A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology

J Am Chem Soc. 2018 Mar 28;140(12):4302-4316. doi: 10.1021/jacs.7b13292. Epub 2018 Mar 16.

Abstract

Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species ( Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aminoglycosides / biosynthesis
  • Aminoglycosides / chemistry
  • Carbazoles / chemistry
  • Carbazoles / metabolism
  • Computational Biology
  • Cyclohexane Monoterpenes
  • Enediynes / chemistry
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Fatty Alcohols / chemistry
  • Fatty Alcohols / metabolism
  • Furans / chemistry
  • Furans / metabolism
  • Genetic Engineering*
  • Lactones / chemistry
  • Lactones / metabolism
  • Molecular Structure
  • Monoterpenes / chemistry
  • Monoterpenes / metabolism
  • Peptides / chemistry
  • Pressure
  • Pyrimidine Nucleosides / biosynthesis
  • Pyrimidine Nucleosides / chemistry
  • Pyrrolnitrin / biosynthesis
  • Pyrrolnitrin / chemistry
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Streptomyces / genetics*
  • Streptomyces / metabolism
  • Thiazoles / chemistry
  • Thiazoles / metabolism
  • Time Factors
  • Vincristine / biosynthesis
  • Vincristine / chemistry

Substances

  • Aminoglycosides
  • Carbazoles
  • Cyclohexane Monoterpenes
  • Enediynes
  • Fatty Alcohols
  • Furans
  • Lactones
  • Monoterpenes
  • Peptides
  • Pyrimidine Nucleosides
  • Thiazoles
  • barbamide
  • pacidamycin D
  • C 1027
  • tetrahydrofuran
  • Vincristine
  • carvone
  • cetyl alcohol
  • rebeccamycin
  • Pyrrolnitrin