Skip to main content

Systems metabolic engineering, industrial biotechnology and microbial cell factories

Cell factories have been largely exploited for the controlled production of substances of interest for food, pharma and biotech industries. Although human-controlled microbial production and transformation are much older, the cell factory concept was fully established in the 80’s through the intensive public and private investment. Strongly empowered by the then nascent recombinant DNA technologies and supported by the approval of recombinant insulin [1, 2], the principle of controlled biological production as a convenient source of difficult-to-obtain molecules (especially those of high added value) deeply penetrated the industrial tissue, soon becoming a widespread platform aiming at cost-effective large-scale production [3]. The first generation cell factories (mainly composed by plain strains of the bacterium Escherichia coli and the yeast Saccharomyces cerevisae) were soon replaced by engineered variants. Resulting from the application of untargeted mutagenesis and phenotypic selection, conventional genetic modification, metabolic engineering, and more recently by systems metabolic engineering that integrates metabolic engineering with systems biology and synthetic biology, new strains having much enhanced performance have been progressively developed [419]. In parallel, mammalian and insect cells for the production of high quality proteins, and other microbial species appealing from an industrial point of view due to their unusual physiological traits, have been incorporated to the cell factory family [20, 21]. This comprises algae, fungi, psychrophilic bacteria and moss, among others [2226]. On the other hand, a set of food-grade lactic acid bacteria are under development as emerging platforms in food microbiology but also as a novel source of metabolites and proteins [2734]. The physiological diversity of the microbial world offers an intricacy of biosynthetic pathways from which novel bio-products, including nano- or micro-structured materials [3537], offer promises in even more diverse applications.

Still, many substances and materials of industrial interest are nowadays produced by chemical synthesis, and the number of (recombinant) proteins approved for therapeutic use hardly reaches 200, a figure much lower than that initially presumed. However, both environmental concerns and medical and industrial needs strongly push towards a fully sustainable bio-production of a larger spectrum of substances. Then, how much limited is the economic feasibility of microbial production? Have the cell factories reached a plateau in their development? Is there more room for further exploitation of the microbial production?

Systems metabolic engineering [38, 39] offers a set of methodological and strategic tools for the design and optimization of metabolic and gene regulatory networks for the efficient production of chemicals (from pharmaceuticals to bulk chemicals and fuels) and materials (from plastics to high value materials) [57, 40]. Furthermore, creation of new metabolic pathways and fine tuning of the existing ones have become possible [8, 15]. This is already allowing the production of substances so far reluctant to microbial production under industrial requirements and under cost-effective processes, allowing us to overcome limitations of microbial cell factories. In silico genome-scale metabolic modeling and simulation are playing increasingly important roles in system-wide identification of target genes and pathways to be manipulated to enhance production of desired products. Profiling of transcriptome, proteome, metabolome, and/or fluxome is also becoming a routine practice in metabolic engineering for the better understanding of cellular characteristics under given genetic and/or environmental perturbations. Through the system-wide optimized design and development of microbial cell factories, many industrially important chemicals and materials could be efficiently produced. Some example products include, but not limited to, alcohols other than ethanol including propanol, butanol and isobutanol, dicarboxylic acids such as succinic acid, fumaric acid, malic acid and adipic acid, diols such as 1,3-propanediol, 1,2-propanediol, 1,4-butanediol and 2,3-butanediol, diamines such as putrescine and cadaverine, and even polymers including polyhydroxyalkanoates, polylactic acid, spider silk protein, poly-gamma-glutamic acid, and many others [40]. It is expected that increasingly diverse chemicals and materials that are currently produced by petrochemical industry will be produced by employing microbial cell factories.

Improving cell factories by systems biotechnology to an industrially relevant level cannot be successfully reached by individual teams alone. A wide range of expertise is needed for the full development of a novel biotechnological process, including microbiology, chemistry, bioinformatics, biochemical engineering, but also agricultural and plant sciences and economics. After a proof of concept has shown the feasibility of a novel approach for cell factory engineering, large consortia or networks of fully skilled teams should take over in collaboration with Biotech companies to accomplish an economically feasible bioprocess. As an early example, the development of bacteria producing 1,3-propanediol from glucose has been well documented, and required the engineering of more than 70 genes, before process development and scale up were reasonably made [41]. Replacing materials which are produced from mineral oil by biobased products requires not only efficient technology but also the assessment of economical and ecological feasibility, as intensely studied for polylactic acid [42].

