Yeast metabolic engineering

Short description: Design and build of stable yeast cell factories for fragrances, flavours, vitamin precursors, jet-fuel intermediates and secreted food proteins, from genome engineering through to strains ready for scale-up, with genomics, transcriptomics, proteomics, metabolomics and flow cytometry.

I engineer Saccharomyces cerevisiae and methylotrophic yeast cell factories for industrial biomanufacturing: complex genome engineering, stable genetic circuits, relief of metabolic bottlenecks, and assembly of large constructs. Strain selection is closed with genomics, transcriptomics, proteomics, metabolomics and flow cytometry, not titre alone.

The core offer is end-to-end strain development for high-value fermentation products, especially terpenes. The same approach extends to methylotrophic yeasts for precision fermentation. As lead author of a Metabolic Engineering review with Kobe University and Australian partners (Peng et al., Metabolic Engineering 99 (2027) 102532), I set out how Komagataella phaffii and Ogataea (para)polymorpha can be engineered for secreted food proteins: dairy proteins (caseins, lactoferrin), animal-free meat ingredients (leghemoglobin, collagen, albumin, growth factors) and sweet proteins (thaumatin, brazzein). The review covers genome editing where homologous recombination is weak, methanol-inducible and methanol-free expression, promoter engineering and synthetic circuits, secretory-pathway engineering, and glycoengineering where glycosylation affects food function, including C1 and methanol feedstocks.

Enabling methods:

HapAmp, a patented haploinsufficiency-driven amplification method (Nature Communications, 2022), titrates copy number from 3 to 47 copies and supports grams-per-litre limonene production. The same dosage control is relevant where multi-copy arrays in methylotrophic yeasts are unstable under production stress.

A cyanamide-inducible homing-nuclease method (Synthetic and Systems Biotechnology, 2024), adopted by Levur for on-genome large-fragment assembly in S. cerevisiae.

Multi-option inducible expression, including small-molecule, quorum-sensing and temperature inputs, plus inducible protein degradation.

Single-cell reporters and biosensors (ACS Synthetic Biology, 2025), read out by flow cytometry to quantify population heterogeneity, circuit switching and evolutionary drift under stress.

Genomics, transcriptomics, proteomics and metabolomics to locate secretory and metabolic bottlenecks and to guide the next design round.

Genetic-circuit biocomputation coupled to essential-gene metabolic locking against strain degeneration (bioRxiv, 2026).

Yeastlink (https://yeastlink.com), a genome cross-reference for non-conventional yeasts.

Suitable engagements: Sponsored research, co-development, strain design for a defined product, methylotrophic-yeast design for secreted food proteins, genomics, transcriptomics, proteomics, metabolomics, biosensor-based single-cell study.

Industry applications: Precision fermentation; flavours and fragrances; food ingredients; dairy and alternative proteins; highdensity jet-fuel intermediates; methanol- and C1-based biomanufacturing.

Looking for: Companies with a defined yeast product, or a need for stable multi-gene constructs, regulatory circuits, and single-cell or multi-omics characterisation in conventional or methylotrophic yeasts.