Regulating the metabolic flux of pyruvate dehydrogenase bypass to enhance lipid production in Saccharomyces cerevisiae.
Saccharomyces cerevisiae
/ genetics
Pyruvate Dehydrogenase Complex
/ metabolism
Lipid Metabolism
Saccharomyces cerevisiae Proteins
/ metabolism
Lipids
/ biosynthesis
Acetyl Coenzyme A
/ metabolism
Gene Expression Regulation, Fungal
Metabolic Engineering
/ methods
Aldehyde Oxidoreductases
/ metabolism
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
26 Oct 2024
26 Oct 2024
Historique:
received:
09
05
2024
accepted:
18
10
2024
medline:
27
10
2024
pubmed:
27
10
2024
entrez:
27
10
2024
Statut:
epublish
Résumé
To achieve high efficiency in microbial cell factories, it is crucial to redesign central carbon fluxes to ensure an adequate supply of precursors for producing high-value compounds. In this study, we employed a multi-omics approach to rearrange the central carbon flux of the pyruvate dehydrogenase (PDH) bypass, thereby enhancing the supply of intermediate precursors, specifically acetyl-CoA. This enhancement aimed to improve the biosynthesis of acetyl-CoA-derived compounds, such as terpenoids and fatty acid-derived molecules, in Saccharomyces cerevisiae. Through transcriptomic and lipidomic analyses, we identified ALD4 as a key regulatory gene influencing lipid metabolism. Genetic validation demonstrated that overexpression of the mitochondrial acetaldehyde dehydrogenase (ALDH) gene ALD4 resulted in a 20.1% increase in lipid production. This study provides theoretical support for optimising the performance of S. cerevisiae as a "cell factory" for the production of commercial compounds.
Identifiants
pubmed: 39462103
doi: 10.1038/s42003-024-07103-7
pii: 10.1038/s42003-024-07103-7
doi:
Substances chimiques
Pyruvate Dehydrogenase Complex
0
Saccharomyces cerevisiae Proteins
0
Lipids
0
Acetyl Coenzyme A
72-89-9
aldehyde dehydrogenase (NAD(P)+)
EC 1.2.1.5
Aldehyde Oxidoreductases
EC 1.2.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1399Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 11975284
Informations de copyright
© 2024. The Author(s).
Références
Ko, Y. S. et al. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production. Chem. Soc. Rev. 49, 4615–4636 (2020).
pubmed: 32567619
doi: 10.1039/D0CS00155D
Su, B. et al. Engineering a balanced acetyl coenzyme a metabolism in Saccharomyces cerevisiae for lycopene production through rational and evolutionary engineering. J. Agric. Food Chem. 70, 4019–4029 (2022).
pubmed: 35319878
doi: 10.1021/acs.jafc.2c00531
Yuan, J. F. & Ching, C. B. Mitochondrial acetyl-CoA utilization pathway for terpenoid productions. Metab. Eng. 38, 303–309 (2016).
pubmed: 27471067
doi: 10.1016/j.ymben.2016.07.008
Chen, Y., Daviet, L., Schalk, M., Siewers, V. & Nielsen, J. Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metab. Eng. 15, 48–54 (2013).
pubmed: 23164578
doi: 10.1016/j.ymben.2012.11.002
Lin, P. et al. Direct utilization of peroxisomal acetyl-CoA for the synthesis of polyketide compounds in Saccharomyces cerevisiae. ACS Synth. Biol. 12, 1599–1607 (2023).
pubmed: 37172280
doi: 10.1021/acssynbio.2c00678
Xu, Y. P. et al. De novo biosynthesis of salvianolic acid B in Saccharomyces cerevisiae engineered with the rosmarinic acid biosynthetic pathway. J. Agric. Food Chem. 70, 2290–2302 (2022).
pubmed: 35157428
doi: 10.1021/acs.jafc.1c06329
Pronk, J. T., Steensma, H. Y. & vanDijken, J. P. Pyruvate metabolism in Saccharomyces cerevisiae. Yeast 12, 1607–1633 (1996).
pubmed: 9123965
doi: 10.1002/(SICI)1097-0061(199612)12:16<1607::AID-YEA70>3.0.CO;2-4
Liu, W., Zhang, B. & Jiang, R. Improving acetyl-CoA biosynthesis in Saccharomyces cerevisiae via the overexpression of pantothenate kinase and PDH bypass. Biotechnol. Biofuels 10, 41 (2017).