As the progress of industrial biotechnology did not accomplish the desired speed of development [43] academic researchers have teamed up with industry in publicly funded research centers worldwide. To name a few, the Joint BioEnergy Institute (JBEI) in the San Francisco Bay Area, the Novo Nordisk Foundation Center for Biosustainability (CFB) at the Technical University of Denmark, the Metabolic and Biomolecular Engineering Laboratory (MBEL) of the Korea Advanced Institute of Science and Technology (KAIST), the Dutch Klyuver Centre for Genomics of Industrial Fermentation, or the Austrian Centre of Industrial Biotechnology (ACIB) share the mission to speed up development of industrial bioprocesses by joining forces of different academic disciplines with industrial collaborators.

References

  1. ANONIMOUS: Human insulin receives FDA approval. FDA Drug Bull. 1982, 12: 18-19.

    Google Scholar 

  2. Johnson IS: Human insulin from recombinant DNA technology. Science. 1983, 219: 632-637. 10.1126/science.6337396

    Article  CAS  Google Scholar 

  3. Marston FA: The purification of eukaryotic polypeptides synthesized in escherichia coli. Biochem J. 1986, 240: 1-12.

    Article  CAS  Google Scholar 

  4. Makino T, Skretas G, Georgiou G: Strain engineering for improved expression of recombinant proteins in bacteria. Microb Cell Fact. 2011, 10: 32-, 10.1186/1475-2859-10-32

    Article  CAS  Google Scholar 

  5. Lee SY, Lee DY, Kim TY: Systems biotechnology for strain improvement. Trends Biotechnol. 2005, 23: 349-358. 10.1016/j.tibtech.2005.05.003

    Article  CAS  Google Scholar 

  6. Park JH, Lee SY, Kim TY, Kim HU: Application of systems biology for bioprocess development. Trends Biotechnol. 2008, 26: 404-412. 10.1016/j.tibtech.2008.05.001

    Article  CAS  Google Scholar 

  7. Lee SY, Kim HU, Park JH, Park JM, Kim TY: Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov Today. 2009, 14: 78-88. 10.1016/j.drudis.2008.08.004

    Article  CAS  Google Scholar 

  8. Na D, Kim TY, Lee SY: Construction and optimization of synthetic pathways in metabolic engineering. Curr Opin Microbiol. 2010, 13: 363-370. 10.1016/j.mib.2010.02.004

    Article  CAS  Google Scholar 

  9. Lee JW, Kim TY, Jang YS, Choi S, Lee SY: Systems metabolic engineering for chemicals and materials. Trends Biotechnol. 2011, 29: 370-378. 10.1016/j.tibtech.2011.04.001

    Article  CAS  Google Scholar 

  10. Adrio JL, Demain AL: Genetic improvement of processes yielding microbial products. FEMS Microbiol Rev. 2006, 30: 187-214. 10.1111/j.1574-6976.2005.00009.x

    Article  CAS  Google Scholar 

  11. Demain AL, Adrio JL: Strain improvement for production of pharmaceuticals and other microbial metabolites by fermentation. Prog Drug Res. 2008, 65: 251-253–251, 289,, 10.1007/978-3-7643-8117-2_7

    Article  CAS  Google Scholar 

  12. Adrio JL, Demain AL: Recombinant organisms for production of industrial products. Bioeng Bugs. 2010, 1: 116-131. 10.4161/bbug.1.2.10484

    Article  Google Scholar 

  13. Demain AL, Adrio JL: Essential role of genetics in the advancement of biotechnology. Methods Mol Biol. 2012, 898: 1-40. 10.1007/978-1-61779-918-1_1

