# Overcoming the problem of heterologous proteins folding to improve the efficiency of yeast bioproducers

**Authors:** N.V. Dorogova, S.A. Fedorova

PMC · DOI: 10.18699/vjgb-25-140 · Vavilov Journal of Genetics and Breeding · 2025-12-01

## TL;DR

This review discusses how yeast can be engineered to better produce heterologous proteins by improving their folding mechanisms.

## Contribution

The paper provides a comprehensive overview of cellular mechanisms and engineering strategies to enhance protein folding in yeast bioproducers.

## Key findings

- Protein folding limitations in yeast are a major bottleneck for heterologous protein production.
- Engineering techniques like optimal signal peptide selection and co-expression with chaperones improve protein folding efficiency.
- Modifications to protein quality control and proteolysis inhibition enhance yeast's ability to secrete heterologous proteins.

## Abstract

In the last few decades, yeasts have been successfully engineered to be an excellent microbial cell factory for producing recombinant proteins with desired properties. This was due to their cost-effective characteristics and the successful application of genomic modification technologies. In addition, yeasts have a conserved post-translational modification pathway among eukaryotic organisms, which ensures the correct folding of recombinant proteins. However, the folding machinery cannot always cope with the load caused by the overexpression of recombinant genes, leading to the accumulation of misfolded proteins, the formation of aggregates and low production. Therefore, the protein-folding capacity of the endoplasmic reticulum (ER) remains one of the main limitations for heterologous protein production in yeast host organisms. However, thanks to many years of effective research of the fundamental mechanisms of protein folding, these limitations have been largely overcome. The study of folding in both model organisms and bioproducers has allowed to identify the molecular factors and cellular mechanisms that determine how a nascent polypeptide chain acquires its three-dimensional functional structure. This knowledge has become the basis for developing new effective techniques for engineering highly productive yeast strains. In this review, we examined the main cellular mechanisms associated with protein folding, such as ER transition, chaperone binding, oxidative folding, glycosylation, protein quality control. We discuss the effectiveness of applying this knowledge to the development of various engineering techniques aimed at overcoming bottlenecks in the protein folding system. In particular, selection of optimal signal peptides, co-expression with chaperones and foldases, modification of protein quality control, inhibition of proteolysis, and other techniques have allowed to enhance the ability of yeast bioproducers to effectively secrete heterologous proteins.

## Full-text entities

- **Genes:** HAC1 (transcription factor HAC1) [NCBI Gene 850513] {aka ERN4, IRE15}, CNE1 (calnexin) [NCBI Gene 851241] {aka FUN48}, MNL1 (alpha-1,2-mannosidase MNL1) [NCBI Gene 856611] {aka HTM1}, OST1 (dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1) [NCBI Gene 853455] {aka NLT1}, HRD1 (E3 ubiquitin-protein ligase HRD1) [NCBI Gene 854149] {aka DER3}, KAR2 (Hsp70 family ATPase KAR2) [NCBI Gene 853418] {aka GRP78}, UBI4 (ubiquitin) [NCBI Gene 850620] {aka SCD2, UB14}, MSB2 (Msb2p) [NCBI Gene 852897], ROT2 (glucan 1,3-alpha-glucosidase ROT2) [NCBI Gene 852530] {aka GLS2}, UBC7 (E2 ubiquitin-conjugating protein UBC7) [NCBI Gene 855036] {aka DER2, QRI8}, DAN4 (Dan4p) [NCBI Gene 853616], SCJ1 (Scj1p) [NCBI Gene 855254], JEM1 (Jem1p) [NCBI Gene 853372] {aka KAR8}, ERO1 (ER oxidoreductin) [NCBI Gene 854909], YDJ1 (type I HSP40 co-chaperone YDJ1) [NCBI Gene 855661] {aka HSP40, MAB3, MAS5}, SIL1 (Sil1p) [NCBI Gene 854126] {aka SLS1}, PDI1 (protein disulfide isomerase PDI1) [NCBI Gene 850314] {aka MFP1, TRG1}, HRD3 (ubiquitin ligase complex subunit HRD3) [NCBI Gene 850904], GAS1 (1,3-beta-glucanosyltransferase GAS1) [NCBI Gene 855355] {aka CWH52, GGP1}, USA1 (Usa1p) [NCBI Gene 854979], MFA1 (mating pheromone a) [NCBI Gene 852072], LHS1 (Hsp70 family chaperone LHS1) [NCBI Gene 853789] {aka CER1, SSI1}, BLZF1 (basic leucine zipper nuclear factor 1) [NCBI Gene 8548] {aka GOLGIN-45, JEM-1, JEM-1s, JEM1}, FRE2 (ferric/cupric-chelate reductase) [NCBI Gene 853660], EGH1 (hydrolase) [NCBI Gene 854824], CWH41 (mannosyl-oligosaccharide glucosidase) [NCBI Gene 852857] {aka DER7, GLS1}, MPD1 (protein disulfide isomerase MPD1) [NCBI Gene 854462], TRL1 (tRNA ligase) [NCBI Gene 853358] {aka LIG1, RLG1}, MNS1 (mannosyl-oligosaccharide 1,2-alpha-mannosidase) [NCBI Gene 853595], IRE1 (bifunctional endoribonuclease/protein kinase IRE1) [NCBI Gene 856478] {aka ERN1}, YOS9 (Yos9p) [NCBI Gene 851627], DER1 (derlin) [NCBI Gene 852500]
- **Diseases:** congenital (MESH:D008209), ERAD (MESH:D055959)
- **Chemicals:** Glycans (MESH:D011134), dithiols (MESH:C004848), asparagine (MESH:D001216), mannose (MESH:D008358), cystine (MESH:D003553), starch (MESH:D013213), disulfide (MESH:D004220), oligosaccharide (MESH:D009844), Glc3Man9GlcNAc2-oligosaccharide (-), dolichol diphosphate (MESH:C026406), thiol (MESH:D013438), Glc1Man9GlcNAc2 oligosaccharide (MESH:C092383), cysteine (MESH:D003545), glucose (MESH:D005947), xylan (MESH:D014990), calcium (MESH:D002118), nitrogen (MESH:D009584), GlcNAc (MESH:D000117)
- **Species:** Komagataella pastoris (species) [taxon 4922], Candida albicans (species) [taxon 5476], Homo sapiens (human, species) [taxon 9606], Kluyveromyces lactis (species) [taxon 28985], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Schizosaccharomyces pombe (fission yeast, species) [taxon 4896], Lyssavirus rabies (species) [taxon 11292], Ogataea angusta (species) [taxon 870730], Trichoderma reesei (species) [taxon 51453], Pichia (genus) [taxon 4919], Lodderomyces parapsilosis (species) [taxon 5480], Necator americanus (New World hookworm, species) [taxon 51031], Yarrowia lipolytica (species) [taxon 4952], Bacillus subtilis (species) [taxon 1423], Komagataella phaffii (species) [taxon 460519], Citrobacter amalonaticus (species) [taxon 35703]

## Full text

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Source: https://tomesphere.com/paper/PMC12876926