland, WA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Sandia National Laboratories (SNL-CA), Livermore, CA (United States)

Sponsoring Organization:: USDOE; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830; NA0003525

OSTI ID:: 1993646

Report Number(s):: PNNL-SA--177272; SAND--2023-09654J; 144; PII: 2148

Journal Information:: Microbial Cell Factories, Journal Name: Microbial Cell Factories Journal Issue: 1 Vol. 22; ISSN 1475-2859

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (59)

Enabling xylose utilization in Yarrowia lipolytica for lipid production Li, Haibo; Alper, Hal S. Biotechnology Journal, Vol. 11, Issue 9 https://doi.org/10.1002/biot.201600210	journal	July 2016
The baffled microtiter plate: Increased oxygen transfer and improved online monitoring in small scale fermentations Funke, Matthias; Diederichs, Sylvia; Kensy, Frank Biotechnology and Bioengineering, Vol. 103, Issue 6 https://doi.org/10.1002/bit.22341	journal	August 2009
Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides Liu, Di; Geiselman, Gina M.; Coradetti, Samuel Biotechnology and Bioengineering, Vol. 117, Issue 5 https://doi.org/10.1002/bit.27285	journal	February 2020
A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments Matzke, Melissa M.; Brown, Joseph N.; Gritsenko, Marina A. PROTEOMICS, Vol. 13, Issue 3-4 https://doi.org/10.1002/pmic.201200269	journal	November 2012
Cloning and evaluation of different constitutive promoters in the oleaginous yeast Rhodosporidium toruloides : Evaluation of five constitutive promoters in Wang, Yanan; Lin, Xinping; Zhang, Sufang Yeast, Vol. 33, Issue 3 https://doi.org/10.1002/yea.3145	journal	January 2016
The zinc cluster transcriptional regulator Asg1 transcriptionally coordinates oleate utilization and lipid accumulation in Saccharomyces cerevisiae Jansuriyakul, Siripat; Somboon, Pichayada; Rodboon, Napachai Applied Microbiology and Biotechnology, Vol. 100, Issue 10 https://doi.org/10.1007/s00253-016-7356-4	journal	February 2016
Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation Zhang, Shuyan; Ito, Masakazu; Skerker, Jeffrey M. Applied Microbiology and Biotechnology, Vol. 100, Issue 21 https://doi.org/10.1007/s00253-016-7815-y	journal	September 2016
Production of d-arabitol from d-xylose by the oleaginous yeast Rhodosporidium toruloides IFO0880 Jagtap, Sujit Sadashiv; Rao, Christopher V. Applied Microbiology and Biotechnology, Vol. 102, Issue 1 https://doi.org/10.1007/s00253-017-8581-1	journal	November 2017
Induction of resistance mechanisms in Rhodotorula toruloides for growth in sugarcane hydrolysate with high inhibitor content Lopes, Helberth Júnnior Santos; Bonturi, Nemailla; Miranda, Everson Alves Applied Microbiology and Biotechnology, Vol. 105, Issue 24 https://doi.org/10.1007/s00253-021-11687-z	journal	November 2021
Fatty alcohols production by oleaginous yeast Fillet, Sandy; Gibert, Jordi; Suárez, Beatriz Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 11 https://doi.org/10.1007/s10295-015-1674-x	journal	August 2015
Rhodotorula toruloides: an ideal microbial cell factory to produce oleochemicals, carotenoids, and other products Zhao, Yu; Song, Baocai; Li, Jing World Journal of Microbiology and Biotechnology, Vol. 38, Issue 1 https://doi.org/10.1007/s11274-021-03201-4	journal	December 2021
Insights from enzymatic degradation of cellulose and hemicellulose to fermentable sugars– a review Houfani, Aicha Asma; Anders, Nico; Spiess, Antje C. Biomass and Bioenergy, Vol. 134 https://doi.org/10.1016/j.biombioe.2020.105481	journal	March 2020
Adaptive laboratory evolution of Rhodosporidium toruloides to inhibitors derived from lignocellulosic biomass and genetic variations behind evolution Liu, Zhijia; Radi, Mohammad; Mohamed, Elsayed T. T. Bioresource Technology, Vol. 333 https://doi.org/10.1016/j.biortech.2021.125171	journal	August 2021
MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC–MS(/MS) features Monroe, Matthew E.; Shaw, Jason L.; Daly, Don S. Computational Biology and Chemistry, Vol. 32, Issue 3 https://doi.org/10.1016/j.compbiolchem.2008.02.006	journal	June 2008
Harnessing xylose pathways for biofuels production Li, Xiaowei; Chen, Yun; Nielsen, Jens Current Opinion in Biotechnology, Vol. 57 https://doi.org/10.1016/j.copbio.2019.01.006	journal	June 2019
Direct production of fatty alcohols from glucose using engineered strains of Yarrowia lipolytica Cordova, Lauren T.; Butler, Jonathan; Alper, Hal S. Metabolic Engineering Communications, Vol. 10 https://doi.org/10.1016/j.mec.2019.e00105	journal	June 2020
Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks d’Espaux, Leo; Ghosh, Amit; Runguphan, Weerawat Metabolic Engineering, Vol. 42 https://doi.org/10.1016/j.ymben.2017.06.004	journal	July 2017
Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics Callister, Stephen J.; Barry, Richard C.; Adkins, Joshua N. Journal of Proteome Research, Vol. 5, Issue 2 https://doi.org/10.1021/pr050300l	journal	February 2006
Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data Webb-Robertson, Bobbie-Jo M.; McCue, Lee Ann; Waters, Katrina M. Journal of Proteome Research, Vol. 9, Issue 11 https://doi.org/10.1021/pr1005247	journal	November 2010
ProteomeXchange provides globally coordinated proteomics data submission and dissemination Vizcaíno, Juan A.; Deutsch, Eric W.; Wang, Rui Nature Biotechnology, Vol. 32, Issue 3 https://doi.org/10.1038/nbt.2839	journal	March 2014
MS-GF+ makes progress towards a universal database search tool for proteomics Kim, Sangtae; Pevzner, Pavel A. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6277	journal	October 2014
EUF1 – a newly identified gene involved in erythritol utilization in Yarrowia lipolytica Rzechonek, Dorota A.; Neuvéglise, Cécile; Devillers, Hugo Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12715-7	journal	October 2017
DMR (deacetylation and mechanical refining) processing of corn stover achieves high monomeric sugar concentrations (230 g L ⁻¹ ) during enzymatic hydrolysis and high ethanol concentrations (>10% v/v) during fermentation without hydrolysate purification or concentration Chen, Xiaowen; Kuhn, Erik; Jennings, Edward W. Energy & Environmental Science, Vol. 9, Issue 4 https://doi.org/10.1039/C5EE03718B	journal	January 2016
Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides Wehrs, Maren; Gladden, John M.; Liu, Yuzhong Green Chemistry, Vol. 21, Issue 12 https://doi.org/10.1039/C9GC00920E	journal	January 2019
Engineering of yeast hexose transporters to transport D-xylose without inhibition by D-glucose Farwick, A.; Bruder, S.; Schadeweg, V. Proceedings of the National Academy of Sciences, Vol. 111, Issue 14 https://doi.org/10.1073/pnas.1323464111	journal	March 2014
The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus Wu, Vincent W.; Thieme, Nils; Huberman, Lori B. Proceedings of the National Academy of Sciences, Vol. 117, Issue 11 https://doi.org/10.1073/pnas.1915611117	journal	February 2020
Two glucose transporters in Saccharomyces cerevisiae are glucose sensors that generate a signal for induction of gene expression. Ozcan, S.; Dover, J.; Rosenwald, A. G. Proceedings of the National Academy of Sciences, Vol. 93, Issue 22 https://doi.org/10.1073/pnas.93.22.12428	journal	October 1996
Saccharomyces cerevisiae Forms d-2-Hydroxyglutarate and Couples Its Degradation to d-Lactate Formation via a Cytosolic Transhydrogenase Becker-Kettern, Julia; Paczia, Nicole; Conrotte, Jean-François Journal of Biological Chemistry, Vol. 291, Issue 12 https://doi.org/10.1074/jbc.M115.704494	journal	March 2016
DAnTE: a statistical tool for quantitative analysis of -omics data Polpitiya, A. D.; Qian, W. -J.; Jaitly, N. Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn217	journal	May 2008
Improved quality control processing of peptide-centric LC-MS proteomics data Matzke, Melissa M.; Waters, Katrina M.; Metz, Thomas O. Bioinformatics, Vol. 27, Issue 20 https://doi.org/10.1093/bioinformatics/btr479	journal	August 2011
Cha4p of Saccharomyces cerevisiae Activates Transcription Via Serine/Threonine Response Elements Holmberg, Steen; Schjerling, Peter Genetics, Vol. 144, Issue 2 https://doi.org/10.1093/genetics/144.2.467	journal	October 1996
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix Price, M. N.; Dehal, P. S.; Arkin, A. P. Molecular Biology and Evolution, Vol. 26, Issue 7 https://doi.org/10.1093/molbev/msp077	journal	April 2009
UniProt: the universal protein knowledgebase in 2021 Bateman, Alex; Martin, Maria-Jesus; Orchard, Sandra Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1100	journal	November 2020
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 49, Issue W1 https://doi.org/10.1093/nar/gkab301	journal	April 2021
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Katoh, K. Nucleic Acids Research, Vol. 30, Issue 14 https://doi.org/10.1093/nar/gkf436	journal	July 2002
MycoCosm portal: gearing up for 1000 fungal genomes Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1183	journal	December 2013
Metabolic Engineering of Ammonium Assimilation in Xylose-Fermenting Saccharomyces cerevisiae Improves Ethanol Production Roca, Christophe; Nielsen, Jens; Olsson, Lisbeth Applied and Environmental Microbiology, Vol. 69, Issue 8 https://doi.org/10.1128/AEM.69.8.4732-4736.2003	journal	August 2003
Upc2p and Ecm22p, Dual Regulators of Sterol Biosynthesis in Saccharomyces cerevisiae Vik, Åshild; Rine, Jasper Molecular and Cellular Biology, Vol. 21, Issue 19 https://doi.org/10.1128/MCB.21.19.6395-6405.2001	journal	October 2001
