Abstract
Malonyl-CoA is the essential building block of natural products such as fatty acids, polyketides, and flavonoids. Engineering the biosynthesis of fatty acids is important for biofuel production while that of polyketides provides precursors of medicines and nutritional supplements. However, microorganisms maintain a small amount of cellular malonyl-CoA, which could limit production of lipid and polyketides under certain conditions. Malonyl-CoA concentration is regulated by multiple pathways and signals, and changes in intracellular malonyl-CoA often lead to complex alterations in metabolism. In the present work, overexpression of a plant malonyl-CoA synthetase gene (AAE13) in Saccharomyces cerevisiae resulted in 1.6- and 2.4-fold increases in lipid and resveratrol accumulation simultaneously. We also demonstrated that AAE13 partially complemented the temperature-sensitive acc1 mutant, replacing this key enzyme in central metabolism. Mechanistic analysis by CoA quantification and transcriptomic measurement suggested that increases in malonyl-CoA concentration were coupled with drastic reductions in other major CoA compounds and clear suppression of tricarboxylic acid cycle-related genes. These results suggest that malonyl-CoA is a critical target for fatty acid and polyketide engineering and that overexpression of malonyl-CoA synthetic enzymes needs to be combined with upregulation of CoA synthesis to maintain metastasis of central metabolism.
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References
An JH, Kim YS (1998) A gene cluster encoding malonyl-CoA decarboxylase (MatA), malonyl-CoA synthetase (MatB) and a putative dicarboxylate carrier protein (MatC) in Rhizobium trifolii—cloning, sequencing, and expression of the enzymes in Escherichia coli. Eur J Biochem 257(2):395–402
Blobel F, Erdmann R (1996) Identification of a yeast peroxisomal member of the family of AMP-binding proteins. Eur J Biochem 240(2):468–476
Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW (2005) Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J Exp Bot 56(410):323–336
Chen H, Kim HU, Weng H, Browse J (2011) Malonyl-CoA synthetase, encoded by ACYL ACTIVATING ENZYME13, is essential for growth and development of Arabidopsis. Plant Cell 23(6):2247–2262
Chen WN, Tan KY (2013) Malonate uptake and metabolism in Saccharomyces cerevisiae. Appl Biochem Biotechnol 171(1):44–62
Chohnan S, Furukawa H, Fujio T, Nishihara H, Takamura Y (1997) Changes in the size and composition of intracellular pools of nonesterified coenzyme A and coenzyme A thioesters in aerobic and facultatively anaerobic bacteria. Appl Environ Microbiol 63(2):553–560
Daum G, Paltauf F (1980) Triacylglycerols as fatty acid donors for membrane phospholipid biosynthesis in yeast. Monatsh Chem 111:355–363
Davis MS, Solbiati J, Cronan JE Jr (2000) Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J Biol Chem 275(37):28593–28598
Ekhterae D, Tae HJ, Daniel S, Moller DE, Kim KH (1996) Regulation of acetyl coenzyme-A carboxylase gene in a transgenic animal model. Biochem Biophys Res Commun 227(2):547–552
Folmes CD, Lopaschuk GD (2007) Role of malonyl-CoA in heart disease and the hypothalamic control of obesity. Cardiovasc Res 73(2):278–287
Fowler ZL, Gikandi WW, Koffas MA (2009) Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production. Appl Environ Microbiol 75(18):5831–5839
Halls C, Yu O (2008) Potential for metabolic engineering of resveratrol biosynthesis. Trends Biotechnol 26(2):77–81
Hasslacher M, Ivessa AS, Paltauf F, Kohlwein SD (1993) Acetyl-CoA carboxylase from yeast is an essential enzyme and is regulated by factors that control phospholipid metabolism. J Biol Chem 268(15):10946–10952
Hayashi E, Hasegawa R, Tomita T (1976) Accumulation of neutral lipids in Saccharomyces carlsbergensis by myo-inositol deficiency and its mechanism. Reciprocal regulation of yeast acetyl-CoA carboxylase by fructose bisphosphate and citrate. J Biol Chem 251(18):5759–5769
Hoja U, Marthol S, Hofmann J, Stegner S, Schulz R, Meier S, Greiner E, Schweizer E (2004) HFA1 encoding an organelle-specific acetyl-CoA carboxylase controls mitochondrial fatty acid synthesis in Saccharomyces cerevisiae. J Biol Chem 279(21):21779–21786