pubmed: 28239413
pmcid: 5316175
doi: 10.1186/s13068-017-0726-z
van Rossum, H. M., Kozak, B. U., Pronk, J. T. & van Maris, A. J. A. Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metab. Eng. 36, 99–115 (2016).
pubmed: 27016336
doi: 10.1016/j.ymben.2016.03.006
Koivuranta, K. et al. Enhanced triacylglycerol production with genetically modified Trichosporon oleaginosus. Front. Microbiol. 9, 1337 (2018).
pubmed: 29977232
pmcid: 6021488
doi: 10.3389/fmicb.2018.01337
Boubekeur, S. et al. A mitochondrial pyruvate dehydrogenase bypass in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 274, 21044–21048 (1999).
pubmed: 10409655
doi: 10.1074/jbc.274.30.21044
Navarro-Avino, J. P., Prasad, R., Miralles, V. J., Benito, R. M. & Serrano, R. A proposal for nomenclature of aldehyde dehydrogenases in Saccharomyces cerevisiae and characterization of the stress-inducible ALD2 and ALD3 genes. Yeast 15, 829–842 (1999).
pubmed: 10407263
doi: 10.1002/(SICI)1097-0061(199907)15:10A<829::AID-YEA423>3.0.CO;2-9
Meaden, P. G. et al. The ALD6 gene of Saccharomyces cerevisiae encodes a cytosolic, Mg
pubmed: 9392076
doi: 10.1002/(SICI)1097-0061(199711)13:14<1319::AID-YEA183>3.0.CO;2-T
Tessier, W. D., Meaden, P. G., Dickinson, F. M. & Midgley, M. Identification and disruption of the gene encoding the K
pubmed: 9675847
doi: 10.1111/j.1574-6968.1998.tb13063.x
Wang, X. P., Mann, C. J., Bai, Y. L., Ni, L. & Weiner, H. Molecular cloning, characterization, and potential roles of cytosolic and mitochondrial aldehyde dehydrogenases in ethanol metabolism in Saccharomyces cerevisiae. J. Bacteriol. 180, 822–830 (1998).
pubmed: 9473035
pmcid: 106960
doi: 10.1128/JB.180.4.822-830.1998
Wernig, F., Baumann, L., Boles, E. & Oreb, M. Production of octanoic acid in Saccharomyces cerevisiae: investigation of new precursor supply engineering strategies and intrinsic limitations. Biotechnol. Bioeng. 118, 3046–3057 (2021).
pubmed: 34003487
doi: 10.1002/bit.27814
Su, B., Song, D., Yang, F. & Zhu, H. Engineering a growth-phase-dependent biosynthetic pathway for carotenoid production in Saccharomyces cerevisiae. J. Ind. Microbiol. Biotechnol. 47, 383–393 (2020).
pubmed: 32236768
doi: 10.1007/s10295-020-02271-x
Saint-Prix, F., Bonquist, L. & Dequin, S. Functional analysis of the ALD gene family of Saccharomyces cerevisiae during anaerobic growth on glucose: the NADP
pubmed: 15256563
doi: 10.1099/mic.0.26999-0
Remize, F., Andrieu, E. & Dequin, S. Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae: role of the cytosolic Mg
pubmed: 10919763
pmcid: 92127
doi: 10.1128/AEM.66.8.3151-3159.2000
Wang, X., Sa, N., Wang, F. H. & Tian, P. F. Engineered constitutive pathway in Klebsiella pneumoniae for 3-hydroxypropionic acid production and implications for decoupling glycerol dissimilation pathways. Curr. Microbiol. 66, 293–299 (2013).
pubmed: 23192305
doi: 10.1007/s00284-012-0271-8
Chen, L. N., Li, Y. & Tian, P. F. Enhanced promoter activity by replenishment of sigma factor rpoE in Klebsiella pneumoniae. Indian J. Microbiol. 56, 190–197 (2016).
pubmed: 27570311
pmcid: 4984433
doi: 10.1007/s12088-016-0576-6
Holyavkin, C. et al. Genomic, transcriptomic, and metabolic characterization of 2-phenylethanol-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Front. Microbiol. 14, 1148065 (2023).
pubmed: 37113225
pmcid: 10127108
doi: 10.3389/fmicb.2023.1148065
Aranda, A. & del Olmo, M. L. Response to acetaldehyde stress in the yeast Saccharomyces cerevisiae involves a strain-dependent regulation of several ALD genes and is mediated by the general stress response pathway. Yeast 20, 747–759 (2003).