A Fungal Family of Transcriptional Regulators: the Zinc Cluster Proteins MacPherson, S.; Larochelle, M.; Turcotte, B. Microbiology and Molecular Biology Reviews, Vol. 70, Issue 3 https://doi.org/10.1128/MMBR.00015-06	journal	September 2006
p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate Eaton, R. W. Journal of Bacteriology, Vol. 179, Issue 10 https://doi.org/10.1128/jb.179.10.3171-3180.1997	journal	May 1997
Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides Otoupal, Peter B.; Ito, Masakazu; Arkin, Adam P. mSphere, Vol. 4, Issue 2 https://doi.org/10.1128/mSphere.00099-19	journal	March 2019
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C. mSystems, Vol. 1, Issue 3 https://doi.org/10.1128/mSystems.00043-16	journal	May 2016
Molecular characterization of KU70 and KU80 homologues and exploitation of a KU70-deficient mutant for improving gene deletion frequency in Rhodosporidium toruloides Koh, Chong Mei; Liu, Yanbin BMC Microbiology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2180-14-50	journal	January 2014
Lipid production in batch and fed-batch cultures of Rhodosporidium toruloidesfrom 5 and 6 carbon carbohydrates Wiebe, Marilyn G.; Koivuranta, Kari; Penttilä, Merja BMC Biotechnology, Vol. 12, Issue 1 https://doi.org/10.1186/1472-6750-12-26	journal	May 2012
Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae Salusjärvi, Laura; Kankainen, Matti; Soliymani, Rabah Microbial Cell Factories, Vol. 7, Issue 1 https://doi.org/10.1186/1475-2859-7-18	journal	January 2008
Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose Guo, Weihua; Sheng, Jiayuan; Zhao, Huimin Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0423-9	journal	February 2016
Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks Geiselman, Gina M.; Kirby, James; Landera, Alexander Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01456-4	journal	November 2020
Fatty alcohol production in Lipomyces starkeyi and Yarrowia lipolytica Wang, Wei; Wei, Hui; Knoshaug, Eric Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0647-2	journal	October 2016
Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression Wang, Bang; Li, Jingen; Gao, Jingfang Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0705-4	journal	January 2017
Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts Yaegashi, Junko; Kirby, James; Ito, Masakazu Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0927-5	journal	October 2017
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways King, Zachary A.; Dräger, Andreas; Ebrahim, Ali PLOS Computational Biology, Vol. 11, Issue 8 https://doi.org/10.1371/journal.pcbi.1004321	journal	August 2015
The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs Olgeiser, Lilli; Haag, Carl; Boerner, Susan EMBO reports, Vol. 20, Issue 1 https://doi.org/10.15252/embr.201846588	journal	December 2018
Nutritional Control of Growth and Development in Yeast Broach, James R. Genetics, Vol. 192, Issue 1 https://doi.org/10.1534/genetics.111.135731	journal	September 2012
High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces Alexander, W. G.; Doering, D. T.; Hittinger, C. T. Genetics, Vol. 198, Issue 3, p. 859-866 https://doi.org/10.1534/genetics.114.170118	journal	September 2014
Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides Kim, Joonhoon; Coradetti, Samuel T.; Kim, Young-Mo Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.612832	journal	January 2021
Screening and Growth Characterization of Non-conventional Yeasts in a Hemicellulosic Hydrolysate Monteiro de Oliveira, Paola; Aborneva, Daria; Bonturi, Nemailla Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.659472	journal	April 2021
A Role of a Newly Identified Isomerase From Yarrowia lipolytica in Erythritol Catabolism Mirończuk, Aleksandra M.; Biegalska, Anna; Zugaj, Karolina Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01122	journal	May 2018
Evaluating the Potential of Rhodosporidium toruloides-1588 for High Lipid Production Using Undetoxified Wood Hydrolysate as a Carbon Source Saini, Rahul; Hegde, Krishnamoorthy; Osorio-Gonzalez, Carlos Saul Energies, Vol. 13, Issue 22 https://doi.org/10.3390/en13225960	journal	November 2020
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides Coradetti, Samuel T.; Pinel, Dominic; Geiselman, Gina M. eLife, Vol. 7 https://doi.org/10.7554/eLife.32110	journal	March 2018

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59 BASIC BIOLOGICAL SCIENCES
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Title: Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts

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