Production of octanoic acid in Saccharomyces cerevisiae: Investigation of new precursor supply engineering strategies and intrinsic limitations.
acetyl-CoA
octanoic acid
phosphoketolase
phosphotransacetylase
Journal
Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
revised:
08
04
2021
received:
18
01
2021
accepted:
30
04
2021
pubmed:
19
5
2021
medline:
18
1
2022
entrez:
18
5
2021
Statut:
ppublish
Résumé
The eight-carbon fatty acid octanoic acid (OA) is an important platform chemical and precursor of many industrially relevant products. Its microbial biosynthesis is regarded as a promising alternative to current unsustainable production methods. In Saccharomyces cerevisiae, the production of OA had been previously achieved by rational engineering of the fatty acid synthase. For the supply of the precursor molecule acetyl-CoA and of the redox cofactor NADPH, the native pyruvate dehydrogenase bypass had been harnessed, or the cells had been additionally provided with a pathway involving a heterologous ATP-citrate lyase. Here, we redirected the flux of glucose towards the oxidative branch of the pentose phosphate pathway and overexpressed a heterologous phosphoketolase/phosphotransacetylase shunt to improve the supply of NADPH and acetyl-CoA in a strain background with abolished OA degradation. We show that these modifications lead to an increased yield of OA during the consumption of glucose by more than 60% compared to the parental strain. Furthermore, we investigated different genetic engineering targets to identify potential factors that limit the OA production in yeast. Toxicity assays performed with the engineered strains suggest that the inhibitory effects of OA on cell growth likely impose an upper limit to attainable OA yields.
Substances chimiques
Caprylates
0
Saccharomyces cerevisiae Proteins
0
octanoic acid
OBL58JN025
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3046-3057Informations de copyright
© 2021 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals LLC.
Références
Aguilera, A. (1986). Deletion of the phosphoglucose isomerase structural gene makes growth and sporulation glucose dependent in Saccharomyces cerevisiae . Molecular & General Genetics: MGG, 204, 310-316. https://doi.org/10.1007/BF00425515
Alexandre, H. , Mathieu, B. , & Charpentier, C. (1996). Alteration in membrane fluidity and lipid composition, and modulation of H+-ATPase activity in Saccharomyces cerevisiae caused by decanoic acid. Microbiology, 142, 469-475. https://doi.org/10.1099/13500872-142-3-469
Baumann, L. , Doughty, T. , Siewers, V. , Nielsen, J. , Boles, E. , & Oreb, M. (2021). Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production. FEMS Yeast Research, 21, foab011. https://doi.org/10.1093/femsyr/foab011
Baumann, L. , Rajkumar, A. S. , Morrissey, J. P. , Boles, E. , & Oreb, M. (2018). A yeast-based biosensor for screening of short- and medium-chain fatty acid production. ACS Synthetic Biology, 7, 2640-2646. https://doi.org/10.1021/acssynbio.8b00309
Baumann, L. , Wernig, F. , Born, S. , & Oreb, M. (2020). Enigneering Saccaromyces cerevisiae for production of fatty acids and their derivatives. In J. P. Benz , & K. Schipper (Eds.), The Mycota Vol. II: Genetics and biotechnology (3rd ed., pp. 339-368). Springer. https://doi.org/10.1007/978-3-030-49924-2_14
Bergman, A. , Hellgren, J. , Moritz, T. , Siewers, V. , Nielsen, J. , & Chen, Y. (2019). Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae . Microbial Cell Factories, 18, 25. https://doi.org/10.1186/s12934-019-1072-6
Bergman, A. , Siewers, V. , Nielsen, J. , & Chen, Y. (2016). Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae . AMB Express, 6, 115. https://doi.org/10.1186/s13568-016-0290-0
Besada-Lombana, P. B. , Fernandez-Moya, R. , Fenster, J. , & Da Silva, N. A. (2017). Engineering Saccharomyces cerevisiae fatty acid composition for increased tolerance to octanoic acid. Biotechnology and Bioengineering, 114, 1531-1538. https://doi.org/10.1002/bit.26288
