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

Abstract

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.

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References

  • 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 330:70–74

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M (2014) Kinetic models in industrial biotechnology: improving cell factory performance. Metab Eng 24:38–60

    CAS  PubMed  Article  Google Scholar 

  • Avalos JL, Fink GR, Stephanopoulos G (2013) Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol 31:335–341

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 2:727–738

    CAS  PubMed  Article  Google Scholar 

  • 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 29:156–162

    CAS  PubMed  Article  Google Scholar 

  • 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 19:26–32

    CAS  PubMed  Article  Google Scholar 

  • 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 7:271–277

    CAS  PubMed  Article  Google Scholar 

  • Cameron DE, Bashor CJ, Collins JJ (2014) A brief history of synthetic biology. Nat Rev Microbiol 12:381–390

    CAS  PubMed  Article  Google Scholar 

  • 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 25:140–158

    CAS  Article  Google Scholar 

  • 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 24:965–972

    CAS  PubMed  Article  Google Scholar 

  • Chen Z, Zeng AP (2013) Protein design in systems metabolic engineering for industrial strain development. Biotechnol J 8:523–533

    PubMed  Article  Google Scholar 

  • 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 19:10–16

    CAS  PubMed  Article  Google Scholar 

  • 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 40:1879–1889

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Coussement P, Maertens J, Beauprez J, Van Bellegem W, De Mey M (2014) One step DNA assembly for combinatorial metabolic engineering. Metab Eng 23:70–77

    CAS  PubMed  Article  Google Scholar 

  • Delebecque CJ, Silver PA, Lindner AB (2012) Designing and using RNA scaffolds to assemble proteins in vivo. Nat Protoc 7(10):1797–1807

    CAS  PubMed  Article  Google Scholar 

  • 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 27:753–759

    CAS  PubMed  Article  Google Scholar 

  • 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 24:30–37

    CAS  PubMed  Article  Google Scholar 

  • Gerosa L, Sauer U (2011) Regulation and control of metabolic fluxes in microbes. Curr Opin Biotechnol 22:566–575

    CAS  PubMed  Article  Google Scholar 

  • 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 6:343–345

    CAS  PubMed  Article  Google Scholar 

  • Heinemann M, Sauer U (2010) Systems biology of microbial metabolism. Curr Opin Biotechnol 13:337–343

    CAS  Google Scholar 

  • 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 164:454–460

    CAS  PubMed  Article  Google Scholar 

  • 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 111:2056–2066

    CAS  PubMed  Article  Google Scholar 

  • 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 78:89–98

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 8:536–546

    CAS  PubMed  Article  Google Scholar 

  • Lee Y, Lafontaine Rivera JG, Liao JC (2014) Ensemble modeling for robustness analysis in engineering non-native metabolic pathways. Metab Eng 25:63–71

    CAS  PubMed  Article  Google Scholar 

  • 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 107:13654–13659

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 13:55

    PubMed Central  PubMed  Article  Google Scholar 

  • Li S, Xu N, Liu L, Chen J (2014b) Engineering of carboligase activity reaction in Candida glabrata for acetoin production. Metab Eng 22:32–39

    CAS  PubMed  Article  Google Scholar 

  • Link H, Christodoulou D, Sauer U (2014) Advancing metabolic models with kinetic information. Curr Opin Biotechnol 29:8–14

    CAS  PubMed  Article  Google Scholar 

  • 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 19:107–115

    PubMed  Article  Google Scholar 

  • 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 23:42–52

    CAS  PubMed  Article  Google Scholar 

  • 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 24:61–69

    CAS  PubMed  Article  Google Scholar 

  • 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)

  • 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 24:70–77

    CAS  PubMed  Article  Google Scholar 

  • 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 31:170–174

  • 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 24:129–138

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Paddon CJ, Keasling JD (2014) Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 12:355–367

    CAS  PubMed  Article  Google Scholar 

  • Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–355

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 23:175–184

    CAS  PubMed  Article  Google Scholar 

  • Stephanopoulos G (2012) Synthetic biology and metabolic engineering. ACS Synth Biol 1(11):514–525

    CAS  PubMed  Article  Google Scholar 

  • Tyo KEJ, Ajikumar PK, Stephanopoulos G (2009) Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat Biotechnol 27(8):760–765

    CAS  PubMed  Article  Google Scholar 

  • Wang Y, Yu O (2012) Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J Biotechnol 157:258–260

    CAS  PubMed  Article  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • 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 16:48–55

    PubMed  Article  Google Scholar 

  • 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 167:404–411

    CAS  PubMed  Article  Google Scholar 

  • 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:e52086

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 97:519–539

    CAS  PubMed  Article  Google Scholar 

  • 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 9:205–216

    CAS  PubMed  Article  Google Scholar 

  • 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 4:1409

    PubMed  Article  Google Scholar 

  • 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 111:11299–11304

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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):734–740

    CAS  PubMed  Article  Google Scholar 

  • 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 7:445–452

    CAS  PubMed  Article  Google Scholar 

  • 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 108:18643–18648

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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:e98

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 14:521–527

    CAS  PubMed  Article  Google Scholar 

  • 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):1396–1405

    CAS  PubMed  Article  Google Scholar 

  • 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 161:42–48

    CAS  PubMed  Article  Google Scholar 

  • 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 164:503–509

    CAS  PubMed  Article  Google Scholar 

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Acknowledgments

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.

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Correspondence to Long Liu.

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Liu, Y., Shin, Hd., Li, J. et al. Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects. Appl Microbiol Biotechnol 99, 1109–1118 (2015). https://doi.org/10.1007/s00253-014-6298-y

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  • DOI: https://doi.org/10.1007/s00253-014-6298-y

Keywords

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