Biotechnology Letters

, Volume 36, Issue 8, pp 1557–1568 | Cite as

The role of malic enzyme as the provider of NADPH in oleaginous microorganisms: a reappraisal and unsolved problems

  • Colin RatledgeEmail author
Review and Discussion Paper


Malic enzyme (ME; NADP+-dependent; EC 1.1.40) provides NADPH for lipid biosynthesis in oleaginous microorganisms. Its role in vivo depends on there being an adequate supply of NADH to drive malate dehydrogenase to convert oxaloacetate to malate as a component of a cycle of three reactions: pyruvate → oxaloacetate → malate and, by the action of ME, back to pyruvate. However, the availability of cytosolic NADH is limited and, consequently, ancillary means of producing NADPH are necessary. Stoichiometries are given for the conversion of glucose to triacylglycerols involving ME with and without the reactions of the pentose phosphate pathway (PPP) as an additional source of NADPH. Some oleaginous microorganisms (such as Yarrowia lipolytica), however, lack a cytosolic ME and, if the PPP is the sole provider of NADPH, the theoretical yield of triacylglycerol from glucose falls to 27.6 % (w/w) from 31.6 % when ME is present. An alternative route for NADPH generation via a cytosolic isocitrate dehydrogenase (NADP+-dependent) is then discussed.


Glucose metabolism Fatty acid biosynthesis Isocitrate dehydrogenase Lipid accumulation Malic enzyme Pentose phosphate pathway Stoichiometries 



I owe a debt of gratitude to Professor Hans van Dijken, The Netherlands, for returning my attention to the unsolved problem of NADPH generation in oleaginous microorganisms that had been highlighted in an earlier review of mine (Ratledge 1997) but then had been somewhat conveniently forgotten in subsequent discussions of this topic. I am also indebted to him for a critical appraisal of the first draft of this review and for bringing to my attention some of the key papers involving the possible synthesis of isocitrate from 2-oxoglutarate in mammalian systems. Any remaining errors and oversights are entirely my own.


