Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products

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1 Engineering Conferences International ECI Digital Archives Metabolic Engineering IX Proceedings Summer Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products Ethal Jackson Du Pont Follow this and additional works at: Part of the Biomedical Engineering and Bioengineering Commons Recommended Citation Ethal Jackson, "Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products" in "Metabolic Engineering IX", E. Heinzle, Saarland Univ.; P. Soucaille, INSA; G. Whited, Danisco Eds, ECI Symposium Series, (2013). This Conference Proceeding is brought to you for free and open access by the Proceedings at ECI Digital Archives. It has been accepted for inclusion in Metabolic Engineering IX by an authorized administrator of ECI Digital Archives. For more information, please contact

2 Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products Ethel Jackson CR&D, E.I. du Pont de Nemours and Company, USA Metabolic Engineering IX, Biarritz, France 2012

3 2 Metabolic Engineering of Yarrowia: Land-based Renewable Source of Omega-3 Current Wild Harvest of Ocean Fish Unsustainable Future Renewable Land-based Fermentation

4 3 Essential Omega-3 Fatty Acids: EPA and DHA EPA & DHA required in diet of humans & animals Total Omega-3 market ~$7B, growing 10-12%/yr. Markets include aquaculture, human nutrition, pharmaceuticals, animal feed, pet food Primary source is wild-caught ocean fish Only synthesized in nature by plankton and algae Small amount DHA from algae fermentation Critical for salmon aquaculture 85% of world market for fish oil No highly productive land-based source of EPA available

5 4 Goal: DuPont s Omega-3 program Develop a clean and sustainable source of Omega-3 and Omega-6 fatty acids by fermentation Approach: Metabolically engineered oleaginous yeast to produce EPA and/or DHA by fermentation. Sugar Yarrowia lipolytica Omega-3 oil OH O Eicosapentaenoic Acid (EPA)

6 5 TOPICS Yarrowia lipolytica good production host for products of metabolic engineering Omega-3 metabolic engineering Omega-3 fermentation process First commercial products Lessons Learned Summary

7 6 Yarrowia lipolytica: : A Good Production Host Safe FDA approved for food-grade citric acid production Good Fermentation Organism - Robust growth - High oil content - Growth on Sugars Conventional strain breeding - Mating types Oil body Oleaginous Yarrowia Useful molecular genetic tools

8 Development of a Comprehensive Genetic Toolbox for Yarrowia lipolytica 7 Genome Sequence Information available 21 Mb; 6 chromosome; 6650 ORFs Transformation System Stable integration into genome or replicating plasmids Selectable Markers No antibiotic resistance genes needed Strategy for Chromosomal Integration of Multiple Foreign Genes Genetic Tools Based on Homologous Recombination Targeted gene deletions Targeted gene integrations Genetic Tools Based on Non-Homologous End Joining Random gene disruptions Random gene integrations Method for Identifying the Chromosomal Locations of Integrated Genes

9 8 Metabolic Engineering of Yarrowia for Production of Omega-3 & Omega-6 Fatty Acids Oleic Acid [C18:1] 9D Stearic Acid [C18:0] C 16/18 E Palmitate [C16:0] C 14/16 E Myristic Acid [C14:0] 12D Linoleic Acid [LA, C18:2] 9E 15D 18:3 (ALA) 9E 20:3 (ETrA) 8D 5D 20:2 (EDA) 20:3 (DGLA) 20:4 (ARA) 8D 17D 20:4 (ETA) 5D 17D 20:5 (EPA) Eicosapentaenoic Acid Yarrowia native pathway Engineered pathway options

10 9 Strategies to Build an EPA Production Strain Build an efficient EPA biosynthetic pathway - Use of different strong promototers - Codon-optimization of heterologous genes - Multiple copies of structural genes - Focus on limiting steps - Push and pull carbon flux Screen for high oil and EPA productivity Eliminate fatty acid β-oxidation and increase oil content - Modification of Peroxisome - Generate mutants with key enzymes of β-oxidation knocked-out Control fatty acid transportation - Fine regulation of acyltransferases - Direct fatty acid flux for increased EPA productivity Manipulating global regulators - Alter nitrogen control of lipid synthesis by Snf1 mutation

