Enhancing biomolecule production through microbial engineering and advanced manufacturing




Yuan, Shuo-Fu

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Sustainable production of biochemicals through microbial fermentation from renewable feedstocks offers an attractive alternative to the chemical synthesis process. In this regard, strategies including harnessing synthetic biology tools and metabolic engineering enable the high-level production of value-added biomolecules. However, sorting large libraries of microbial variants for improving biomolecule production is greatly limited in the throughput of screening. Additionally, most microbial bioprocess applications rely on large-scale suspension fermentation technologies that are not easily portable, reusable, or suitable for on-demand production, especially when large-scale manufacturing infrastructure is scarce and medicines are hard to access in developing nations or on active military missions. To overcome these challenges, we first develop high-throughput screening platforms for maximizing de novo microbial production of a selected non-proteinogenic amino acid β-alanine, which has been widely used in sport supplements. Through evaluation of innate metabolic potential in various Escherichia coli wild-type strains towards generating direct precursor aspartate, utilization of genetic editing tools, directed evolution approach, and in vivo biosensor able to readily transduce β-alanine production levels into stable fluorescent readouts, we identified decreasing the gene expression level of a novel chromosomal target ribonuclease E (rne) is beneficial to β-alanine production. Specifically, the resulting engineered E. coli exhibits a 4.34-fold improvement in β-alanine yield when compared to the parental strain cultivated in a glucose minimal medium. Further redox-cofactor balancing in this background strain and fermentation optimization led to the production of 7.84 g/L of β-alanine in a bioreactor. We next designed a synthetic E. coli-Saccharomyces cerevisiae consortium wherein two metabolically distinct microbes were employed for de novo production of resveratrol, a flavonoid compound exhibiting health-promoting properties. Through modular co-culture engineering, the upstream E. coli module enables glucose-to-p-coumaric acid conversion, and the downstream S. cerevisiae module allows for the transformation of p-coumaric acid into resveratrol. Upon optimization of the initial inoculation ratio of two populations and fermentation parameters, this co-culture approach yielded a final resveratrol titer of 36 mg/L. Finally, we describe an F127-BUM hydrogel system for encapsulating microbes for on-demand small molecule and protein production in microbial mono-culture and consortia. This robust hydrogel system can not only spatially confine independent members of a microbial consortium well-suited for establishing stable fermentative performance but also be used to control end-point dynamics of the consortia. To this end, this platform was utilized for the production of four chemical compounds, a peptide antibiotic, 3 recombinant proteins and carbohydrate catabolism by using either mono-cultures or co-cultures. The printed microbe-laden hydrogel constructs’ efficiency in repeated production phases, both pre- and post-preservation, outperforms traditional suspension fermentation.



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