Methods to Activate and Elucidate Complex Endogenous Sugar Metabolism in Yarrowia lipolytica

Ryu, Seunghyun; Trinh, Cong T.

doi:10.1007/978-1-0716-1414-3_12

Methods to Activate and Elucidate Complex Endogenous Sugar Metabolism in Yarrowia lipolytica

Journal Article · Wed Apr 14 00:00:00 EDT 2021 · Methods in Molecular Biology

DOI:https://doi.org/10.1007/978-1-0716-1414-3_12· OSTI ID:1777841

Ryu, Seunghyun ^[1]; Trinh, Cong T. ^[2]

Univ. of Tennessee, Knoxville, TN (United States); University of Tennessee Knoxville
Univ. of Tennessee, Knoxville, TN (United States)

Yarrowia lipolytica has endogenous metabolism to use complex sugars derived from lignocellulosic biomass. However, many of these pathways are cryptic and hence either inactive or inefficient for xylose, arabinose, and cellobiose assimilation. Furthermore, we present collective methods to activate and elucidate these endogenous sugar pathways by performing short-term growth adaptation, determining the pathway efficiency, and conducting transcriptomic, enzymatic, and metabolic analyses to identify rate limiting steps for enhanced sugar consumption.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Tennessee, Knoxville, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation

Grant/Contract Number:: SC0019412

OSTI ID:: 1777841

Journal Information:: Methods in Molecular Biology, Journal Name: Methods in Molecular Biology Vol. 2307; ISSN 1064-3745

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

References (16)

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
Real-time PCR (qPCR) primer design using free online software Thornton, Brenda; Basu, Chhandak Biochemistry and Molecular Biology Education, Vol. 39, Issue 2 https://doi.org/10.1002/bmb.20461	journal	March 2011
Simultaneous saccharification and fermentation of cellulose in ionic liquid for efficient production of α-ketoglutaric acid by Yarrowia lipolytica Ryu, Seunghyun; Labbé, Nicole; Trinh, Cong T. Applied Microbiology and Biotechnology, Vol. 99, Issue 10 https://doi.org/10.1007/s00253-015-6521-5	journal	March 2015
A survey of yeast from the Yarrowia clade for lipid production in dilute acid pretreated lignocellulosic biomass hydrolysate Quarterman, Josh; Slininger, Patricia J.; Kurtzman, Cletus P. Applied Microbiology and Biotechnology, Vol. 101, Issue 8 https://doi.org/10.1007/s00253-016-8062-y	journal	December 2016
Organic Acid Production by the Yeast Yarrowia lipolytica: A Review of Prospects Finogenova, T. V.; Morgunov, I. G.; Kamzolova, S. V. Applied Biochemistry and Microbiology, Vol. 41, Issue 5 https://doi.org/10.1007/s10438-005-0076-7	journal	September 2005
Reference genes in real-time PCR Kozera, Bartłomiej; Rapacz, Marcin Journal of Applied Genetics, Vol. 54, Issue 4 https://doi.org/10.1007/s13353-013-0173-x	journal	September 2013
Metabolic engineering of Yarrowia lipolytica to produce chemicals and fuels from xylose Ledesma-Amaro, Rodrigo; Lazar, Zbigniew; Rakicka, Magdalena Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.07.001	journal	November 2016
Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica Xue, Zhixiong; Sharpe, Pamela L.; Hong, Seung-Pyo Nature Biotechnology, Vol. 31, Issue 8 https://doi.org/10.1038/nbt.2622	journal	July 2013
Comparative genomics of biotechnologically important yeasts Riley, Robert; Haridas, Sajeet; Wolfe, Kenneth H. Proceedings of the National Academy of Sciences, Vol. 113, Issue 35 https://doi.org/10.1073/pnas.1603941113	journal	August 2016
Rewiring Yarrowia lipolytica toward triacetic acid lactone for materials generation Markham, Kelly A.; Palmer, Claire M.; Chwatko, Malgorzata Proceedings of the National Academy of Sciences, Vol. 115, Issue 9 https://doi.org/10.1073/pnas.1721203115	journal	February 2018
Understanding Functional Roles of Native Pentose-Specific Transporters for Activating Dormant Pentose Metabolism in Yarrowia lipolytica Ryu, Seunghyun; Trinh, Cong T. Applied and Environmental Microbiology, Vol. 84, Issue 3 https://doi.org/10.1128/aem.02146-17	journal	November 2017
Activating and Elucidating Metabolism of Complex Sugars in Yarrowia lipolytica Ryu, Seunghyun; Hipp, Julie; Trinh, Cong T. Applied and Environmental Microbiology, Vol. 82, Issue 4 https://doi.org/10.1128/aem.03582-15	journal	December 2015
Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae Teste, Marie-Ange; Duquenne, Manon; François, Jean M. BMC Molecular Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2199-10-99	journal	January 2009
Development of cellobiose-degrading ability in Yarrowia lipolytica strain by overexpression of endogenous genes Guo, Zhongpeng; Duquesne, Sophie; Bozonnet, Sophie Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0289-9	journal	August 2015
Engineering of a high lipid producing Yarrowia lipolytica strain Friedlander, Jonathan; Tsakraklides, Vasiliki; Kamineni, Annapurna Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0492-3	journal	March 2016
Engineering xylose utilization in Yarrowia lipolytica by understanding its cryptic xylose pathway Rodriguez, Gabriel M.; Hussain, Murtaza Shabbir; Gambill, Lauren Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0562-6	journal	July 2016