pubmed: 12794936
doi: 10.1002/yea.991
Parmar, J. H., Bhartiya, S. & Venkatesh, K. V. Characterization of the adaptive response and growth upon hyperosmotic shock in Saccharomyces cerevisiae. Mol. Biosyst. 7, 1138–1148 (2011).
pubmed: 21234493
doi: 10.1039/c0mb00224k
Singh, S. et al. Aldehyde dehydrogenases in cellular responses to oxidative/electrophilic stress. Free Radic. Bio. Med. 56, 89–101 (2013).
doi: 10.1016/j.freeradbiomed.2012.11.010
Guo, X. P. et al. Quantitative multi-omics analysis of the effects of mitochondrial dysfunction on lipid metabolism in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 104, 1211–1226 (2020).
pubmed: 31832712
doi: 10.1007/s00253-019-10260-z
Ganesan, S., Shabits, B. N. & Zaremberg, V. Tracking diacylglycerol and phosphatidic acid pools in budding yeast. Lipid Insights 8, 75–85 (2015).
pubmed: 27081314
Boubekeur, S., Camougrand, N., Bunoust, O., Rigoulet, M. & Guerin, B. Participation of acetaldehyde dehydrogenases in ethanol and pyruvate metabolism of the yeast Saccharomyces cerevisiae. Eur. J. Biochem. 268, 5057–5065 (2001).
pubmed: 11589696
doi: 10.1046/j.1432-1033.2001.02418.x
Miyagi, H., Kawai, S. & Murata, K. Two sources of mitochondrial NADPH in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 284, 7553–7560 (2009).
pubmed: 19158096
pmcid: 2658050
doi: 10.1074/jbc.M804100200
Chen, Y., Zhang, Y., Siewers, V. & Nielsen, J. Ach1 is involved in shuttling mitochondrial acetyl units for cytosolic C2 provision in Saccharomyces cerevisiae lacking pyruvate decarboxylase. FEMS Yeast Res. 15, fov015 (2015).
pubmed: 25852051
doi: 10.1093/femsyr/fov015
Milke, L., Aschenbrenner, J., Marienhagen, J. & Kallscheuer, N. Production of plant-derived polyphenols in microorganisms: current state and perspectives. Appl. Microbiol. Biotechnol. 102, 1575–1585 (2018).
pubmed: 29340710
doi: 10.1007/s00253-018-8747-5
Milke, L. & Marienhagen, J. Engineering intracellular malonyl-CoA availability in microbial hosts and its impact on polyketide and fatty acid synthesis. Appl. Microbiol. Biotechnol. 104, 6057–6065 (2020).
pubmed: 32385515
pmcid: 7316851
doi: 10.1007/s00253-020-10643-7
Zhang, Q., Zeng, W. Z., Xu, S. & Zhou, J. W. Metabolism and strategies for enhanced supply of acetyl-CoA in Saccharomyces cerevisiae. Bioresour. Technol. 342, 125978 (2021).
pubmed: 34598073
doi: 10.1016/j.biortech.2021.125978
Lian, J. Z., Si, T., Nair, N. U. & Zhao, H. M. Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. Metab. Eng. 24, 139–149 (2014).
pubmed: 24853351
doi: 10.1016/j.ymben.2014.05.010
Xiao, T., Khan, A., Shen, Y., Chen, L. & Rabinowitz, J. D. Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast. Nat. Chem. Biol. 18, 1380–1387 (2022).
pubmed: 35970997
doi: 10.1038/s41589-022-01091-7
Shiba, Y., Paradise, E. M., Kirby, J., Ro, D. K. & Keasing, J. D. Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab. Eng. 9, 160–168 (2007).
pubmed: 17196416
doi: 10.1016/j.ymben.2006.10.005
Li, X. W. et al. Overproduction of fatty acids in engineered Saccharomyces cerevisiae. Biotechnol. Bioeng. 111, 1841–1852 (2014).
pubmed: 24752690
doi: 10.1002/bit.25239
Qiu, J. et al. Boosting the cannabidiol production in engineered Saccharomyces cerevisiae by harnessing the vacuolar transporter BPT1. J. Agric. Food Chem. 70, 12055–12064 (2022).
pubmed: 36122349
doi: 10.1021/acs.jafc.2c05468
Shi, L. & Tu, B. P. Acetyl-CoA and the regulation of metabolism: mechanisms and consequences. Curr. Opin. Cell Biol. 33, 125–131 (2015).
