Synthetic Biology for Sustainable Bioproduction Systems

Abstract

Synthetic biology--the application of engineering principles including standardisation, modularity, and
design-build-test-learn cycles to the construction of novel biological systems--offers transformative potential for
sustainable bioproduction of chemicals, fuels, materials, and therapeutics that currently depend on fossil-derived
feedstocks and resource-intensive chemical synthesis routes. This study designs, constructs, and optimises three
synthetic metabolic pathways in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BY4741 for the biosynthesis
of three high-value industrial compounds: lycopene (terpenoid antioxidant, EUR 800/kg), muconic acid (nylon precursor,
EUR 2,400/kg), and PHB (polyhydroxybutyrate, biodegradable polymer, EUR 4,000/kg). Using a
Design-Build-Test-Learn (DBTL) framework integrating metabolic modelling (COBRA v3.0), combinatorial promoter/RBS
optimisation (Anderson promoter library, 5'-UTR calculator), flux balance analysis (FBA)-guided gene knockout selection,
and adaptive laboratory evolution (ALE, 30 serial passages), final engineered strains achieved titres of 847 mg/L
lycopene (E. coli, 14.2-fold improvement over wild-type MEP pathway baseline), 18.4 g/L muconic acid (E. coli, 92% of
theoretical maximum yield), and 62.4% PHB cell dry weight (E. coli, 98.1% substrate conversion efficiency). Multi-omics
characterisation of evolved strains (transcriptomics, metabolomics, proteomics) revealed the molecular basis of
performance gains and identified seven novel regulatory targets for future strain improvement. Techno-economic
analysis confirmed positive net present value (NPV = EUR 28.4M at 10-year horizon) for lycopene and muconic acid
bioproduction at demonstration scale (100 m3 fermenter), providing a blueprint for industrial synthetic biology scale-up.