Methylotrophic yeast engineering for secreted protein production via precision fermentation: food ingredient proteins and synthetic biology strategies.
Aug 2026· Metabolic Engineering· Vol 99, pp.
102532
· 1 citation· 198 references
Medicine
TL;DR
Recent advances and future potential in engineering methylotrophic yeasts for food protein production, with particular focus on Komagataella phaffii are reviewed, addressing the dual goals of improving both yield and quality.
Abstract
Methylotrophic yeasts are outstanding platforms for the production of recombinant proteins through precision fermentation. Growing demand for protein-based food ingredients requires economically viable secretion efficiency and space-time yields, as well as correct post-translational modifications to ensure proper food functionality. Here, we review recent advances and future potential in engineering methylotrophic yeasts for food protein production, with particular focus on Komagataella phaffii. We first summarise the production of three categories of protein food ingredients: recombinant dairy proteins, proteins for plant-based and cultivated meat applications, and sweet-tasting proteins. Addressing the dual goals of improving both yield and quality, we then review synthetic biology and metabolic engineering strategies in methylotrophic yeasts, with emphasis on genome engineering and gene expression tools, protein secretory pathway engineering, and glycoengineering. Further advances in synthetic biology, integrated with industrial process development, will be critical to unlocking future precision fermentation systems based on methylotrophic yeasts.
Yeast-based single-cell protein (SCP) has emerged as a promising sustainable protein source due to its high protein content, favorable nutritional profile, and ability to utilize renewable feedstocks. The conversion of food-processing wastes, agricultural by-products, and one-carbon substrates into protein-rich biomass supports waste valorization and circular bioeconomy strategies. However, efficient utilization of these diverse feedstocks remains challenging due to variations in substrate composition and microbial metabolic capacity. Recent advances in metabolic engineering, cell wall engineering, adaptive laboratory evolution, random mutagenesis, and fermentation optimization have improved substrate utilization, biomass formation, and protein accumulation in yeasts. These developments have expanded the potential applications of yeast-based SCP in protein supplements, meat products, flavoring agents, and animal feed. This review provides a comprehensive overview of yeast species for SCP production, renewable feedstock utilization, engineering approaches for enhancing biomass and protein accumulation, and the emerging applications of yeast-based SCP in sustainable food and feed systems.
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The escalating global population and the environmentally inefficient nature of livestock-based protein production are intensifying demand for sustainable and scalable protein alternatives. Microbial biosynthesis, employing engineered cell factories, represents a pivotal strategy for producing functional proteins with a reduced ecological footprint. This review comprehensively examines the biosynthesis of alternative proteins (APs) via microbial precision fermentation, encompassing diverse categories including coloring proteins, flavoring and taste proteins, structuring and texturizing proteins, nutritional and functional proteins, food processing and enabling proteins, and special functional proteins. Enabling technologies, from fermentation feedstock and microbial host selection to genome/metabolic engineering, bioprocess optimization via response surface methodology/artificial neural networks, and downstream purification, are critically analyzed. Emerging strategies demonstrate substantial progress in enhancing microbial titers, achieving functional mimicry, and advancing regulatory readiness. However, persistent challenges include precise flavor replication, nutritional completeness, and food safety concerns such as allergenicity and process contaminants. Potential solutions, including advanced metabolic engineering, refined protein extraction, biocontainment strategies, and transparent regulatory frameworks, are discussed. By integrating technological innovation with targeted application mapping and regulatory foresight, this review outlines a roadmap toward scalable, safe, and functionally robust microbial AP platforms, thereby contributing to the transition toward a sustainable food system.
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Dairy proteins are among the most nutritionally and functionally valuable proteins used in food, clinical nutrition, and infant nutrition, yet their supply remains structurally linked to livestock production and dairy processing streams. Precision fermentation offers, based on proven technology, a route to produce individual milk proteins independently of animal agriculture while preserving their molecular identity and application potential. Recent advances in host engineering, secretion capacity, and bioprocess optimization have moved recombinant milk proteins from proof-of-concept toward industrial relevance. However, not all milk proteins are equally tractable fermentation targets. In this opinion article, we examine β-lactoglobulin, α-lactalbumin, and caseins through the lens of nutritional value, functionality, manufacturing complexity, and commercial readiness. We argue that future success will depend less on sequence expression alone than on scalable biomanufacturing technology and know-how, post-translational fidelity, and application-driven target prioritization.
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