Cited By (31)

Trichoderma mediate early and enhanced lignifications in chickpea during Fusarium oxysporum f. sp. ciceris infection Meshram, Shweta; Patel, Jai Singh; Yadav, Sudheer K. Journal of Basic Microbiology, Vol. 59, Issue 1 https://doi.org/10.1002/jobm.201800212	journal	October 2018
Intranasal delivery of human umbilical cord Wharton's jelly mesenchymal stromal cells restores lung alveolarization and vascularization in experimental bronchopulmonary dysplasia Moreira, Alvaro; Winter, Caitlyn; Joy, Jooby STEM CELLS Translational Medicine, Vol. 9, Issue 2 https://doi.org/10.1002/sctm.18-0273	journal	November 2019
N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae Cellini, Antonio; Donati, Irene; Fiorentini, Luca Microbial Ecology, Vol. 79, Issue 2 https://doi.org/10.1007/s00248-019-01416-5	journal	July 2019
Identification and quantification of Aphelenchoides besseyi from rice using qPCR Çelik, Elvan Sert; Devran, Zübeyir European Journal of Plant Pathology, Vol. 154, Issue 3 https://doi.org/10.1007/s10658-019-01692-4	journal	February 2019
Fine mapping of the tomato yellow leaf curl virus resistance gene Ty-2 on chromosome 11 of tomato Yang, Xiaohui; Caro, Myluska; Hutton, Samuel F. Molecular Breeding https://doi.org/10.1007/s11032-014-0072-9	journal	March 2014
Real-time polymerase chain reaction assays for rapid detection and virulence evaluation of the environmental Pseudomonas aeruginosa isolates Golpayegani, Abdolali; Nodehi, Ramin Nabizadeh; Rezaei, Farhad Molecular Biology Reports, Vol. 46, Issue 4 https://doi.org/10.1007/s11033-019-04855-y	journal	May 2019
Stress induced biofilm formation in Propionibacterium acidipropionici and use in propionic acid production Cavero-Olguin, Victor Hugo; Hatti-Kaul, Rajni; Cardenas-Alegria, Oscar Victor World Journal of Microbiology and Biotechnology, Vol. 35, Issue 7 https://doi.org/10.1007/s11274-019-2679-9	journal	June 2019
Domestication history and geographical adaptation inferred from a SNP map of African rice Meyer, Rachel S.; Choi, Jae Young; Sanches, Michelle Nature Genetics, Vol. 48, Issue 9 https://doi.org/10.1038/ng.3633	journal	August 2016
Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features Döring, Matthias; Kreer, Christoph; Lehnen, Nathalie Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-47173-w	journal	July 2019
Identification, characterization and expression profiles of Fusarium udum stress-responsive WRKY transcription factors in Cajanus cajan under the influence of NaCl stress and Pseudomonas fluorescens OKC Kumar, Gagan; Bajpai, Raina; Sarkar, Ankita Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-50696-x	journal	October 2019
Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes Tafolla-Arellano, Julio C.; Zheng, Yi; Sun, Honghe Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep46163	journal	April 2017
Wolbachia Infection Differs Among Divergent Mitochondrial Haplotypes of Bactericera cockerelli (Hemiptera: Triozidae) Cooper, W. R.; Swisher, K. D.; Garczynski, S. F. Annals of the Entomological Society of America, Vol. 108, Issue 2 https://doi.org/10.1093/aesa/sau048	journal	February 2015