Borrull, A. , Lopez-Martinez, G. , Poblet, M. , Cordero-Otero, R. , & Rozes, N. (2015). New insights into the toxicity mechanism of octanoic and decanoic acids on Saccharomyces cerevisiae . Yeast (Chichester, England), 32, 451-460. https://doi.org/10.1002/yea.3071
Brachmann C. B. , Davies A. , Cost G. J. , Caputo E. , Li J. , Hieter P. , Boeke J. D. (1998). Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast, 14(2), 115-132. https://doi.org/10.1002/(sici)1097-0061(19980130)14:2%3C115::aid-yea204%3E3.0.co;2-2
Brinsmade, S. R. , & Escalante-Semerena, J. C. (2004). The eutD gene of Salmonella enterica encodes a protein with phosphotransacetylase enzyme activity. Journal of Bacteriology, 186, 1890-1892. https://doi.org/10.1128/jb.186.6.1890-1892.2004
Bruder, S. , Reifenrath, M. , Thomik, T. , Boles, E. , & Herzog, K. (2016). Parallelised online biomass monitoring in shake flasks enables efficient strain and carbon source dependent growth characterisation of Saccharomyces cerevisiae . Microbial Cell Factories, 15, 127. https://doi.org/10.1186/s12934-016-0526-3
Cabral, M. G. , Viegas, C. A. , & Sá-Correia, I. (2001). Mechanisms underlying the acquisition of resistance to octanoic-acid-induced-death following exposure of Saccharomyces cerevisiae to mild stress imposed by octanoic acid or ethanol. Archives of Microbiology, 175, 301-307. https://doi.org/10.1007/s002030100269
Chen, Y. , Siewers, V. , & Nielsen, J. (2012). Profiling of cytosolic and peroxisomal acetyl-CoA metabolism in Saccharomyces cerevisiae . PLoS One, 7, e42475. https://doi.org/10.1371/journal.pone.0042475
Demeke, M. M. , Dietz, H. , Li, Y. , Foulquié-Moreno, M. R. , Mutturi, S. , Deprez, S. , Den Abt, T. , Bonini, B. M. , Liden, G. , Dumortier, F. , Verplaetse, A. , Boles, E. , & Thevelein, J. M. (2013). Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnology for Biofuels, 6, 89. https://doi.org/10.1186/1754-6834-6-89
Van Dijken, J. P. , Bauer, J. , Brambilla, L. , Duboc, P. , Francois, J. M. , Gancedo, C. , Giuseppin, M. L. , Heijnen, J. J. , Hoare, M. , Lange, H. C. , Madden, E. A. , Niederberger, P. , Nielsen, J. , Parrou, J. L. , Petit, T. , Porro, D. , Reuss, M. , van Riel, N. , Rizzi, M. , … Pronk, J. T. (2000). An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme and Microbial Technology, 26, 706-714. https://doi.org/10.1016/S0141-0229(00)00162-9
Gajewski, J. , Pavlovic, R. , Fischer, M. , Boles, E. , & Grininger, M. (2017). Engineering fungal de novo fatty acid synthesis for short chain fatty acid production. Nature Communications, 8, 14650. https://doi.org/10.1038/ncomms14650
Generoso, W. C. , Gottardi, M. , Oreb, M. , & Boles, E. (2016). Simplified CRISPR-Cas genome editing for Saccharomyces cerevisiae . Journal of Microbiological Methods, 127, 203-205. https://doi.org/10.1016/j.mimet.2016.06.020
Giaever, G. , Chu, A. M. , Ni, L. , Connelly, C. , Riles, L. , Véronneau, S. , Dow, S. , Lucau-Danila, A. , Anderson, K. , André, B. , Arkin, A. P. , Astromoff, A. , El-Bakkoury, M. , Bangham, R. , Benito, R. , Brachat, S. , Campanaro, S. , Curtiss, M. , Davis, K. , … Johnston, M. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387-391. https://doi.org/10.1038/nature00935
Gietz, R. D. , & Schiestl, R. H. (2007). Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method. Nature Protocols, 2, 1-4. https://doi.org/10.1038/nprot.2007.17
Grabowska, D. , & Chelstowska, A. (2003). The ALD6 gene product is indispensable for providing NADPH in yeast cells lacking glucose-6-phosphate dehydrogenase activity. The Journal of Biological Chemistry, 278, 13984-13988. https://doi.org/10.1074/jbc.M210076200
Hamacher, T. , Becker, J. , Gardonyi, M. , Hahn-Hägerdal, B. , & Boles, E. (2002). Characterization of the xylose-transporting properties of yeast hexose transporters and their influence on xylose utilization. Microbiology, 148, 2783-2788. https://doi.org/10.1099/00221287-148-9-2783