    Article  CAS  Google Scholar 

  14. Chen Z, Wilmanns M, Zeng AP: Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development. Trends Biotechnol. 2010, 28: 534-542. 10.1016/j.tibtech.2010.07.004

    Article  CAS  Google Scholar 

  15. Kondo A, Ishii J, Hara KY, Hasunuma T, Matsuda F: Development of microbial cell factories for bio-refinery through synthetic bioengineering. J Biotechnol. 2012, [Epub ahead of print]

    Google Scholar 

  16. Lee JH, Sung BH, Kim MS, Blattner FR, Yoon BH, Kim JH, et al: Metabolic engineering of a reduced-genome strain of escherichia coli for L-threonine production. Microb Cell Fact. 2009, 8: 2-, 10.1186/1475-2859-8-2

    Article  Google Scholar 

  17. Ferndahl C, Bonander N, Logez C, Wagner R, Gustafsson L, Larsson C, et al: Increasing cell biomass in saccharomyces cerevisiae increases recombinant protein yield: the use of a respiratory strain as a microbial cell factory. Microb Cell Fact. 2010, 9: 47-, 10.1186/1475-2859-9-47

    Article  Google Scholar 

  18. Hasunuma T, Sanda T, Yamada R, Yoshimura K, Ishii J, Kondo A: Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of saccharomyces cerevisiae. Microb Cell Fact. 2011, 10: 2-, 10.1186/1475-2859-10-2

    Article  CAS  Google Scholar 

  19. Krainer FW, Dietzsch C, Hajek T, Herwig C, Spadiut O, Glieder A: Recombinant protein expression in pichia pastoris strains with an engineered methanol utilization pathway. Microb Cell Fact. 2012, 11: 22-, 10.1186/1475-2859-11-22

    Article  CAS  Google Scholar 

  20. Ferrer-Miralles N, Domingo-Espin J, Corchero JL, Vazquez E, Villaverde A: Microbial factories for recombinant pharmaceuticals. Microb Cell Fact. 2009, 8: 17-, 10.1186/1475-2859-8-17

    Article  Google Scholar 

  21. Gasser B, Saloheimo M, Rinas U, Dragosits M, Rodriguez-Carmona E, Baumann K, et al: Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microb Cell Fact. 2008, 7: 11-, 10.1186/1475-2859-7-11

    Article  Google Scholar 

  22. Corchero JL, Gasser B, Resina D, Smith W, Parrilli E, Vazquez F, et al: Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics. Biotechnol Adv. 2012, S0734 (12): 00151-6. 10.1016/j.biotechadv.2012.09.001. 10.1016/j.biotechadv.2012.09.001

    Google Scholar 

  23. Gong Y, Hu H, Gao Y, Xu X, Gao H: Microalgae as platforms for production of recombinant proteins and valuable compounds: progress and prospects. J Ind Microbiol Biotechnol. 2011,

    Google Scholar 

  24. Hempel F, Bozarth AS, Lindenkamp N, Klingl A, Zauner S, Linne U, et al: Microalgae as bioreactors for bioplastic production. Microb Cell Fact. 2011, 10: 81-, 10.1186/1475-2859-10-81

    Article  CAS  Google Scholar 

  25. Meyer V, Wu B, Ram AF: Aspergillus as a multi-purpose cell factory: current status and perspectives. Biotechnol Lett. 2011, 33: 469-476. 10.1007/s10529-010-0473-8

    Article  CAS  Google Scholar 

  26. Spadiut O, Olsson L, Brumer III H: A comparative summary of expression systems for the recombinant production of galactose oxidase. Microb Cell Fact. 2010, 9: 68-, 10.1186/1475-2859-9-68

    Article  Google Scholar 

  27. Le LY, Azevedo V, Oliveira SC, Freitas DA, Miyoshi A, Bermudez-Humaran LG, et al: Protein secretion in lactococcus lactis: an efficient way to increase the overall heterologous protein production. Microb Cell Fact. 2005, 4: 2-, 10.1186/1475-2859-4-2

