Periodic Reporting for period 2 - SHIKIFACTORY100 (Modular cell factories for the production of 100 compounds from the shikimate pathway)
Berichtszeitraum: 2020-07-01 bis 2021-12-31
However, to support this significant market trend, it is important to develop scalable technologies that can offer efficient biological processes for compounds that can be scaled-up respecting environmental and social aspects. In many cases where the chemical synthesis has been put in place, the complexity of the molecules leads to prices that, although lower than most of the ones associated with natural products, are still within the same order of magnitude.
Combining the latest advances on synthetic biology, systems biology and rapid prototyping the project SHIKIFACTORY100 seeks the rapid and cost-effective development of biological alternatives, which can be used to create resource-efficient and cost-effective microbial processes for the production of novel compounds or compounds that are currently only produced by petrochemical processes or limited to plant extraction.
The overall objective of SHIKIFACTORY100 is empowering cost-effective synthesis of >100 compounds derived from shikimate to expand diversity of nature's chemical production. This project proposes a complete pipeline taking advantage of emerging synthetic biology and rapid prototyping techniques combined with knowledge of synthetic chemistry, enzyme engineering, systems biology and bioinformatics.
The main technical objectives (vectors) of the project are (Figure 1):
● DISCOVERY - Collection of natural and non-natural reactions and compounds as well as the discovery and ranking of novel pathways for the production of the target compounds.
● DESIGN - In silico and in vivo design, rapid prototyping for the pathways selected in the previous vector and optimization efforts toward chassis and advancing production strains.
● APPLICATION - Application and initial upscaling for a subset of compounds and sustainability appraisal.
In summary:
● common pipeline established for the generation of potential biosynthetic pathways
● generated potential pathways for 106 compounds.
● creation of ShikiAtlas and ARBRE, tools that allow to explore >400k reactions and 62k compounds obtainable from the shikimate pathway.
● developed a deep learning pipeline to design new chemical structures
● synthesis of 48 potential sweeteners, 3 identified as sweet and non-toxic and 2 with potential biosynthetic pathways identified
● established a framework for cell factory design and SDDB - a centralized database for strain designs
● a new large-scale multi-compartment model for S. cerevisiae was developed
● preliminary chassis cells for E. coli and S. cerevisiae are available
● frameworks for gene discovery and computational protein engineering were developed and applied
● >600 synbio parts made available on ICE
● implemented prototype strains for 53 of the 100 compounds
● 1 patent finalized, 1 submitted and potential for at least 9 more is being evaluated.