Henritzi, S. , Fischer, M. , Grininger, M. , Oreb, M. , & Boles, E. (2018). An engineered fatty acid synthase combined with a carboxylic acid reductase enables de novo production of 1-octanol in Saccharomyces cerevisiae . Biotechnology for Biofuels, 11, 150. https://doi.org/10.1186/s13068-018-1149-1
Ichihara, K. , & Fukubayashi, Y. (2010). Preparation of fatty acid methyl esters for gas-liquid chromatography. Journal of Lipid Research, 51, 635-640. https://doi.org/10.1194/jlr.D001065
De Jong, B. W. , de, Shi, S. , Siewers, V. , & Nielsen, J. (2014). Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway. Microbial Cell Factories, 13, 39. https://doi.org/10.1186/1475-2859-13-39
Karim, A. S. , Curran, K. A. , & Alper, H. S. (2013). Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications. FEMS Yeast Research, 13, 107-116. https://doi.org/10.1111/1567-1364.12016
Krivoruchko, A. , Serrano-Amatriain, C. , Chen, Y. , Siewers, V. , & Nielsen, J. (2013). Improving biobutanol production in engineered Saccharomyces cerevisiae by manipulation of acetyl-CoA metabolism. Journal of Industrial Microbiology & Biotechnology, 40, 1051-1056. https://doi.org/10.1007/s10295-013-1296-0
Krivoruchko, A. , Zhang, Y. , Siewers, V. , Chen, Y. , & Nielsen, J. (2015). Microbial acetyl-CoA metabolism and metabolic engineering. Metabolic Engineering, 28, 28-42. https://doi.org/10.1016/j.ymben.2014.11.009
Kwak, S. , Yun, E. J. , Lane, S. , Oh, E. J. , Kim, K. H. , & Jin, Y.-S. (2019). Redirection of the glycolytic flux enhances isoprenoid production in Saccharomyces cerevisiae . Biotechnology Journal, 15, e1900173. https://doi.org/10.1002/biot.201900173
Leber, C. , Choi, J. W. , Polson, B. , & Da Silva, N. A. (2016). Disrupted short chain specific beta-oxidation and improved synthase expression increase synthesis of short chain fatty acids in Saccharomyces cerevisiae . Biotechnology and Bioengineering, 113, 895-900. https://doi.org/10.1002/bit.25839
Lee, M. E. , DeLoache, W. C. , Cervantes, B. , & Dueber, J. E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. ACS Synthetic Biology, 4, 975-986. https://doi.org/10.1021/sb500366v
Legras, J. L. , Erny, C. , Le Jeune, C. , Lollier, M. , Adolphe, Y. , Demuyter, C. , Delobel, P. , Blondin, B. , & Karst, F. (2010). Activation of two different resistance mechanisms in Saccharomyces cerevisiae upon exposure to octanoic and decanoic acids. Applied and Environmental Microbiology, 76, 7526-7535. https://doi.org/10.1128/AEM.01280-10
Li, X. , Guo, D. , Cheng, Y. , Zhu, F. , Deng, Z. , & Liu, T. (2014). Overproduction of fatty acids in engineered Saccharomyces cerevisiae . Biotechnology and Bioengineering, 111, 1841-1852. https://doi.org/10.1002/bit.25239
Lian, J. , Si, T. , Nair, N. U. , & Zhao, H. (2014). Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. Metabolic Engineering, 24, 139-149. https://doi.org/10.1016/j.ymben.2014.05.010
Liu, P. , Chernyshov, A. , Najdi, T. , Fu, Y. , Dickerson, J. , Sandmeyer, S. , & Jarboe, L. (2013). Membrane stress caused by octanoic acid in Saccharomyces cerevisiae . Applied Microbiology and Biotechnology, 97, 3239-3251. https://doi.org/10.1007/s00253-013-4773-5
Meadows, A. L. , Hawkins, K. M. , Tsegaye, Y. , Antipov, E. , Kim, Y. , Raetz, L. , Dahl, R. H. , Tai, A. , Mahatdejkul-Meadows, T. , Xu, L. , Zhao, L. , Dasika, M. S. , Murarka, A. , Lenihan, J. , Eng, D. , Leng, J. S. , Liu, C. L. , Wenger, J. W. , Jiang, H. , … Tsong, A. E. (2016). Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature, 537, 694-697. https://doi.org/10.1038/nature19769
Niehus, X. , Crutz-Le Coq, A. M. , Sandoval, G. , Nicaud, J. M. , & Ledesma-Amaro, R. (2018). Engineering Yarrowia lipolytica to enhance lipid production from lignocellulosic materials. Biotechnology for Biofuels, 11, 11. https://doi.org/10.1186/s13068-018-1010-6
Nielsen, J. (2014). Synthetic biology for engineering acetyl coenzyme A metabolism in yeast. mBio, 5, e02153. https://doi.org/10.1128/mBio.02153-14