Gut Content Analysis of a Phloem-Feeding Insect, Bactericera cockerelli (Hemiptera: Triozidae) Cooper, W. Rodney; Horton, David R.; Unruh, Thomas R. Environmental Entomology, Vol. 45, Issue 4 https://doi.org/10.1093/ee/nvw060	journal	June 2016
Bystander inhibition of humoral immune responses by Epstein–Barr virus LMP1 Tsai, Chao-Yuan; Sakakibara, Shuhei; Yasui, Teruhito International Immunology https://doi.org/10.1093/intimm/dxy053	journal	August 2018
In vivo properties of the disaggregase function of J‐proteins and Hsc70 in Caenorhabditis elegans stress and aging Kirstein, Janine; Arnsburg, Kristin; Scior, Annika Aging Cell, Vol. 16, Issue 6 https://doi.org/10.1111/acel.12686	journal	October 2017
Induced thiacloprid insensitivity in honeybees ( A pis mellifera L.) is associated with up-regulation of detoxification genes: Induced thiacloprid insensitivity in A. mellifera Alptekin, S.; Bass, C.; Nicholls, C. Insect Molecular Biology, Vol. 25, Issue 2 https://doi.org/10.1111/imb.12211	journal	January 2016
Engineering d -limonene synthase down-regulation in orange fruit induces resistance against the fungus Phyllosticta citricarpa through enhanced accumulation of monoterpene alcohols and activation of defence : Linalool defence against Rodríguez, Ana; Kava, Vanessa; Latorre-García, Lorena Molecular Plant Pathology, Vol. 19, Issue 9 https://doi.org/10.1111/mpp.12681	journal	May 2018
Amino Acid Biosynthetic Pathways Are Required for Klebsiella pneumoniae Growth in Immunocompromised Lungs and Are Druggable Targets during Infection Silver, Rebecca J.; Paczosa, Michelle K.; McCabe, Anne L. Antimicrobial Agents and Chemotherapy, Vol. 63, Issue 8 https://doi.org/10.1128/aac.02674-18	journal	August 2019
History, epidemiology and diagnostics of dengue in the American and Brazilian contexts: a review Salles, Tiago Souza; da Encarnação Sá-Guimarães, Thayane; de Alvarenga, Evelyn Seam Lima Parasites & Vectors, Vol. 11, Issue 1 https://doi.org/10.1186/s13071-018-2830-8	journal	April 2018
Identification of putative adhesins of Actinobacillus suis and their homologues in other members of the family Pasteurellaceae Bujold, Adina R.; MacInnes, Janet I. BMC Research Notes, Vol. 8, Issue 1 https://doi.org/10.1186/s13104-015-1659-x	journal	November 2015
Stress amplifies sex differences in primate prefrontal profiles of gene expression Lee, Alex G.; Hagenauer, Megan; Absher, Devin Biology of Sex Differences, Vol. 8, Issue 1 https://doi.org/10.1186/s13293-017-0157-3	journal	November 2017
High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice Amanzougaghene, Nadia; Mumcuoglu, Kosta Y.; Fenollar, Florence PLOS ONE, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pone.0164659	journal	October 2016
Genomic profiling supports the diagnosis of primary ciliary dyskinesia and reveals novel candidate genes and genetic variants Andjelkovic, Marina; Minic, Predrag; Vreca, Misa PLOS ONE, Vol. 13, Issue 10 https://doi.org/10.1371/journal.pone.0205422	journal	October 2018
