Applied Microbiology and Biotechnology

, Volume 99, Issue 3, pp 1109–1118 | Cite as

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

  • Yanfeng Liu
  • Hyun-dong Shin
  • Jianghua Li
  • Long LiuEmail author


Metabolic engineering facilitates the rational development of recombinant bacterial strains for metabolite overproduction. Building on enormous advances in system biology and synthetic biology, novel strategies have been established for multivariate optimization of metabolic networks in ensemble, spatial, and dynamic manners such as modular pathway engineering, compartmentalization metabolic engineering, and metabolic engineering guided by genome-scale metabolic models, in vitro reconstitution, and systems and synthetic biology. Herein, we summarize recent advances in novel metabolic engineering strategies. Combined with advancing kinetic models and synthetic biology tools, more efficient new strategies for improving cellular properties can be established and applied for industrially important biochemical production.


System metabolic engineering Modular pathway engineering Synthetic biology Genome-scale metabolic model Spatial engineering 



This work was financially supported by the Enterprise-university-research prospective program, Jiangsu Province (BY2012054), 111 Project (111-2-06), and 973 project (2012CB720806). We are also thankful for the constructive advice of Prof. Uwe Sauer from ETH Zürich.


  1. Ajikumar PK, Xiao WH, Tyo KEJ, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330:70–74PubMedCentralPubMedCrossRefGoogle Scholar
  2. Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M (2014) Kinetic models in industrial biotechnology: improving cell factory performance. Metab Eng 24:38–60PubMedCrossRefGoogle Scholar
  3. Avalos JL, Fink GR, Stephanopoulos G (2013) Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol 31:335–341PubMedCentralPubMedCrossRefGoogle Scholar
  4. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2:727–738PubMedCrossRefGoogle Scholar
  5. Biggs BW, De Paepe B, Santos CNS, De Mey M, Kumaran Ajikumar P (2014) Multivariate modular metabolic engineering for pathway and strain optimization. Curr Opin Biotechnol 29:156–162PubMedCrossRefGoogle Scholar
  6. Blumhoff ML, Steiger MG, Mattanovich D, Sauer M (2013) Targeting enzymes to the right compartment: Metabolic engineering for itaconic acid production by Aspergillus niger. Metab Eng 19:26–32PubMedCrossRefGoogle Scholar
  7. Bujara M, Schümperli M, Pellaux R, Heinemann M, Panke S (2011) Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis. Nat Chem Biol 7:271–277PubMedCrossRefGoogle Scholar
  8. Cameron DE, Bashor CJ, Collins JJ (2014) A brief history of synthetic biology. Nat Rev Microbiol 12:381–390PubMedCrossRefGoogle Scholar
  9. Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM (2014) Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm. GEM-Path Metab Eng 25:140–158CrossRefGoogle Scholar
  10. Chen Y, Nielsen J (2013) Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks. Curr Opin Biotechnol 24:965–972PubMedCrossRefGoogle Scholar
  11. Chen Z, Zeng AP (2013) Protein design in systems metabolic engineering for industrial strain development. Biotechnol J 8:523–533PubMedCrossRefGoogle Scholar
  12. Chen X, Xu G, Xu N, Zou W, Zhu P, Liu L, Chen J (2013) Metabolic engineering of Torulopsis glabrata for malate production. Metab Eng 19:10–16PubMedCrossRefGoogle Scholar
  13. Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Koprivnjak T (2012) DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40:1879–1889PubMedCentralPubMedCrossRefGoogle Scholar
  14. Coussement P, Maertens J, Beauprez J, Van Bellegem W, De Mey M (2014) One step DNA assembly for combinatorial metabolic engineering. Metab Eng 23:70–77PubMedCrossRefGoogle Scholar
  15. Delebecque CJ, Silver PA, Lindner AB (2012) Designing and using RNA scaffolds to assemble proteins in vivo. Nat Protoc 7(10):1797–1807PubMedCrossRefGoogle Scholar
  16. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KLJ, Keasling JD (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27:753–759PubMedCrossRefGoogle Scholar
