Engineered microbes and methods for microbial oil production

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Title: Engineered microbes and methods for microbial oil production

Patent · Tue Feb 10 00:00:00 EST 2015

OSTI ID:1169615

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

View Patent

Cite

Export

Save

Research Organization:: Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AR0000059

Assignee:: Massachusetts Institute of Technology (Cambridge, MA)

Patent Number(s):: 8,951,776

Application Number:: 13/656,086

OSTI ID:: 1169615

Country of Publication:: United States

Language:: English

References (68)

Metabolically engineered cells for the production of polyunsaturated fatty acids Gunnarsson, Nina Katarina; Forster, Jochen; Nielsen, Jens Bredal https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20060051847 US Patent Document 11/146428; 20060051847	patent-application	March 2006
Acyltransferases for alteration of polyunsaturated fatty acids and oil content in oleaginous yeasts Yadav, Narendra; Zhang, Hongxiang https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20060160193 US Patent Document 10/882760; 20060160193	patent-application	July 2006
Diacylglycerol Acyltransferases for Alteration of Polyunsaturated Fatty Acids and Oil Content in Oleaginous Organisms Yadav, Narendra; Xue, Zhixiong; Zhang, Hongxiang https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20090104674 US Patent Document 12/338536; 20090104674	patent-application	April 2009
Bioprocess and Microbe Engineering for Total Carbon Utilization in Biofuel Production Stephanopoulos, Gregory https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20110177564 US Patent Document 13/007325; 20110177564	patent-application	July 2011
Microbial Engineering for the Production of Fatty Acids and Fatty Acid Derivatives Stephanopoulos, Gregory; Abidi, Syed Hussain Imam https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20110223641 US Patent Document 13/039227; 20110223641	patent-application	September 2011
Engineered Microbes and Methods for Microbial Oil Overproduction from Cellulosic Materials Stephanopoulos, Gregory; Tai, Mitchell https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20130344548 US Patent Document 13/923607; 20130344548	patent-application	December 2013
Yarrowia lipolytica as a model for bio-oil production Beopoulos, Athanasios; Cescut, Julien; Haddouche, Ramdane Progress in Lipid Research, Vol. 48, Issue 6, p. 375-387 https://doi.org/10.1016/j.plipres.2009.08.005	journal	November 2009
Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production Tai, Mitchell; Stephanopoulos, Gregory Metabolic Engineering, Vol. 15, p. 1-9 https://doi.org/10.1016/j.ymben.2012.08.007	journal	January 2013
Toward a science of metabolic engineering Bailey, J. E. Science, Vol. 252, Issue 5013, p. 1668-1675 https://doi.org/10.1126/science.2047876	journal	June 1991
Control of Lipid Accumulation in the Yeast Yarrowia lipolytica Beopoulos, A.; Mrozova, Z.; Thevenieau, F. Applied and Environmental Microbiology, Vol. 74, Issue 24, p. 7779-7789 https://doi.org/10.1128/AEM.01412-08	journal	October 2008
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts Blank, Lars M.; Lehmbeck, Frank; Sauer, Uwe FEMS Yeast Research, Vol. 5, Issue 6-7, p. 545-558 https://doi.org/10.1016/j.femsyr.2004.09.008	journal	April 2005
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns Bon, Elisabeth Nucleic Acids Research, Vol. 31, Issue 4, p. 1121-1135 https://doi.org/10.1093/nar/gkg213	journal	February 2003
Correlation of Lipid Accumulation in Yeasts with Possession of ATP: Citrate Lyase Boulton, Christopher A.; Ratledge, C. Microbiology, Vol. 127, Issue 1, p. 169-176 https://doi.org/10.1099/00221287-127-1-169	journal	November 1981