11 Metabolic Engineering Generation of The First Commercial Production Strain 10 ATCC Wild typey. lipolytica Each Step: 1,500 GC Y2224 Y4001 Y4001U1 Y4036 Y4036U Integrate multiple genes into host s genome by homologous & non-homologous recombination Y4070 Y4086 Y4086U1 Y4128 Y4128U3 Y4217 Y4217U Y4259 Y4259U2 Y % EPA Y4305 (56% EPA) 15 Steps, 8 Generations 32 copies of 9 different genes No antibiotic marker

12 11 EPA/Oil Biosynthesis A Complex Process in Engineered Yarrowia Cell Glucose Pyruvate Acetyl-CoA Oxaloacetate Citrate Isocitrate Malate α-ketoglutarate Fumarate Succinate Mitochondrion Pentose phosphate shunt ER NADPH Acetyl-CoA Citrate Oxaloacetate EPA-CoA Acyl (C16)-CoA Malonyl-CoA TAGs (Oil) EPA/TAGs Fatty Acids Lipid Body X Fatty Acids Acetyl-CoA Oxaloacetate Malate Acetyl -CoA Glyoxylate Peroxisome Citrate Isocitrate Succinate Cytoplasm

13 12 Pex10 Gene Function Member of peroxin class of proteins involved in peroxisome biogenesis Identified Pex10 knockout that blocked β-oxidation pathway (key to keeping oil and EPA high) EPA/TAGs Fatty Acids X Fatty Acids Lipid Body Acetyl-CoA Oxaloacetate Citrate Acetyl-CoA Malate Isocitrate P M N NE CW V peroxisome mitochondrion nucleus nuclear envelope cell wall vacuole Electron micrograph of Yarrowia lipolytica Glyoxylate Peroxisome Succinate

14 13 Peroxisome Mutations Increase EPA Titer Knock out of the Pex10 gene resulted in an EPA titer increase >2X 50 EPA% of FAME PEX Pex Y4127 Y4128 Strains

15 14 Control the Carbon Flux for Enhanced EPA Production % of To otal Lipids C16: 4% 3 1 Pushing Pulling C18: <24% Fatty Acids 56 EPA TAG Sink

16 Searching for A Global Regulator of Lipid Metabolism in Yarrowia 15 Glucose Pentose phosphate shunt NADPH Pyruvate ER EPA-CoA Acyl (C14)-CoA TAGs (Oil) EPA/TAGs Fatty Acids Lipid Body Acetyl-CoA Acetyl-CoA Malonyl-CoA Fatty Acids Acetyl-CoA Oxaloacetate Citrate Isocitrate Malate a-ketoglutarate Fumarate Succinate Mitochondrion Citrate Oxaloacetate Global Regulator? Cytoplasm Oxaloacetate Citrate Acetyl-CoA Malate Isocitrate Glyoxylate Peroxisome Succinate

17 Yarrowia SNF1: Global Regulator of Lipid Accumulation 16 Lipid %D DCW High Medium Low snf1 Control Days in oleaginous phase

18 Three DAG Acyltransferases for Oil Biosynthesis 17 E P E R P E R R P E R R TAG biosynthesis E R R R G3P LPA PA DAG TAG Glycerol G3PAT LPAAT PC-DAG exchange CPT1 18:1 18:2 20:2 20:3 20:4 20:5 EPA biosynthesis PC pool. E R R PDAT PC DGAT2 DGAT1 FAS LPCAT/ LPAAT 16:0 18:0 18:1 18:2 EPA 20:2 20:5 PC recycling CoA pool PEX β-oxidation GPAT DGAT CPT LPAAT LPCAT PDAT Glycerol-3-phosphate acyltransferase Diacylglycerol acyltransferase CDP-choline:diacylglycerol cholinephosphotransferase Lysophosphatidic Acid Acyltransferase acyl-coa::lyso-phosphatidylcholine acltransferase phopholipid::diacylglycerol acyltransferase