Field performance of hermaphrodite papaya plants obtained through molecular selection and micropropagation Araya-Valverde, Emanuel; Bogantes, Antonio; Holst, Andrea Crop Breeding and Applied Biotechnology, Vol. 19, Issue 4 https://doi.org/10.1590/1984-70332019v19n4a59	journal	December 2019
Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary Siboni, Nachshon; Balaraju, Varunan; Carney, Richard Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00460	journal	April 2016
The Prevalence of Colistin Resistant Strains and Antibiotic Resistance Gene Profiles in Funan River, China Tuo, Hongmei; Yang, Yanxian; Tao, Xi Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03094	journal	December 2018
Pseudomonas fluorescens and Trichoderma asperellum Enhance Expression of Gα Subunits of the Pea Heterotrimeric G-protein during Erysiphe pisi Infection Patel, Jai S.; Sarma, Birinchi K.; Singh, Harikesh B. Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.01206	journal	January 2016
Increased Plasma Circulating Cell-Free DNA Could Be a Potential Marker for Oral Cancer Lin, Li-Han; Chang, Kuo-Wei; Kao, Shou-Yen International Journal of Molecular Sciences, Vol. 19, Issue 11 https://doi.org/10.3390/ijms19113303	journal	October 2018
Anti-Obesity Effects of Lactobacillus fermentum CQPC05 Isolated from Sichuan Pickle in High-Fat Diet-Induced Obese Mice through PPAR-α Signaling Pathway Zhu, Kai; Tan, Fang; Mu, Jianfei Microorganisms, Vol. 7, Issue 7 https://doi.org/10.3390/microorganisms7070194	journal	July 2019
Identification of Factors Linked to Higher Water-Deficit Stress Tolerance in Amaranthus hypochondriacus Compared to Other Grain Amaranths and A. hybridus, Their Shared Ancestor González-Rodríguez, Tzitziki; Cisneros-Hernández, Ismael; Acosta Bayona, Jonathan Plants, Vol. 8, Issue 7 https://doi.org/10.3390/plants8070239	journal	July 2019
Characterization of the salivary microbiome in patients with pancreatic cancer Torres, Pedro J.; Fletcher, Erin M.; Gibbons, Sean M. PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1373	journal	January 2015

Similar Records

Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates

Journal Article · Mon Nov 11 23:00:00 EST 2024 · Bioresource Technology · OSTI ID:2502088

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

Technical Report · Thu Feb 13 23:00:00 EST 2025 · OSTI ID:2516696

Heterologous expression of xylanase enzymes in lipogenic yeast Yarrowia lipolytica

Journal Article · Mon Dec 01 23:00:00 EST 2014 · PLoS ONE · OSTI ID:1169214

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Adaptation
Beta-glucosidase
Cellobiose
D-glucose
D-xylitol dehydrogenase
D-xylose
D-xylose reductase
D-xylulokinase
L-arabinose
L-arabinose reductase
L-arabitol dehydrogenase
L-xylulose reductase
Yarrowia lipolytica

Methods to Activate and Elucidate Complex Endogenous Sugar Metabolism in Yarrowia lipolytica

Citation Formats

References (16)

Cited By (31)

Similar Records

Related Subjects