Introns increase gene expression in cultured maize cells. Callis, J.; Fromm, M.; Walbot, V. Genes & Development, Vol. 1, Issue 10, p. 1183-1200 https://doi.org/10.1101/gad.1.10.1183	journal	December 1987
Increasing unsaturated fatty acid contents in Escherichia coli by coexpression of three different genes Cao, Yujin; Yang, Jianming; Xian, Mo Applied Microbiology and Biotechnology, Vol. 87, Issue 1, p. 271-280 https://doi.org/10.1007/s00253-009-2377-x	journal	February 2010
Hydrophobic substrate utilisation by the yeast Yarrowia lipolytica, and its potential applications Fickers, P.; Benetti, P.; Wache, Y. FEMS Yeast Research, Vol. 5, Issue 6-7, p. 527-543 https://doi.org/10.1016/j.femsyr.2004.09.004	journal	April 2005
Promoter proximal splice sites enhance transcription Furger, Andre; O‘Sullivan, Justin M.; Binnie, Alexandra Genes & Development, Vol. 16, Issue 21, p. 2792-2799 https://doi.org/10.1101/gad.983602	journal	November 2002
Design of an efficient medium for heterologous protein production in Yarrowia lipolytica: case of human interferon alpha 2b Gasmi, Najla; Ayed, Atef; Nicaud, Jean-Marc Microbial Cell Factories, Vol. 10, Issue 1, Article No. 38 https://doi.org/10.1186/1475-2859-10-38	journal	January 2011
Elevated stearoyl-CoA desaturase-1 expression in skeletal muscle contributes to abnormal fatty acid partitioning in obese humans Hulver, Matthew W.; Berggren, Jason R.; Carper, Michael J. Cell Metabolism, Vol. 2, Issue 4, p. 251-261 https://doi.org/10.1016/j.cmet.2005.09.002	journal	October 2005
Perspectives of microbial oils for biodiesel production Li, Qiang; Du, Wei; Liu, Dehua Applied Microbiology and Biotechnology, Vol. 80, Issue 5, p. 749-756 https://doi.org/10.1007/s00253-008-1625-9	journal	August 2008
Fatty acid production in genetically modified cyanobacteria Liu, X.; Sheng, J.; Curtiss III, R. Proceedings of the National Academy of Sciences, Vol. 108, Issue 17, p. 6899-6904 https://doi.org/10.1073/pnas.1103014108	journal	April 2011
Transcriptomic Analyses during the Transition from Biomass Production to Lipid Accumulation in the Oleaginous Yeast Yarrowia lipolytica Morin, Nicolas; Cescut, Julien; Beopoulos, Athanasios PLoS ONE, Vol. 6, Issue 11, Article No. e27966 https://doi.org/10.1371/journal.pone.0027966	journal	November 2011
Comparison of expression systems in the yeastsSaccharomyces cerevisiae, Hansenula polymorpha, Klyveromyces lactis, Schizosaccharomyces pombe andYarrowia lipolytica. Cloning of two novel promoters fromYarrowia lipolytica Müller, Sven; Sandal, Thomas; Kamp-Hansen, Peter Yeast, Vol. 14, Issue 14, p. 1267-1283 https://doi.org/10.1002/(SICI)1097-0061(1998100)14:14<1267::AID-YEA327>3.0.CO;2-2	journal	October 1998
Protein expression and secretion in the yeast Yarrowia lipolytica Nicaud, Jean-Marc; Madzak, Catherine; van den Broek, Peter FEMS Yeast Research, Vol. 2, Issue 3, p. 371-379 https://doi.org/10.1016/S1567-1356(02)00082-X	journal	August 2002
Regulation of stearoyl-CoA desaturases and role in metabolism Ntambi, James M.; Miyazaki, Makoto Progress in Lipid Research, Vol. 43, Issue 2, p. 91-104 https://doi.org/10.1016/S0163-7827(03)00039-0	journal	March 2004
The DGA1 Gene Determines a Second Triglyceride Synthetic Pathway in Yeast Oelkers, Peter; Cromley, Debra; Padamsee, Mahajabeen Journal of Biological Chemistry, Vol. 277, Issue 11, p. 8877-8881 https://doi.org/10.1074/jbc.M111646200	journal	December 2001
Single cell oil production by Yarrowia lipolytica growing on an industrial derivative of animal fat in batch cultures Papanikolaou, S.; Chevalot, I.; Komaitis, M. Applied Microbiology and Biotechnology, Vol. 58, Issue 3, p. 308-312 https://doi.org/10.1007/s00253-001-0897-0	journal	March 2002
