Prospecting Biochemical Pathways to Implement Microbe-Based Production of the New-to-Nature Platform Chemical Levulinic Acid

Levulinic acid is a versatile platform
molecule with potential
to be used as an intermediate in the synthesis of many value-added
products used across different industries, from cosmetics to fuels.
Thus far, microbial biosynthetic pathways having levulinic acid as
a product or an intermediate are not known, which restrains the development
and optimization of a microbe-based process envisaging the sustainable
bioproduction of this chemical. One of the doors opened by synthetic
biology in the design of microbial systems is the implementation of
new-to-nature pathways, that is, the assembly of combinations of enzymes
not observed in vivo, where the enzymes can use not
only their native substrates but also non-native ones, creating synthetic
steps that enable the production of novel compounds. Resorting to
a combined approach involving complementary computational tools and
extensive manual curation, in this work, we provide a thorough prospect
of candidate biosynthetic pathways that can be assembled for the production
of levulinic acid in Escherichia coli or Saccharomyces cerevisiae. Out
of the hundreds of combinations screened, five pathways were selected
as best candidates on the basis of the availability of substrates
and of candidate enzymes to catalyze the synthetic steps (that is,
those steps that involve conversions not previously described). Genome-scale
metabolic modeling was used to assess the performance of these pathways
in the two selected hosts and to anticipate possible bottlenecks.
Not only does the herein described approach offer a platform for the
future implementation of the microbial production of levulinic acid
but also it provides an organized research strategy that can be used
as a framework for the implementation of other new-to-nature biosynthetic
pathways for the production of value-added chemicals, thus fostering
the emerging field of synthetic industrial microbiotechnology.