  17. Gao L, Hu Y, Liu J, Du G, Zhou J, Chen J (2014) Stepwise metabolic engineering of Gluconobacter oxydans WSH-003 for the direct production of 2-keto-l-gulonic acid from D-sorbitol. Metab Eng 24:30–37PubMedCrossRefGoogle Scholar
  18. Gerosa L, Sauer U (2011) Regulation and control of metabolic fluxes in microbes. Curr Opin Biotechnol 22:566–575PubMedCrossRefGoogle Scholar
  19. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343–345PubMedCrossRefGoogle Scholar
  20. Heinemann M, Sauer U (2010) Systems biology of microbial metabolism. Curr Opin Biotechnol 13:337–343Google Scholar
  21. Huang Z, Zou W, Liu J, Liu L (2013) Glutathione enhances 2-keto-l-gulonic acid production based on Ketogulonicigenium vulgare model iWZ663. J Biotechnol 164:454–460PubMedCrossRefGoogle Scholar
  22. Ip K, Donoghue N, Kim MK, Lun DS (2014) Constraint-based modeling of heterologous pathways: application and experimental demonstration for overproduction of fatty acids in Escherichia coli. Biotechnol Bioeng 111:2056–2066PubMedCrossRefGoogle Scholar
  23. Juminaga D, Baidoo EE, Redding-Johanson AM, Batth TS, Burd H, Mukhopadhyay A, Petzold CJ, Keasling JD (2012) Modular engineering of L-tyrosine production in Escherichia coli. Appl Environ Microbiol 78:89–98PubMedCentralPubMedCrossRefGoogle Scholar
  24. Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8:536–546PubMedCrossRefGoogle Scholar
  25. Lee Y, Lafontaine Rivera JG, Liao JC (2014) Ensemble modeling for robustness analysis in engineering non-native metabolic pathways. Metab Eng 25:63–71PubMedCrossRefGoogle Scholar
  26. Leonard E, Ajikumar PK, Thayer K, Xiao W-H, Mo JD, Tidor B, Stephanopoulos G, Prather KL (2010) Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci U S A 107:13654–13659PubMedCentralPubMedCrossRefGoogle Scholar
  27. Li S, Gao X, Xu N, Liu L, Chen J (2014a) Enhancement of acetoin production in Candida glabrata by in silico-aided metabolic engineering. Microb Cell Fact 13:55PubMedCentralPubMedCrossRefGoogle Scholar
  28. Li S, Xu N, Liu L, Chen J (2014b) Engineering of carboligase activity reaction in Candida glabrata for acetoin production. Metab Eng 22:32–39PubMedCrossRefGoogle Scholar
  29. Link H, Christodoulou D, Sauer U (2014) Advancing metabolic models with kinetic information. Curr Opin Biotechnol 29:8–14PubMedCrossRefGoogle Scholar
  30. Liu Y, Liu L, H-d S, Chen RR, Li J, Du G, Chen J (2013) Pathway engineering of Bacillus subtilis for microbial production of N-acetylglucosamine. Metab Eng 19:107–115PubMedCrossRefGoogle Scholar
  31. Liu Y, Zhu Y, Li J, H-d S, Chen RR, Du G, Liu L, Chen J (2014a) Modular pathway engineering of Bacillus subtilis for improved N-acetylglucosamine production. Metab Eng 23:42–52PubMedCrossRefGoogle Scholar
  32. Liu Y, Zhu Y, Ma W, H-d S, Li J, Liu L, Du G, Chen J (2014b) Spatial modulation of key pathway enzymes by DNA-guided scaffold system and respiration chain engineering for improved N-acetylglucosamine production by Bacillus subtilis. Metab Eng 24:61–69PubMedCrossRefGoogle Scholar
  33. McCloskey D, Palsson BØ, Feist AM (2013) Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol. 9(1)Google Scholar
  34. Myung S, Rollin J, You C, Sun F, Chandrayan S, Adams MW, Zhang Y-HP (2014) In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose. Metab Eng 24:70–77PubMedCrossRefGoogle Scholar
  35. Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 31:170–174Google Scholar
  36. Nocon J, Steiger MG, Pfeffer M, Sohn SB, Kim TY, Maurer M, Rußmayer H, Pflügl S, Ask M, Haberhauer-Troyer C (2014) Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metab Eng 24:129–138PubMedCentralPubMedCrossRefGoogle Scholar
  37. Paddon CJ, Keasling JD (2014) Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 12:355–367PubMedCrossRefGoogle Scholar
  38. Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–355PubMedCentralPubMedCrossRefGoogle Scholar
  39. Soma Y, Tsuruno K, Wada M, Yokota A, Hanai T (2014) Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metab Eng 23:175–184PubMedCrossRefGoogle Scholar