Yarrowia lipolytica as a potential producer of citric acid from raw glycerol Papanikolaou, S.; Muniglia, L.; Chevalot, I. Journal of Applied Microbiology, Vol. 92, Issue 4, p. 737-744 https://doi.org/10.1046/j.1365-2672.2002.01577.x	journal	April 2002
Targeting of the Arabidopsis Homomeric Acetyl-Coenzyme A Carboxylase to Plastids of Rapeseeds Roesler, K.; Shintani, D.; Savage, L. Plant Physiology, Vol. 113, Issue 1, p. 75-81 https://doi.org/10.1104/pp.113.1.75	journal	January 1997
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli Shen, Claire R.; Lan, Ethan I.; Dekishima, Yasumasa Applied and Environmental Microbiology, Vol. 77, Issue 9, p. 2905-2915 https://doi.org/10.1128/AEM.03034-10	journal	March 2011
Fatty acid synthesis and elongation in yeast Tehlivets, Oksana; Scheuringer, Kim; Kohlwein, Sepp D. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1771, Issue 3, p. 255-270 https://doi.org/10.1016/j.bbalip.2006.07.004	journal	March 2007
Alternative routes of acetyl-CoA synthesis identified by comparative genomic analysis: involvement in the lipid production of oleaginous yeast and fungi Vorapreeda, T.; Thammarongtham, C.; Cheevadhanarak, S. Microbiology, Vol. 158, Issue 1, p. 217-228 https://doi.org/10.1099/mic.0.051946-0	journal	October 2011
Three diacylglycerol acyltransferases contribute to oil biosynthesis and normal growth in Yarrowia lipolytica DAG acyltransferases, growth and oil biosynthesis in Y. lipolytica Zhang, Hongxiang; Damude, Howard G.; Yadav, Narendra S. Yeast, Vol. 29, Issue 1, p. 25-38 https://doi.org/10.1002/yea.1914	journal	December 2011
Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction Zhao, Sheng; Fernald, Russell D. Journal of Computational Biology, Vol. 12, Issue 8, p. 1047-1064 https://doi.org/10.1089/cmb.2005.12.1047	journal	October 2005
Enhancement of single cell oil production by Yarrowia lipolytica growing in the presence of Teucrium polium L. aqueous extract Aggelis, George; Komaitis, Michael Biotechnology Letters, Vol. 21, Issue 9, p. 747-749 https://doi.org/10.1023/A:1005591127592	journal	January 1999
Tobacco as a production platform for biofuel overexpression of Arabidopsis DGAT and LEC2 genes increases accumulation and shifts the composition of lipids in green biomass Andrianov, Vyacheslav; Borisjuk, Nikolai; Pogrebnyak, Natalia Plant Biotechnology Journal, Vol. 8, Issue 3, p. 277-287 https://doi.org/10.1111/j.1467-7652.2009.00458.x	journal	April 2010
Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source Athenstaedt, Karin; Jolivet, Pascale; Boulard, Céline PROTEOMICS, Vol. 6, Issue 5, p. 1450-1459 https://doi.org/10.1002/pmic.200500339	journal	March 2006
Lignocellulosic Biomass Pretreatment Using AFEX Balan, Venkatesh; Bals, Bryan; Chundawat, Shishir P. S. Biofuels, p. 61-77 https://doi.org/10.1007/978-1-60761-214-8_5	book	January 2009
Physiology and genetics of the dimorphic fungus Yarrowia lipolytica Barth, Gerold; Gaillardin, Claude FEMS Microbiology Reviews, Vol. 19, Issue 4, p. 219-237 https://doi.org/10.1111/j.1574-6976.1997.tb00299.x	journal	April 1997
An overview of lipid metabolism in yeasts and its impact on biotechnological processes Beopoulos, Athanasios; Nicaud, Jean-Marc; Gaillardin, Claude Applied Microbiology and Biotechnology, Vol. 90, Issue 4, p. 1193-1206 https://doi.org/10.1007/s00253-011-3212-8	journal	March 2011
Regulation of acetyl-CoA carboxylase Table 1 Brownsey, R.W.; Boone, A.N.; Elliott, J.E. Biochemical Society Transactions, Vol. 34, Issue 2, p. 223-227 https://doi.org/10.1042/BST0340223	journal	April 2006
