CHE.496/2008/Schedule/Metabolic pathway engineering

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CHE.496: Biological Systems Design Seminar

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Metabolic pathway engineering

  • Discussion leader: Patrick

  • Bioengineering novel in vitro metabolic pathways using synthetic biology link

    • Chemical routes instead of enzymatic routes prevail in industry because assembly of enzymes are expensive, the biological system is complex and not well understood, cellular systems go for homeostasis. Multiple enzyme systems have been designed and built with favorable results – however other circumstances prevent the use of these systems in industry.
    • This paper presents an approach to the design of gene systems that code enzymes to produce desired molecules.
    • Figure 2: a diagram of what the design cycle is for designing these systems of enzymes
      • Start out with the assembly of the system (overexpression of required genes, dna synthesis, etc.)
      • collect concentration data on intermediates, products
      • fit a model to the data to predict behaviors
      • determine points in the system where further expression, etc. can be used to increase product
      • adapt the kinetics of system members and loop back to the beginning
    • For experimental modeling of metabolic systems - there are many kinetic parameters for purified proteins, but their is a big lack of data comprising of the kinetics of metabolic pathways (there a a few exceptions to this - E.Coli, yeast, etc.
    • The modeling of the data produced and subsequent analysis of the forces (van der waals, etc.) can be used to predict behaviors and subsequently devise a manner to increase the desired product in the metabolic pathway.
  • Synthetic biology for synthetic chemistry link
    • Synthetic biology impacts the development of the components to engineer cellular metabolism and chassis that hosts the chemistry. Metabolic engineering begins with the introduction of genes that encode enzymes which take advantage of locally produced molecules in the chassis metabolic network to produce desired molecules.Enzymes can catalyze in a single step what may require many steps utilizing synthetic chemistry methodologies. Coupling multiple enzymes eliminates the need for purification of intermediates.
    • The Essential Components Required for Chemical Production: that are described in the article
      • Chassis
      • Vectors
      • Promoters
      • Simultaneous Engagement of Multiple Genes
      • CAD Tools
      • Debugging Routines
    • Example Case: Artemisinic Acid produced via E.Coli
      • the methodology of utilizing the mevalonate pathway in E.Coli is listed with a diagram provided. You guys already know this from my presentation.
      • There are much better articles that describe this particular project in far more detail (contact me for pdf's or look it up on google)