pubmed: 25703630
pmcid: 4380630
doi: 10.1016/j.ceb.2015.02.003
Liu, K., Zhang, X., Sumanasekera, C., Lester, R. L. & Dickson, R. C. Signalling functions for sphingolipid long-chain bases in Saccharomyces cerevisiae. Biochem. Soc. Trans. 33, 1170–1173 (2005).
pubmed: 16246074
doi: 10.1042/BST0331170
Mao, C. G., Xu, R. J., Bielawska, A. & Obeid, L. M. Cloning of an alkaline ceramidase from Saccharomyces cerevisiae: an enzyme with reverse (CoA-independent) ceramide synthase activity. J. Biol. Chem. 275, 6876–6884 (2000).
pubmed: 10702247
doi: 10.1074/jbc.275.10.6876
Giudetti, A. M., Stanca, E., Siculella, L., Gnoni, G. V. & Damiano, F. Nutritional and hormonal regulation of citrate and carnitine/acylcarnitine transporters: two mitochondrial carriers involved in fatty acid metabolism. Int. J. Mol. Sci. 17, 817–817 (2016).
pubmed: 27231907
pmcid: 4926351
doi: 10.3390/ijms17060817
Dong, Y., Hu, J., Fan, L. & Chen, Q. RNA-Seq-based transcriptomic and metabolomic analysis reveal stress responses and programmed cell death induced by acetic acid in Saccharomyces cerevisiae. Sci. Rep. 7, 42659–42659 (2017).
pubmed: 28209995
pmcid: 5314350
doi: 10.1038/srep42659
Hiltunen, J. K., Chen, Z. J., Haapalainen, A. M., Wierenga, R. K. & Kastaniotis, A. J. Mitochondrial fatty acid synthesis - an adopted set of enzymes making a pathway of major importance for the cellular metabolism. Prog. Lipid Res. 49, 27–45 (2010).
pubmed: 19686777
doi: 10.1016/j.plipres.2009.08.001
Henderson, C. M., Lozada-Contreras, M., Naravane, Y., Longo, M. L. & Block, D. E. Analysis of major phospholipid species and ergosterol in fermenting industrial yeast strains using atmospheric pressure ionization ion-trap mass spectrometry. J. Agric. Food Chem. 59, 12761–12770 (2011).
pubmed: 21995817
doi: 10.1021/jf203203h
Sitepu, I. R. et al. Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeast species. Bioresour. Technol. 144, 360–369 (2013).
pubmed: 23891835
doi: 10.1016/j.biortech.2013.06.047
Klug, L. & Daum, G. Yeast lipid metabolism at a glance. FEMS Yeast Res. 14, 369–388 (2014).
pubmed: 24520995
doi: 10.1111/1567-1364.12141
Tang, X. L., Feng, H. X. & Chen, W. N. Metabolic engineering for enhanced fatty acids synthesis in Saccharomyces cerevisiae. Metab. Eng. 16, 95–102 (2013).
pubmed: 23353549
doi: 10.1016/j.ymben.2013.01.003
Lin, H., Castro, N. M., Bennett, G. N. & San, K. Y. Acetyl-CoA synthetase overexpression in Escherichia coli demonstrates more efficient acetate assimilation and lower acetate accumulation: a potential tool in metabolic engineering. Appl. Microbiol. Biotechnol. 71, 870–874 (2006).
pubmed: 16496143
doi: 10.1007/s00253-005-0230-4
Ni, J., Zhang, G., Qin, L., Li, J. & Li, C. Simultaneously down-regulation of multiplex branch pathways using CRISPRi and fermentation optimization for enhancing β-amyrin production in Saccharomyces cerevisiae. Synth. Syst. Biotechnol. 4, 79–85 (2019).
pubmed: 30949594
pmcid: 6428687
doi: 10.1016/j.synbio.2019.02.002
Shi, B. et al. Systematic metabolic engineering of Saccharomyces cerevisiae for lycopene overproduction. J. Agric. Food Chem. 67, 11148–11157 (2019).
pubmed: 31532654
doi: 10.1021/acs.jafc.9b04519
de Jong, B. W., Shi, S., Siewers, V. & Nielsen, J. 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. Microb. Cell Fact. 13, 39 (2014).
pubmed: 24618091
pmcid: 3995654
doi: 10.1186/1475-2859-13-39
Cardenas, J. & Da Silva, N. A. Engineering cofactor and transport mechanisms in Saccharomyces cerevisiae for enhanced acetyl-CoA and polyketide biosynthesis. Metab. Eng. 36, 80–89 (2016).