One-step transformation of the dimorphic yeast Yarrowia lipolytica Chen, D.-C.; Beckerich, J.-M.; Gaillardin, C. Applied Microbiology and Biotechnology, Vol. 48, Issue 2, p. 232-235 https://doi.org/10.1007/s002530051043	journal	August 1997
Co-expression of heterologous desaturase genes in Yarrowia lipolytica Chuang, Lu-Te; Chen, Dzi-Chi; Nicaud, Jean-Marc New Biotechnology, Vol. 27, Issue 4, p. 277-282 https://doi.org/10.1016/j.nbt.2010.02.006	journal	September 2010
Enhancement of lipid production using biochemical, genetic and transcription factor engineering approaches Courchesne, Noémie Manuelle Dorval; Parisien, Albert; Wang, Bei Journal of Biotechnology, Vol. 141, Issue 1-2, p. 31-41 https://doi.org/10.1016/j.jbiotec.2009.02.018	journal	April 2009
Direct conversion of inulin into single cell protein by the engineered Yarrowia lipolytica carrying inulinase gene Cui, Wei; Wang, Qi; Zhang, Fang Process Biochemistry, Vol. 46, Issue 7, p. 1442-1448 https://doi.org/10.1016/j.procbio.2011.03.017	journal	July 2011
The role of stearoyl-CoA desaturase in the control of metabolism Dobrzyn, Agnieszka; Ntambi, James M. Prostaglandins, Leukotrienes and Essential Fatty Acids, Vol. 73, Issue 1, p. 35-41 https://doi.org/10.1016/j.plefa.2005.04.011	journal	July 2005
Involvement of the G3P shuttle and β-oxidation pathway in the control of TAG synthesis and lipid accumulation in Yarrowia lipolytica Dulermo, Thierry; Nicaud, Jean-Marc Metabolic Engineering, Vol. 13, Issue 5, p. 482-491 https://doi.org/10.1016/j.ymben.2011.05.002	journal	September 2011
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli Feist, Adam M.; Zielinski, Daniel C.; Orth, Jeffrey D. Metabolic Engineering, Vol. 12, Issue 3, p. 173-186 https://doi.org/10.1016/j.ymben.2009.10.003	journal	May 2010
Selection of Direct Transesterification as the Preferred Method for Assay of Fatty Acid Content of Microalgae Griffiths, M. J.; van Hille, R. P.; Harrison, S. T. L. Lipids, Vol. 45, Issue 11, p. 1053-1060 https://doi.org/10.1007/s11745-010-3468-2	journal	September 2010
Conversion of proteins into biofuels by engineering nitrogen flux Huo, Yi-Xin; Cho, Kwang Myung; Rivera, Jimmy G Lafontaine Nature Biotechnology, Vol. 29, Issue 4, p. 346-351 https://doi.org/10.1038/nbt.1789	journal	March 2011
Improving the lipid accumulation properties of the yeast cells for biodiesel production using molasses Karatay, Sevgi Ertuğrul; Dönmez, Gönül Bioresource Technology, Vol. 101, Issue 20, p. 7988-7990 https://doi.org/10.1016/j.biortech.2010.05.054	journal	October 2010
Manufacturing Molecules Through Metabolic Engineering Keasling, Jay D. Science, Vol. 330, Issue 6009, p. 1355-1358 https://doi.org/10.1126/science.1193990	journal	December 2010
Yarrowia lipolytica, a yeast genetic system to study mitochondrial complex I Kerscher, Stefan; Dröse, Stefan; Zwicker, Klaus Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1555, Issue 1-3, p. 83-91 https://doi.org/10.1016/S0005-2728(02)00259-1	journal	September 2002
Increased fatty acid production in potato by engineering of acetyl-CoA carboxylase Klaus, Dorte; Ohlrogge, John B.; Neuhaus, H. Ekkehard Planta, Vol. 219, Issue 3, p. 389-396 https://doi.org/10.1007/s00425-004-1236-3	journal	March 2004
Lipid-induced cell dysfunction and cell death: Lessons from yeast Kohlwein, Sepp D.; Petschnigg, Julia Current Hypertension Reports, Vol. 9, Issue 6, p. 455-461 https://doi.org/10.1007/s11906-007-0084-5	journal	December 2007
How introns influence and enhance eukaryotic gene expression Le Hir, Hervé; Nott, Ajit; Moore, Melissa J. Trends in Biochemical Sciences, Vol. 28, Issue 4, p. 215-220 https://doi.org/10.1016/S0968-0004(03)00052-5	journal	April 2003
