Producing high-value chemicals in Escherichia coli through synthetic biology and metabolic Engineering

Helena Shomar Monges

Research output: ThesisDissertation (TU Delft)

107 Downloads (Pure)


For millennia, humans have used microbes to produce industrial products of social and economical value through fermentation processes. In recent years, the application of engineering principles to microbiology have dramatically expanded our ability to modify and optimize microbes for the production of a wide variety of commercial products from renewable feedstocks: food and commodity chemicals, to biofuels and fine chemicals such as pharmaceuticals, fragrances, cosmetics or dyes. The use of microbial bioprocesses for the production of natural products represents an attractive and sustainable alternative to current industrial production methods, which mainly rely on chemical synthesis and/ or extraction from native producers. Advanced biomanufacturing technologies would not only provide sustainable economic benefits (by reducing the monetary cost of production of useful chemicals), but also offer social and environmental benefits. Synthetic biology has allowed engineering the production of many industrial compounds within microbes that do not naturally produce them – this is called “heterologous microbial biosynthesis”. In addition to replacing current manufacturing processes, heterologous microbial biosynthesis likely offers the only viable platform to produce certain natural products at industrial scales. Indeed, many relevant compounds cannot be viably manufactured through chemical synthesis, and/or are produced at undetectable/insufficient levels in native organisms. However, many heterologous bioprocesses remain in their infancy to fully enable an economically viable delivery of relevant natural products to the market. In order to build and sustain the promise of a bioeconomy for the 21st century, metabolic engineering is under pressure to continue to provide largescale, sustainable and cost-competitive bioprocesses that meet global needs. In this thesis, we focus on the development of microbial strains to accelerate the microbial production of 2 different families of high-value compounds of prominent biotechnological relevance within the established microbial chassis Escherichia coli: antibiotics and isoprenoids. The fight against antimicrobial resistance is considered one of the greatest public health challenges of the 21st century. Recent technologies have uncovered new antibiotics that, if harnessed, might help alleviate this crisis. However, most of these new antibiotic compounds are far too complex for economical chemical synthesis, and are naturally produced by unculturable and/or genetically intractable microbes. Developing new heterologous microbial platforms for antibiotic production may be an efficient solution for harnessing the clinical potential of these molecules and their commercialization. Isoprenoids represent one of the largest families of natural compounds (over 50,000 molecules) with an incredible number of practical uses, and of great commercial value: from high-value compounds such as many pharmaceuticals, fragrances and flavors, to commodity chemicals such as solvents, rubber or advanced biofuels. We focus in particular on relevant obstacles associated with the development of proof-of-principle strains for the laboratory-scale production of these high-value chemicals.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Delft University of Technology
  • Dogterom, A.M., Supervisor
  • Bokinsky, G.E., Advisor
Award date28 Mar 2019
Print ISBNs978-90-8593-386-1
Publication statusPublished - 2019


  • Synthetic biology
  • metabolic engineering
  • biomanufacturing
  • antibiotics
  • carbapenems
  • ironsulfur cluster enzymes
  • metalloenzymes


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