pubmed: 26969250
doi: 10.1016/j.ymben.2016.02.009
Hiltunen, J. K. et al. The biochemistry of peroxisomal β-oxidation in the yeast Saccharomyces cerevisiae. FEMS Microbiol. Rev. 27, 35–64 (2003).
pubmed: 12697341
doi: 10.1016/S0168-6445(03)00017-2
Dimmer, K. S. et al. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol. Biol. Cell 13, 847–853 (2002).
pubmed: 11907266
pmcid: 99603
doi: 10.1091/mbc.01-12-0588
Vamecq, J. et al. Mitochondrial dysfunction and lipid homeostasis. Curr. Drug Metab. 13, 1388–1400 (2012).
pubmed: 22978394
doi: 10.2174/138920012803762792
Aon, M. A., Bhatt, N. & Cortassa, S. C. Mitochondrial and cellular mechanisms for managing lipid excess. Front. Physiol. 5, 282 (2014).
pubmed: 25132820
pmcid: 4116787
doi: 10.3389/fphys.2014.00282
Chen, X., Li, S. & Liu, L. Engineering redox balance through cofactor systems. Trends Biotechnol. 32, 337–343 (2014).
pubmed: 24794722
doi: 10.1016/j.tibtech.2014.04.003
Cha, S., Hong, C. P., Kang, H. A. & Hahn, J. S. Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae. Nucleic Acids Res. 49, 745–759 (2021).
pubmed: 33367825
doi: 10.1093/nar/gkaa1221
Kursu, V. A. S. et al. Defects in mitochondrial fatty acid synthesis result in failure of multiple aspects of mitochondrial biogenesis in Saccharomyces cerevisiae. Mol. Microbiol. 90, 824–840 (2013).
pubmed: 24102902
pmcid: 4153884
doi: 10.1111/mmi.12402
Van Vranken, J. G. et al. ACP acylation is an acetyl-CoA-dependent modification required for electron transport chain assembly. Mol. Cell 71, 567–580 (2018).
pubmed: 30118679
pmcid: 6104058
doi: 10.1016/j.molcel.2018.06.039
Kastaniotis, A. J. et al. Mitochondrial fatty acid synthesis, fatty acids and mitochondrial physiology. Biochim. Biophys. Acta Mol. Cell Biol. Lipids 1862, 39–48 (2017).
pubmed: 27553474
doi: 10.1016/j.bbalip.2016.08.011
Masud, A. J., Kastaniotis, A. J., Rahman, M. T., Autio, K. J. & Hiltunen, J. K. Mitochondrial acyl carrier protein (ACP) at the interface of metabolic state sensing and mitochondrial function. Biochim. Biophys. Acta Mol. Cell Res. 1866, 118540 (2019).
pubmed: 31473256
doi: 10.1016/j.bbamcr.2019.118540
Gietz, D., Stjean, A., Woods, R. A. & Schiestl, R. H. Improved method for high-efficiency transformation of intact yeast-cells. Nucleic Acids Res. 20, 1425–1425 (1992).
pubmed: 1561104
pmcid: 312198
doi: 10.1093/nar/20.6.1425
Varga, E., Klinke, H. B., Réczey, K. & Thomsen, A. B. High solid simultaneous saccharification and fermentation of wet oxidized corn stover to ethanol. Biotechnol. Bioeng. 88, 567–574 (2004).
pubmed: 15470714
doi: 10.1002/bit.20222
Bradford, M. M. Rapid and sensitive method for quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal. Biochem. 72, 248–254 (1976).
pubmed: 942051
doi: 10.1016/0003-2697(76)90527-3
Modig, T., Lidén, G. & Taherzadeh, M. J. Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase. Biochem. J. 363, 769–776 (2002).
pubmed: 11964178
pmcid: 1222530
doi: 10.1042/bj3630769
Dickinson, F. M. The purification and some properties of the Mg
pubmed: 8615805
pmcid: 1217208
doi: 10.1042/bj3150393
Larroy, C., Fernández, M. R., González, E., Parés, X. & Biosca, J. A. Characterization of the Saccharomyces cerevisiae YMR318C (ADH6) gene product as a broad specificity NADPH-dependent alcohol dehydrogenase: relevance in aldehyde reduction. Biochem. J. 361, 163–172 (2002).
pubmed: 11742541
pmcid: 1222291
doi: 10.1042/bj3610163
Wang, D. et al. Metabolic engineering of Saccharomyces cerevisiae for accumulating pyruvic acid. Ann. Microbiol. 65, 2323–2331 (2015).
doi: 10.1007/s13213-015-1074-5