Hughes AJ, Keatinge-Clay A (2011) Enzymatic extender unit generation for in vitro polyketide synthase reactions: structural and functional showcasing of Streptomyces coelicolor MatB. Chem Biol 18(2):165–176
Jin YS, Alper H, Yang YT, Stephanopoulos G (2005) Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol 71(12):8249–8256
Kamisaka Y, Noda N, Sakai T, Kawasaki K (1999) Lipid bodies and lipid body formation in an oleaginous fungus, Mortierella ramanniana var. angulispora. Biochim Biophys Acta 1438(2):185–198
Kamisaka Y, Noda N, Tomita N, Kimura K, Kodaki T, Hosaka K (2006) Identification of genes affecting lipid content using transposon mutagenesis in Saccharomyces cerevisiae. Biosci Biotechnol Biochem 70(3):646–653
Kaya K, Sano T (1996) Algicidal compounds in yeast extract as a component of microbial culture media. Phycologia 35(6S):117–119
Leonard E, Yan Y, Fowler ZL, Li Z, Lim CG, Lim KH, Koffas MA (2008) Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol Pharm 5(2):257–265
Leonardi R, Zhang YM, Rock CO, Jackowski S (2005) Coenzyme A: back in action. Prog Lipid Res 44(2–3):125–153
Li Y, Han D, Hu G, Sommerfeld M, Hu Q (2010) Inhibition of starch synthesis results in overproduction of lipids in Chlamydomonas reinhardtii. Biotechnol Bioeng 107(2):258–268
Miyahisa I, Kaneko M, Funa N, Kawasaki H, Kojima H, Ohnishi Y, Horinouchi S (2005) Efficient production of (2S)-flavanones by Escherichia coli containing an artificial biosynthetic gene cluster. Appl Microbiol Biotechnol 68(4):498–504
Nakamura T, Pluskal T, Nakaseko Y, Yanagida M (2012) Impaired coenzyme A synthesis in fission yeast causes defective mitosis, quiescence-exit failure, histone hypoacetylation and fragile DNA. Open Biol 2(9):120117
Olzhausen J, Schübbe S, Schüller HJ (2009) Genetic analysis of coenzyme A biosynthesis in the yeast Saccharomyces cerevisiae: identification of a conditional mutation in the pantothenate kinase gene CAB1. Curr Genet 55(2):163–173
Park SR, Ahn MS, Han AR, Park JW, Yoon YJ (2011) Enhanced flavonoid production in Streptomyces venezuelae via metabolic engineering. J Microbiol Biotechnol 21(11):1143–1146
Perera MA, Choi SY, Wurtele ES, Nikolau BJ (2009) Quantitative analysis of short-chain acyl-coenzyme As in plant tissues by LC-MS-MS electrospray ionization method. J Chromatogr B Anal Technol Biomed Life Sci 877(5–6):482–488
Ralston L, Subramanian S, Matsuno M, Yu O (2005) Partial reconstruction of flavonoid and isoflavonoid biosynthesis in yeast using soybean type I and type II chalcone isomerases. Plant Physiol 137(4):1375–1388
Roesler K, Shintani D, Savage L, Boddupalli S, Ohlrogge J (1997) Targeting of the Arabidopsis homomeric acetyl-coenzyme A carboxylase to plastids of rapeseeds. Plant Physiol 113(1):75–81
Ruenwai R, Cheevadhanarak S, Laoteng K (2009) Overexpression of acetyl-CoA carboxylase gene of Mucor rouxii enhanced fatty acid content in Hansenula polymorpha. Mol Biotechnol 42(3):327–332
Saggerson D (2008) Malonyl-CoA, a key signaling molecule in mammalian cells. Annu Rev Nutr 28:253–272
Schneiter R, Hitomi M, Ivessa AS, Fasch EV, Kohlwein SD, Tartakoff AM (1996) A yeast acetyl coenzyme A carboxylase mutant links very-long-chain fatty acid synthesis to the structure and function of the nuclear membrane-pore complex. Mol Cell Biol 16(12):7161–7172
Schneiter R, Guerra CE, Lampl M, Tatzer V, Zellnig G, Klein HL, Kohlwein SD (2000) A novel cold-sensitive allele of the rate-limiting enzyme of fatty acid synthesis, acetyl coenzyme A carboxylase, affects the morphology of the yeast vacuole through acylation of Vac8p. Mol Cell Biol 20(9):2984–2995
Shin GH, Veen M, Stahl U, Lang C (2012) Overexpression of genes of the fatty acid biosynthetic pathway leads to accumulation of sterols in Saccharomyces cerevisiae. Yeast 29(9):371–383
Shintani D, Roesler K, Shorrosh B, Savage L, Ohlrogge J (1997) Antisense expression and overexpression of biotin carboxylase in tobacco leaves. Plant Physiol 114(3):881–886
Shockey JM, Fulda MS, Browse J (2003) Arabidopsis contains a large superfamily of acyl-activating enzymes. Phylogenetic and biochemical analysis reveals a new class of acyl-coenzyme a synthetases. Plant Physiol 132(2):1065–1076