19 18 Oil Content In Y.. lipolytica DAG AT Mutants TAG Oil conten nt, TF % dcw (% WT) ATCC Std Oil WT S d1 S-DT1 d2 S-DT2 S-PT p S-DT1 d1 S-DT1 d1 S-DT2 d2 Std S-DT2 d2 S-PT p S-PT p Single mutants Double mutants S-DT1 d1 S-DT2 d2 S-PT p

20 19 Over-Expression of DGAT and PDAT Improves Oil 70 Total Lipids as Dr ry Cell Weight (%) Y9502 Y PDAT Y DGAT2 Strain Comparison

21 20 Omega-3 Fermentation Research: Strain Evaluation and Process Development Glucose feed Cell Density and Byprod ducts (g/l) Cell Density Excreted Byproducts Lipid Content (% DCW) EPA Content (% DCW) Lipid an nd EPA content (% DCW) + + NH 4 4 Fermentation Time Air

22 21 Process Flow for Strain Evaluation by Fermentation 1,500 50, Micro-24 Bioreactor Air * Numbers refer to the strains tested

23 22 Micro-24 Bioreactor vs. Lab-Scale Fermentor Vessel/ Reactor Controllability Experimental Data Work Capacity 24 reactors, 3-7 ml Online process- T, Individual ph, po2 T, ph, po 2 Final point titer, rate, yield 1000 individual experiments /year/person Single reactor, 2-10 L T, ph, po 2 feeding Online process- T, ph, po2, feeding Time course titer, rate, yield 40 individual experiments /year/person

24 23 Micro-24 Bioreactor - bridge between shake flask and fermentor Strain #1 Flask mico-24 2-L fermentor 0 cell density product#1 product #2 product # Strain #2 Flask mico-24 2-L fermentor cell density product#1 product #2 product #3

25 24 Micro-24 Bioreactor - help identify the best strain and condition Identify the best production strain Identify the best fermentation conditions

26 25 Products: Current Omega-3 Market Oil Concentrates Pharmaceuticals Dietary Supplements Yarrowia Biomass Processed Biomass Extracted Oil Functional Foods Medical Foods & Pharma Aquaculture Terrestrial Animal Agriculture Pet Foods Industrial Applications Omega-3 market growing 12-15%/year

27 26 newharvest Vegetarian, renewable source - made from yeast, not fish Highly concentrated for convenient dosage Avoids fishy taste and burps No cholesterol. No PCBs. Strategic Partners Active Ingredient Natural Marketer Channel Partner

28 27 Verlasso s Harmoniously Raised Fish (Salmon) A new category of premium farmed salmon that is beyond sustainable farming practices Raised on a diet rich in omega-3 Fish in Fish out ratio 1 to 1 vs. 4 to 1 One of the lowest pen densities No hormones or preventative antibiotics Partnership between DuPont and AquaChile Validated through extensive market research National Market Test in 5 US Cities Marketing Support Building the Brand Partnership with the retailers 27

29 28 MY LESSONS LEARNED Project choice: make sure the view is worth the climb - No well-established chemical process - Multiple different products possible Collaboration is key: integrate metabolic engineering and fermentation engineering research - Strain, construction and process research should be integrated from the start - Results determine production strain attributes and process parameters Cost is king - Capital investment barrier must optimize fermentation productivity - Raw material cost There s no substitute for good science

30 29 Summary Yarrowia lipolytica is a useful host for metabolic engineering Powerful genetic tool box for metabolic engineering Robust, safe fermentation production organism Engineered production strains are stable without antibiotic selection DuPont s process is a sustainable alternative for Omega-3s Land-based fermentation from renewable resources at commercial scale Naturally contaminant free, no DHA Versatile technology enables production of tailored oil compositions, different PUFA s and multiple product applications Launched two commercial products NewHarvet TM EPA Oil Verlasso TM Salmon EPA Biomass DuPont will continue to drive lower costs and broaden the platform