Jonghyeok Shin

Yeast platforms are rapidly transitioning from traditional eukaryotic model organisms to versatile, programmable chassis for next-generation human health applications. This review systematically examines the translational evolution of conventional and non-conventional yeasts including Saccharomyces cerevisiae, Komagataella phaffii, Saccharomyces boulardii, and Yarrowia lipolytica and redefines them as scalable biomanufacturing factories and advanced living therapeutics. We highlight milestone advancements in synthetic biology toolkits that lower technical barriers, such as CRISPR-mediated multiplex editing, modular cloning frameworks, and high-throughput secretion screening. We focus on sophisticated glycoengineering strategies for humanized N-glycosylation, alongside data-driven paradigms that leverage artificial intelligence to predict gene expression and streamline strain design. In clinical domains, we detail the established success of yeast in producing subunit or virus-like particle vaccines (e.g. HBV and HPV) and therapeutic enzymes (e.g. ecallantide), alongside its emerging role as gut-adapted live biotherapeutic products (LBPs) engineered for in situ delivery and biosensing. Finally, we explore specialized non-conventional platforms, focusing on lipid- and acetyl-CoA-rich hosts for lipophilic drug discovery, and stress-tolerant systems optimized for economical, feedstock-flexible bioprocesses. In summary, this review underscores the integrated value of yeast systems across disease modeling, industrial manufacturing, and clinical intervention, charting future directions to address global health challenges.

Efficiently building metabolic pathways via multigene assembly has long been constrained by the limitations of traditional cloning techniques, necessitating a breakthrough in gene assembly methods. Notably, various in vitro gene assembly methods have been developed to simplify the construction of an expression-tunable library. However, in vitro gene assembly requires a tedious multistep construction process, making it time-consuming and labor-intensive. Therefore, in this study, we developed an automated one-step multigene assembly method for constructing an expression-tunable library based on in vivo homologous recombination. We optimized the shuttle vector for in vivo homologous recombination to improve the assembly efficiency. We also scaled down the whole assembly method for a high-throughput gene assembly. Finally, the developed method demonstrated the construction of the expression-tunable multigene library in the biofoundry. Therefore, this study offers a versatile strategy for parallel and high-throughput genetic engineering in synthetic biology.

Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

A bstract: Simultaneous intracellular depolymerization of xylo-oligosaccharides (XOS) and acetate fermentation by engineered Saccharomyces cerevisiae offers an advance towards more cost-effective second-generation (2G) ethanol production. As xylan is one of the most abundant polysaccharides present in lignocellulosic residues, the transport and breakdown of XOS in an intracellular environment might bring a competitive advantage for recombinant strains in competition with contaminating microbes, which are always present in fermentation tanks; furthermore, acetic acid is a ubiquitous toxic component in lignocellulosic hydrolysates, deriving from hemicellulose and lignin breakdown. In the present work, the previously engineered S. cerevisiae strain, SR8A6S3, expressing NADPH-linked xylose reductase (XR), NAD ⁺ -linked xylitol dehydrogenase (XDH) (for xylose assimilation), as well as NADH-linked acetylating acetaldehyde dehydrogenase (AADH) and acetyl-CoA synthetase (ACS) (for an NADH-dependent acetate reduction pathway), was used as the host for expressing of two β-xylosidases, GH43-2 and GH43-7 , and a xylodextrin transporter, CDT-2 , from Neurospora crassa , yielding the engineered strain SR8A6S3-CDT ₂ -GH43 _2/7 . Both β-xylosidases and the transporter were introduced by replacing two endogenous genes, GRE3 and SOR1 , that encode aldose reductase and sorbitol (xylitol) dehydrogenase, respectively, which catalyse steps in xylitol production. Xylitol accumulation during xylose fermentation is a problem for 2G ethanol production since it reduces final ethanol yield. The engineered strain, SR8A6S3-CDT ₂ -GH43 _2/7 , produced ethanol through simultaneous co-utilization of XOS, xylose, and acetate. The mutant strain produced 60% more ethanol and 12% less xylitol than the control strain when a hemicellulosic hydrolysate was used as a mono- and oligosaccharide source. Similarly, the ethanol yield was 84% higher for the engineered strain using hydrolysed xylan compared with the parental strain. The consumption of XOS, xylose, and acetate expands the capabilities of S. cerevisiae for utilization of all of the carbohydrate in lignocellulose, potentially increasing the efficiency of 2G biofuel production. Highlights: Integration of XOS pathway in an acetate-xylose-consuming S. cerevisiae strain; Intracellular fermentation of XOS, acetate and xylose improved ethanol production; Deletion of both sor1 Δ and gre3 Δ reduced xylitol production.