  40. Stephanopoulos G (2012) Synthetic biology and metabolic engineering. ACS Synth Biol 1(11):514–525PubMedCrossRefGoogle Scholar
  41. Tyo KEJ, Ajikumar PK, Stephanopoulos G (2009) Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat Biotechnol 27(8):760–765PubMedCrossRefGoogle Scholar
  42. Wang Y, Yu O (2012) Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J Biotechnol 157:258–260PubMedCrossRefGoogle Scholar
  43. Weaver LJ, Sousa MM, Wang G, Baidoo E, Petzold CJ, Keasling JD (2014) A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli. Biotechnol Bioeng. doi: 10.1002/bit.25323 PubMedGoogle Scholar
  44. Wu J, Du G, Zhou J, Chen J (2013a) Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy. Metab Eng 16:48–55PubMedCrossRefGoogle Scholar
  45. Wu J, Liu P, Fan Y, Bao H, Du G, Zhou J, Chen J (2013b) Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine. J Biotechnol 167:404–411PubMedCrossRefGoogle Scholar
  46. Xu G, Zou W, Chen X, Xu N, Liu L, Chen J (2012) Fumaric acid production in Saccharomyces cerevisiae by in silico aided metabolic engineering. PLoS One 7:e52086PubMedCentralPubMedCrossRefGoogle Scholar
  47. Xu C, Liu L, Zhang Z, Jin D, Qiu J, Chen M (2013a) Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl Microbiol Biotechnol 97:519–539PubMedCrossRefGoogle Scholar
  48. Xu N, Liu L, Zou W, Liu J, Hua Q, Chen J (2013b) Reconstruction and analysis of the genome-scale metabolic network of Candida glabrata. Mol Biosyst 9:205–216PubMedCrossRefGoogle Scholar
  49. Xu P, Gu Q, Wang W, Wong L, Bower AG, Collins CH, Koffas MA (2013c) Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun 4:1409PubMedCrossRefGoogle Scholar
  50. Xu P, Li L, Zhang F, Stephanopoulos G, Koffas M (2014) Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci U S A 111:11299–11304PubMedCentralPubMedCrossRefGoogle Scholar
  51. Xue Z, Sharpe PL, Hong S-P, Yadav NS, Xie D, Short DR, Damude HG, Rupert RA, Seip JE, Wang J (2013) Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nat Biotechnol 31(8):734–740PubMedCrossRefGoogle Scholar
  52. Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, Boldt J, Khandurina J, Trawick JD, Osterhout RE, Stephen R (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7:445–452PubMedCrossRefGoogle Scholar
  53. Yu X, Liu T, Zhu F, Khosla C (2011) In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli. Proc Natl Acad Sci U S A 108:18643–18648PubMedCentralPubMedCrossRefGoogle Scholar
  54. Zelcbuch L, Antonovsky N, Bar-Even A, Levin-Karp A, Barenholz U, Dayagi M, Liebermeister W, Flamholz A, Noor E, Amram S (2013) Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res 41:e98PubMedCentralPubMedCrossRefGoogle Scholar
  55. Zhang C, Liu L, Teng L, Chen J, Liu J, Li J, Du G, Chen J (2012) Metabolic engineering of Escherichia coli BL21 for biosynthesis of heparosan, a bioengineered heparin precursor. Metab Eng 14:521–527PubMedCrossRefGoogle Scholar
  56. Zhu F, Zhong X, Hu M, Lu L, Deng Z, Liu T (2014) In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli. Biotechnol Bioeng 111(7):1396–1405PubMedCrossRefGoogle Scholar
  57. Zou W, Liu L, Zhang J, Yang H, Zhou M, Hua Q, Chen J (2012) Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001. J Biotechnol 161:42–48PubMedCrossRefGoogle Scholar
  58. Zou W, Zhou M, Liu L, Chen J (2013) Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model. J Biotechnol 164:503–509PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Yanfeng Liu
    • 1
    • 2
    • 3
  • Hyun-dong Shin
    • 4
  • Jianghua Li
    • 1
    • 2
    • 3
  • Long Liu
    • 1
    • 2
    • 3
    Email author
  1. 1.Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of Education, Jiangnan UniversityWuxiChina
  2. 2.Key Laboratory of Industrial BiotechnologyMinistry of Education, Jiangnan UniversityWuxiChina
  3. 3.Synergetic Innovation Center of Food Safety and NutritionWuxiChina
  4. 4.School of Chemical and Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUSA

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