  1. Beopoulos A, Cescut J, Haddouche R, Uribelarrea JL, Molina-Jouve C, Nicaud JM (2009) Yarrowia lipolytica as a model for bio-oil production. Prog Lipid Res 48:375–387PubMedCrossRefGoogle Scholar
  2. Beopoulos A, Nicaud JM, Gaillardin C (2011) An overview of lipid metabolism in yeasts and its impact on biotechnological processes. Appl Microbiol Biotechnol 90:1193–1206PubMedCrossRefGoogle Scholar
  3. Botham P, Ratledge C (1979) A biochemical explanation for lipid accumulation in Candida 107 and other oleaginous microorganisms. J Gen Microbiol 114:361–375PubMedCrossRefGoogle Scholar
  4. Boulton C (1982) The biochemistry of lipid accumulation in oleaginous yeasts. PhD thesis; University of Hull, HullGoogle Scholar
  5. Dujon B, Sherman D, Fischer G et al (2004) Genome evolution in yeasts. Nature 430:35–44PubMedCrossRefGoogle Scholar
  6. Evans CT, Ratledge C (1983) Biochemical activities during lipid accumulation in Candida curvata. Lipids 18:630–635PubMedCrossRefGoogle Scholar
  7. Evans CT, Ratledge C (1984) Phosphofructokinase and the regulation of the flux of carbon from glucose to lipid in the oleaginous yeast Rhodosporidium toruloides. J Gen Microbiol 130:3251–3264Google Scholar
  8. Evans CT, Ratledge C (1985a) The role of the mitochondrial NAD+: isocitrate dehydrogenase in lipid accumulation by the oleaginous yeast Rhodosporidium toruloides CBS 14. Can J Microbiol 31:845–850CrossRefGoogle Scholar
  9. Evans CT, Ratledge C (1985b) Possible regulatory roles of ATP:citrate lyase, malic enzyme and AMP deaminase in lipid accumulation by Rhodosporidium toruloides CBS 14. Can J Microbiol 31:1000–1005CrossRefGoogle Scholar
  10. Fernie AR, Martinoia E (2009) Malate. Jack of all trades or master of few? Phytochemistry 70:828–832PubMedCrossRefGoogle Scholar
  11. Galvez S, Gadal P (1995) On the function of the NADP-dependent isocitrate dehydrogenase isoenzyme in living organisms. Plant Sci 105:1–14CrossRefGoogle Scholar
  12. Gill CO, Hall MJ, Ratledge C (1977) Lipid accumulation in an oleaginous yeast (Candida 107) growing on glucose in single-stage continuous culture. Appl Environ Microbiol 33:231–239PubMedCentralPubMedGoogle Scholar
  13. Gujjarri P, Suh SO, Coumes K, Zhou JJ (2011) Charcterization of oleaginous yeasts revealed two novel species: Trichosporon cacoliposimilis sp. nov. and Trichosporon oleaginosus sp. nov. Mycologia 103:1110–1118CrossRefGoogle Scholar
  14. Hassan M, Blanc PJ, Granger LM, Pareilleux A, Goma G (1993) Lipid production by an unsaturated fatty acid auxotroph of the oleaginous yeast Apiotrichum curvatum growing in a single-stage continous culture. Appl Microbiol Biotechnol 40:483–488CrossRefGoogle Scholar
  15. Hong SP, Xue Z, Zhu QQ (2011) Pentose phosphate pathway upregulation to increase production of non-native products of interest in transgenic microorganisms. US Patent 2011/0244512Google Scholar
  16. Keech DB, Mattoo AK, Carabott MJJ, Wallace JC (1976) The ATP-dependent reductive carboxylation of 2-oxoglutarate using cytosol from rat liver. Biochem Biophys Res Commun 71:712–718PubMedCrossRefGoogle Scholar
  17. Kendrick A, Ratledge C (1992) Desaturation of polyunsaturated fatty acids in Mucor circinelloides and the involvement of a novel membrane-bound malic enzyme. Eur J Biochem 209:667–673PubMedCrossRefGoogle Scholar
  18. Li X, Wang P, Ge Y, Wang W, Abbas A, Zhu G (2013a) NADP+-Specific isocitrate dehydrogenase from oleaginous yeast Yarrowia lipolytica CLIB122: biochemical characterization and coenzyme sites evaluation. Appl Biochem Biotechnol 171:403–416PubMedCrossRefGoogle Scholar
  19. Li Z, Sun H, Mo X, Li X, Xu B, Tian P (2013b) Overexpression of malic enzyme (ME) of Mucor circinelloides improved lipid accumulation in engineered Rhodotorual glutinis. Appl Microbiol Biotechnol 97:4927–4936PubMedCrossRefGoogle Scholar
  20. Liang MH, Jiang JG (2013) Advancing oleaginous microorganisms to produce lipid via metabolic engineering technology. Prog Lipid Res 52:395–408PubMedCrossRefGoogle Scholar
  21. Li-Beisson Y, Peltier G (2013) Third-generation biofuels: current and future research on microalgal lipid technology. OCL 20(6):D606CrossRefGoogle Scholar
  22. Lin H, Wang Q, Shen Q, Zhan J, Zhao Y (2013) Genetic engineering of microorganisms for biodiesel production. Bioengineered 4:292–304PubMedCrossRefGoogle Scholar
  23. Macool DJ, Xue Z, Zhu QQ (2013) Expression of cytosolic malic enzyme in transgenic Yarrowia to increase lipid production. US Patent 2013/0260427Google Scholar
  24. Metallo CM, Gameiro PA, Bell EL, Mattaini KR et al (2012) Reversible glutamine metabolism by IDH1 mediated lipogenesis under hypoxia. Nature 481:380–384Google Scholar
  25. Metz JG, Roessler P, Facciotti D, Levering C et al (2001) Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes. Science 293:290–293PubMedCrossRefGoogle Scholar
  26. Ochoa-Estopier A, Guillouet SE (2014) D-stat culture for studying the metabolic shifts from oxidative metabolism to lipid accumulation and citric acid production in Yarrowia lipolytica. J Biotechnol 170:35–41PubMedCrossRefGoogle Scholar