Heterologous protein expression and secretion in the non-conventional yeast Yarrowia lipolytica: a review Madzak, Catherine; Gaillardin, Claude; Beckerich, Jean-Marie Journal of Biotechnology, Vol. 109, Issue 1-2, p. 63-81 https://doi.org/10.1016/j.jbiotec.2003.10.027	journal	April 2004
Accumulation of a Cocoa-Butter-Like Lipid by Yarrowia lipolytica Cultivated on Agro-Industrial Residues Papanikolaou, Seraphim; Muniglia, Lionel; Chevalot, Isabelle Current Microbiology, Vol. 46, Issue 2, p. 124-130 https://doi.org/10.1007/s00284-002-3833-3	journal	February 2003
Influence of Glucose and Saturated Free-Fatty Acid Mixtures on Citric Acid and Lipid Production by Yarrowia lipolytica Papanikolaou, Seraphim; Galiotou-Panayotou, Maria; Chevalot, Isabelle Current Microbiology, Vol. 52, Issue 2, p. 134-142 https://doi.org/10.1007/s00284-005-0223-7	journal	January 2006
Lipid production by Yarrowia lipolytica growing on industrial glycerol in a single-stage continuous culture Papanikolaou, Seraphim; Aggelis, George Bioresource Technology, Vol. 82, Issue 1, p. 43-49 https://doi.org/10.1016/S0960-8524(01)00149-3	journal	March 2002
Modeling Lipid Accumulation and Degradation in Yarrowia lipolytica Cultivated on Industrial Fats Papanikolaou, Seraphim; Aggelis, George Current Microbiology, Vol. 46, Issue 6, p. 398-402 https://doi.org/10.1007/s00284-002-3907-2	journal	June 2003
Overexpression of Acetyl-CoA Carboxylase Gene of Mucor rouxii Enhanced Fatty Acid Content in Hansenula polymorpha Ruenwai, Rawisara; Cheevadhanarak, Supapon; Laoteng, Kobkul Molecular Biotechnology, Vol. 42, Issue 3, p. 327-332 https://doi.org/10.1007/s12033-009-9155-y	journal	March 2009
The use of Yarrowia lipolytica to reduce pollution in olive mill wastewaters Scioli, Custode; Vollaro, Lucia Water Research, Vol. 31, Issue 10, p. 2520-2524 https://doi.org/10.1016/S0043-1354(97)00083-3	journal	October 1997
Challenges in Engineering Microbes for Biofuels Production Stephanopoulos, Gregory Science, Vol. 315, Issue 5813, p. 801-804 https://doi.org/10.1126/science.1139612	journal	February 2007
Lipid production from Yarrowia lipolytica Po1g grown in sugarcane bagasse hydrolysate Tsigie, Yeshitila Asteraye; Wang, Chun-Yuan; Truong, Chi-Thanh Bioresource Technology, Vol. 102, Issue 19, p. 9216-9222 https://doi.org/10.1016/j.biortech.2011.06.047	journal	October 2011
Expanding the metabolic engineering toolbox more options to engineer cells Tyo, Keith E.; Alper, Hal S.; Stephanopoulos, Gregory N. Trends in Biotechnology, Vol. 25, Issue 3, p. 132-137 https://doi.org/10.1016/j.tibtech.2007.01.003	journal	March 2007
Dilute Acid and Autohydrolysis Pretreatment Yang, Bin; Wyman, Charles E.; Mielenz, Jonathan R. Biofuels, Vol. 581, p 103-114 https://doi.org/10.1007/978-1-60761-214-8_8	book	August 2009
Expression of inulinase gene in the oleaginous yeast Yarrowia lipolytica and single cell oil production from inulin-containingmaterials Zhao, Chun-Hai; Cui, Wei; Liu, Xiao-Yan Metabolic Engineering, Vol. 12, Issue 6, p. 510-517 https://doi.org/10.1016/j.ymben.2010.09.001	journal	November 2010

Similar Records

Engineered microbes and methods for microbial oil production

Patent · Tue Jan 09 00:00:00 EST 2018 · OSTI ID:1169615

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols

Journal Article · Fri Jun 01 00:00:00 EDT 2018 · Metabolic Engineering Communications · OSTI ID:1169615

Ferreira, Raphael; Teixeira, Paulo Gonçalves; Gossing, Michael; +3 more

ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae

Journal Article · Thu Mar 03 00:00:00 EST 2016 · Microbial Cell Factories · OSTI ID:1169615

Rodriguez, Sarah; Denby, Charles M.; Van Vu, T.; +3 more

Related Subjects

09 BIOMASS FUELS

Title: Engineered microbes and methods for microbial oil production

Citation Formats

References (68)

Similar Records

Related Subjects