Oldenburg, K. R. , Vo, K. T. , Michaelis, S. , & Paddon, C. (1997). Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Research, 25, 451-452. https://doi.org/10.1093/nar/25.2.451
Paquin, C. E. , & Williamson, V. M. (1986). Ty insertions at two loci account for most of the spontaneous antimycin A resistance mutations during growth at 15°C of Saccharomyces cerevisiae strains lacking ADHI. Molecular and Cellular Biology, 6, 70-79. https://doi.org/10.1128/MCB.6.1.70
Pronk, J. T. , Steensma, H. Y. , & van Dijken, J. P. (1996). Pyruvate metabolism in Saccharomyces cerevisiae . Yeast, 12, 1607-1633. https://doi.org/10.1002/(sici)1097-0061(199612)12:16%3C;1607::aid-yea70%3E;3.0.co;2-4
Van Rossum, H. M. , Kozak, B. U. , Pronk, J. T. , & van Maris, A. J. A. (2016). Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: Pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metabolic Engineering, 36, 99-115. https://doi.org/10.1016/j.ymben.2016.03.006
Runguphan, W. , & Keasling, J. D. (2014). Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals. Metabolic Engineering, 21, 103-113. https://doi.org/10.1016/j.ymben.2013.07.003
Shiba, Y. , Paradise, E. M. , Kirby, J. , Ro, D.-K. , & Keasling, J. D. (2007). Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metabolic Engineering, 9(2), 160-168. https://doi.org/10.1016/j.ymben.2006.10.005
Starai, V. J. , Gardner, J. G. , & Escalante-Semerena, J. C. (2005). Residue Leu-641 of acetyl-CoA synthetase is critical for the acetylation of residue Lys-609 by the protein acetyltransferase enzyme of Salmonella enterica . The Journal of Biological Chemistry, 280, 26200-26205. https://doi.org/10.1074/jbc.M504863200
Valle-Rodríguez, J. O. , Shi, S. , Siewers, V. , & Nielsen, J. (2014). Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid ethyl esters, an advanced biofuel, by eliminating non-essential fatty acid utilization pathways. Applied Energy, 115, 226-232. https://doi.org/10.1016/j.apenergy.2013.10.003
Viegas, C. A. , Rosa, M. F. , Sà-Correia, I. , & Novais, J. M. (1989). Inhibition of yeast growth by octanoic and decanoic acids produced during ethanolic fermentation. Applied and Environmental Microbiology, 55, 21-28. https://doi.org/10.1128/AEM.55.1.21-28.1989
Viegas, C. A. , & Sá-Correia, I. (1997). Effects of low temperatures (9-33°C) and pH (3.3-5.7) in the loss of Saccharomyces cerevisiae viability by combining lethal concentrations of ethanol with octanoic and decanoic acids. International Journal of Food Microbiology, 34, 267-277. https://doi.org/10.1016/s0168-1605(96)01200-7
Wernig, F. , Born, S. , Boles, E. , Grininger, M. , & Oreb, M. (2020). Fusing α and β subunits of the fungal fatty acid synthase leads to improved production of fatty acids. Scientific Reports, 10, 9780. https://doi.org/10.1038/s41598-020-66629-y
Xu, P. , Qiao, K. , Ahn, W. S. , & Stephanopoulos G . (2016). Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals. Proceedings of the National Academy of Sciences of the United States of America, 113(39), 10848-10853. https://doi.org/10.1073/pnas.1607295113
Yu, T. , Zhou, Y. , Wenning, L. , Liu, Q. , Krivoruchko, A. , Siewers, V. , Nielsen, J. , & David, F. (2017). Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nature Communications, 8, 15587. https://doi.org/10.1038/ncomms15587
Yu, T. , Zhou, Y. J. , Huang, M. , Liu, Q. , Pereira, R. , David, F. , & Nielsen, J. (2018). Reprogramming yeast metabolism from alcoholic fermentation to lipogenesis. Cell, 174, 1549-1558. https://doi.org/10.1016/j.cell.2018.07.013
Zhou, Y. J. , Buijs, N. A. , Zhu, Z. , Qin, J. , Siewers, V. , & Nielsen, J. (2016). Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories. Nature Communications, 7, 11709. https://doi.org/10.1038/ncomms11709
Zhu, Z. , Hu, Y. , Teixeira, P. G. , Pereira, R. , Chen, Y. , Siewers, V. , & Nielsen, J. (2020). Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids. Nature Catalysis, 3, 64-74. https://doi.org/10.1038/s41929-019-0409-1