  27. Ratledge C (1982) Microbial oils and fats: an assessment of their commercial potential. Prog Indust Microbiol 16:119–206Google Scholar
  28. Ratledge C (1997) Microbial lipids. In: Rehm HJ, Reed G (eds) Biotechnology, vol 7, 2nd edn. VCH, Weinheim, pp 133–197CrossRefGoogle Scholar
  29. Ratledge C (2004) Fatty acid biosynthesis in microorganisms being used for single cell oil production. Biochimie 86:807–815PubMedCrossRefGoogle Scholar
  30. Ratledge C (2013) Microbial production of polyunsaturated fatty acids as neutraceuticals. In: McNeil B, Archer D, Giavasis I, Harvey L (eds) Microbial production of food ingredients, enzymes and nutraceuticals. Woodhead Publ Ltd, Cambridge, pp 531–558CrossRefGoogle Scholar
  31. Ratledge C, Wynn JP (2002) The biochemistry and molecular biology of lipid accumulation in oleaginous microorganisms. Adv Appl Microbiol 51:1–51PubMedCrossRefGoogle Scholar
  32. Runguphan W, Keasling JD (2014) Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals. Metab Eng 21:103–113PubMedCrossRefGoogle Scholar
  33. Satoh Y, Nakamura Y (1984) Characteristics of the reverse reaction of NADP+-isocitrate dehydrogenase from castor bean. Physiol Plant 62:561–565CrossRefGoogle Scholar
  34. Shang C, Zhu S, Yuan Z, Wang Z (2012) Molecular cloning and characterization of malic enzyme gene from Dunaliella parva. Adv Mater Res 347–353:2536–2540Google Scholar
  35. Shen H, Gong Z, Yang X, Jin G, Bai F, Zhao ZK (2013) Kinetics of continous cultivation of the oleaginous yeast Rhodosporidium toruloides. J Biotechnol 168:85–89PubMedCrossRefGoogle Scholar
  36. Sijtsma L, Anderson AJ, Ratledge C (2010) Alternative carbon sources for heterotrophic production of docosahexaenoic acid by the marine alga Crypthecodium cohnii. In: Cohen Z, Ratledge C (eds) Single cell oils, 2nd edn. AOCS Press, Urbana, pp 131–149Google Scholar
  37. Song YD, Wynn JP, Li YJ, Grantham D, Ratledge C (2001) A pregenetic study of the isoforms of malic enzyme associated with lipid accumulation in Mucor circinelloides. Microbiology 147:1507–1515PubMedGoogle Scholar
  38. Srere PA, Ovadi J (1972) Enzyme-enzyme interactions and their metabolic role. FEBS Lett 268:360–364CrossRefGoogle Scholar
  39. Tai M, Stephanopoulos G (2013) Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. Metab Eng 15:1–9PubMedCrossRefGoogle Scholar
  40. Tang W, Zhang S, Tan H, Zhao ZK (2010) Molecular cloning and characterization of a malic enzyme gene from the oleaginous yeast Lipomyces starkeyi. Mol Biotechnol 45:121–128PubMedCrossRefGoogle Scholar
  41. Vongsangnak W, Zhang Y, Chen W, Ratledge C, Song Y (2012) Annotation and analysis of malic enzyme genes encoding for multiple isoforms in the fungus Mucor circinelloides CBS 277.49. Biotechnol Lett 34:941–947PubMedCrossRefGoogle Scholar
  42. Vorapreeda T, Thammarongtham C, Cheevadhanarak S, Laoteng K (2013) The repertoire of malic enzymes in yeast and fungi: insight into their evolutionary functional and structural significance. Microbiology 159:2548–2557PubMedCrossRefGoogle Scholar
  43. Wang L, Chen W, Feng Y, Ren Y et al (2011) Genome characterization of the oleaginous fungus Mortierella alpina. PLoS ONE 6:e28319PubMedCentralPubMedCrossRefGoogle Scholar
  44. Wu S, Hu C, Jin G, Zhao X, Zhao ZK (2010) Phosphate-limitation mediated lipid production by Rhodosporidium toruloides. Bioresour Technol 101:6124–6129PubMedCrossRefGoogle Scholar
  45. Wynn JP, Kendrick A, Ratledge C (1997) Sesamol as an inhibitor of growth and lipid metabolism in Mucor circinelloides via its action on malic enzyme. Lipids 32:605–610PubMedCrossRefGoogle Scholar
  46. Xue Z, Sharpe PL, Hong SP, Yadav NS et al (2013) Production of omega-3 eicosapentaenoic acid by Yarrowia lipolytica. Nat Biotechnol 31:734–740PubMedCrossRefGoogle Scholar
  47. Yang F, Zhang S, Zhou YJ, Zhu Z, Lin X, Zhao ZK (2012) Characterization of the mitochondrial NAD+-dependent isocitrate dehydrogenase of the oleaginous yeast Rhodosporidium toruloides. Appl Microbiol Biotechnol 94:1095–1105PubMedCrossRefGoogle Scholar
  48. Ykema A, Verbree EC, Kater MM, Smit H (1988) Optimization of lipid production in the oleaginous yeast Apiotrichum curvatum in wheypermeate. Appl Microbiol Biotechnol 29:211–218CrossRefGoogle Scholar
  49. Zhang Y, Adams IP, Ratledge C (2007) Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to 2.5-fold increase in lipid accumulation. Microbiology 153:2013–2025PubMedCrossRefGoogle Scholar
  50. Zhang H, Zhang L, Chen H, Chen YQ, Ratledge C, Song Y, Chen W (2013) Regulatory properties of malic enzyme in the oleaginous yeast, Yarrowia lipolytica, and its non-involvement in lipid accumulation. Biotechnol Lett 35:2091–2098PubMedCrossRefGoogle Scholar
  51. Zhu Z, Zhang S, Liu H, Shen H et al (2012) A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides. Nat Commun 3:1112PubMedCentralPubMedCrossRefGoogle Scholar
  52. Zhu Y, Zhou P, Hu J, Zhang R et al (2013) Characterization of Pythium transcriptome and gene expression analysis at different stages of fermentation. PLoS ONE 8:e65552PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Department of Biological SciencesUniversity of HullHullUK

Personalised recommendations