    Article  Google Scholar 

  28. Morello E, Bermudez-Humaran LG, Llull D, Sole V, Miraglio N, Langella P, et al: Lactococcus lactis, an efficient cell factory for recombinant protein production and secretion. J Mol Microbiol Biotechnol. 2008, 14: 48-58. 10.1159/000106082

    Article  CAS  Google Scholar 

  29. Peterbauer C, Maischberger T, Haltrich D: Food-grade gene expression in lactic acid bacteria. Biotechnol J. 2011, 6: 1147-1161. 10.1002/biot.201100034

    Article  CAS  Google Scholar 

  30. Hu S, Kong J, Sun Z, Han L, Kong W, Yang P: Heterologous protein display on the cell surface of lactic acid bacteria mediated by the S-layer protein. Microb Cell Fact. 2011, 10: 86-, 10.1186/1475-2859-10-86

    Article  CAS  Google Scholar 

  31. De Vos WM: Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact. 2011, 10 (1): S2-, 10.1186/1475-2859-10-S1-S2

    Article  Google Scholar 

  32. Teusink B, Bachmann H, Molenaar D: Systems biology of lactic acid bacteria: a critical review. Microb Cell Fact. 2011, 10 (1): S11-, 10.1186/1475-2859-10-S1-S11

    Article  Google Scholar 

  33. Rhee SJ, Lee JE, Lee CH: Importance of lactic acid bacteria in asian fermented foods. Microb Cell Fact. 2011, 10 (1): S5-, 10.1186/1475-2859-10-S1-S5

    Article  Google Scholar 

  34. Siezen RJ, Van HV: Genomic diversity and versatility of lactobacillus plantarum, a natural metabolic engineer. Microb Cell Fact. 2011, 10 (1): S3-, 10.1186/1475-2859-10-S1-S3

    Article  Google Scholar 

  35. Rodriguez-Carmona E, Villaverde A: Nanostructured bacterial materials for innovative medicines. Trends Microbiol. 2010, 18: 423-430. 10.1016/j.tim.2010.06.007

    Article  CAS  Google Scholar 

  36. Villaverde A: Nanotechnology, bionanotechnology and microbial cell factories. Microb Cell Fact. 2010, 9: 53-, 10.1186/1475-2859-9-53

    Article  Google Scholar 

  37. Vazquez E, Villaverde A: Engineering building blocks for self-assembling protein nanoparticles. Microb Cell Fact. 2010, 9: 101-, 10.1186/1475-2859-9-101

    Article  CAS  Google Scholar 

  38. Lee KH, Park JH, Kim TY, Kim HU, Lee SY: Systems metabolic engineering of escherichia coli for L-threonine production. Mol Syst Biol. 2007, 3: 149-

    Article  CAS  Google Scholar 

  39. Wittmann C, Lee SY (Eds): Systems metabolic engineering. Heidelberg,Germany: Springer; 2012. ISBN 978-94-007-4533-9.

    Book  Google Scholar 

  40. Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY: Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol. 2012, 8: 536-546. 10.1038/nchembio.970

    Article  CAS  Google Scholar 

  41. Liu H, Xu Y, Zheng Z, Liu D: 1, 3-Propanediol and its copolymers: research, development and industrialization. Biotechnol J. 2010, 5: 1137-1148. 10.1002/biot.201000140

    Article  CAS  Google Scholar 

  42. Vink ETH, Glassner DA, Olstad JJWROR: The eco-profiles for current and near-future nature works polylactide (PLA) production. Ind Biotechnol. 2007, 3: 58-81. 10.1089/ind.2007.3.058. 10.1089/ind.2007.3.058

    Article  CAS  Google Scholar 

  43. Chen GQ: New challenges and opportunities for industrial biotechnology. Microb Cell Fact. 2012, 11: 111-, 10.1186/1475-2859-11-111

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Antonio Villaverde.

Rights and permissions

Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and permissions

About this article

Cite this article

Lee, S., Mattanovich, D. & Villaverde, A. Systems metabolic engineering, industrial biotechnology and microbial cell factories. Microb Cell Fact 11, 156 (2012). https://doi.org/10.1186/1475-2859-11-156

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/1475-2859-11-156