Sloan JL, Johnston JJ, Manoli I, Chandler RJ, Krause C, Carrillo-Carrasco N, Chandrasekaran SD, Sysol JR, O'Brien K, Hauser NS, Sapp JC, Dorward HM, Huizing M, Barshop BA, Berry SA, James PM, Champaigne NL, de Lonlay P, Valayannopoulos V, Geschwind MD, Gavrilov DK, Nyhan WL, Biesecker LG, Venditti CP (2011) Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nat Genet 43(9):883–886
Smith CM, Bryla J, Williamson JR (1974) Regulation of mitochondrial α-ketoglutarate metabolism by product inhibition at α-ketoglutarate dehydrogenase. J Biol Chem 249(5):1497–505
Tehlivets O, Scheuringer K, Kohlwein SD (2007) Fatty acid synthesis and elongation in yeast. Biochim Biophys Acta 1771(3):255–270
Tong L (2005) Acetyl-coenzyme A carboxylase: crucial metabolic enzyme and attractive target for drug discovery. Cell Mol Life Sci 62(16):1784–1803
Torres-Giner S, Martinez-Abad A, Ocio MJ, Lagaron JM (2010) Stabilization of a nutraceutical omega-3 fatty acid by encapsulation in ultrathin electrosprayed zein prolamine. J Food Sci 75(6):N69–79
Urban P, Mignotte C, Kazmaier M, Delorme F, Pompon D (1997) Cloning, yeast expression, and characterization of the coupling of two distantly related Arabidopsis thaliana NADPH-cytochrome P450 reductases with P450 CYP73A5. J Biol Chem 272(31):19176–19186
Wang X, Yomano LP, Lee JY, York SW, Zheng H, Mullinnix MT, Shanmugam KT, Ingram LO (2013) Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals. Proc Natl Acad Sci U S A 110(10):4021–4026
Wang Y, Chen H, Yu O (2010) Metabolic engineering of resveratrol and other longevity boosting compounds. Biofactors 36(5):394–400
Wang Y, Chen S, Yu O (2011a) Metabolic engineering of flavonoids in plants and microorganisms. Appl Microbiol Biotechnol 91(4):949–956
Wang Y, Halls C, Zhang J, Matsuno M, Zhang Y, Yu O (2011b) Stepwise increase of resveratrol biosynthesis in yeast Saccharomyces cerevisiae by metabolic engineering. Metab Eng 13(5):455–463
Wawrik B, Kerkhof L, Zylstra GJ, Kukor JJ (2005) Identification of unique type II polyketide synthase genes in soil. Appl Environ Microbiol 71(5):2232–2238
Wink M (2003) Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective. Phytochemistry 64(1):3–19
Witkowski A, Thweatt J, Smith S (2011) Mammalian ACSF3 protein is a malonyl-CoA synthetase that supplies the chain extender units for mitochondrial fatty acid synthesis. J Biol Chem 286(39):33729–33736
Work VH, Radakovits R, Jinkerson RE, Meuser JE, Elliott LG, Vinyard DJ, Laurens LM, Dismukes GC, Posewitz MC (2010) Increased lipid accumulation in the Chlamydomonas reinhardtii sta7-10 starchless isoamylase mutant and increased carbohydrate synthesis in complemented strains. Eukaryot Cell 9(8):1251–1261
Xu P, Ranganathan S, Fowler ZL, Maranas CD, Koffas MA (2011) Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng 13(5):578–587
Xu P, Gu Q, Wang W, Wong L, Bower AG, Collins CH, Koffas MA (2013) Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun 4:1409
Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, Boldt J, Khandurina J, Trawick JD, Osterhout RE, Stephen R, Estadilla J, Teisan S, Schreyer HB, Andrae S, Yang TH, Lee SY, Burk MJ, Van Dien S (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7(7):445–452
Yomano LP, York SW, Shanmugam KT, Ingram LO (2009) Deletion of methylglyoxal synthase gene (mgsA) increased sugar co-metabolism in ethanol-producing Escherichia coli. Biotechnol Lett 31(9):1389–1398
Zha W, Rubin-Pitel SB, Shao Z, Zhao H (2009) Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering. Metab Eng 11(3):192–198
Acknowledgements
We thank Dr. John Browse of Washington State University for the gift of AAE13 gene in pENTR/D-TOPO prior to its publication. This work is support in part by three federal grants: one is from US Department of Energy (DESC0001295), one from National Science Foundation (MCB-0923779), and one from US Department of Agriculture (2010-65116-20514), and National 863 projects (2013AA102801-03).
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Wang, Y., Chen, H. & Yu, O. A plant malonyl-CoA synthetase enhances lipid content and polyketide yield in yeast cells. Appl Microbiol Biotechnol 98, 5435–5447 (2014). https://doi.org/10.1007/s00253-014-5612-z
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DOI: https://doi.org/10.1007/s00253-014-5612-z