Biosynthetic Route Simulator: Functionality

[srhoades10]

High-level functionalities of a biosynthetic route discovery tool

• Multi-objective optimization criteria:
  • Produce product of interest and maintain ATP and/or NAD(P)H supply (whichever might be required energy or reducing equivalents in the route)
• Pathway selection criteria:
  • Minimize metabolic burden (thus requiring estimated transcription/translation load for new or lowly-expressed enzymes)
  • Minimum net Gibbs free energy (most thermodynamically favorable)
  • Carbon or energy efficiency, based on overall pathway stoichiometry or loss of atoms such as CO2
  • Minimum path length
  • Minimum number of heterologous enzymes (if any)
• Post-hoc route analysis:
  • Enzymes within the metabolic network which are net negative towards product production (e.g. enzymes which may be deletion or expression repression candidates)
  • Identify sets of metabolites which may inhibit the biosynthetic route, and the corresponding enzymes which may either produce or metabolize them (repression or overexpression candidates)
  • Estimated flux and/or metabolic control analysis to identify rate-controlling enzyme(s) along the pathway
  • Cost estimates of all precursors and intermediates (if intermediates are to be added exogenously)
  • Necessary co-reactants
• Other capabilities
  • Co-culture opportunities: If a route can be effectively modularized across two organisms, which transporters can be expressed in each organism to connect the routes
  • Creating a biosynthetic route with gaps, and gap-filling with a proposed enzymatic requirement (e.g. if we could engineer an enzyme to do X, what does it need to do?) or one or more heterologous enzymes
  • For reactions which utilize promiscuous enzymes, if the enzyme can act on a metabolite with a non-specific functional group (-R), dynamically expand the metabolite network (e.g. if enzyme can elongate carbon chains C-, C-C, C-C-C, etc...)
  • Ensure carbons from precursor(s) of interest are those found in final product(s). This may require a full atom-mapping reaction network
  • Multi-precursor and multi-product search