Engineering Strategies for Enhanced Heterologous Protein Production by Saccharomyces Cerevisiae

Overview

Journal Microb Cell Fact

Publisher Biomed Central

Specialties Biotechnology
Microbiology

Date 2024 Jan 21

PMID 38247006

Authors

Meirong Zhao

Jianfan Ma

Lei Zhang

Haishan Qi

Affiliations

Soon will be listed here.

Abstract

Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae, a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae. The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.

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References

Rakestraw J, Sazinsky S, Piatesi A, Antipov E, Wittrup K . Directed evolution of a secretory leader for the improved expression of heterologous proteins and full-length antibodies in Saccharomyces cerevisiae. Biotechnol Bioeng. 2009; 103(6):1192-201. PMC: 2847895. DOI: 10.1002/bit.22338. View

Wang C, Zhang W, Tian R, Zhang J, Zhang L, Deng Z . Model-driven design of synthetic N-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnol J. 2022; 17(5):e2100655. DOI: 10.1002/biot.202100655. View

Richardson S, Mitchell L, Stracquadanio G, Yang K, Dymond J, DiCarlo J . Design of a synthetic yeast genome. Science. 2017; 355(6329):1040-1044. DOI: 10.1126/science.aaf4557. View

Feng X, Marchisio M . Promoter Engineering before and during the Synthetic Biology Era. Biology (Basel). 2021; 10(6). PMC: 8229000. DOI: 10.3390/biology10060504. View

Huang M, Bao J, Hallstrom B, Petranovic D, Nielsen J . Efficient protein production by yeast requires global tuning of metabolism. Nat Commun. 2017; 8(1):1131. PMC: 5656615. DOI: 10.1038/s41467-017-00999-2. View

Smith J, Tang B, Robinson A . Protein disulfide isomerase, but not binding protein, overexpression enhances secretion of a non-disulfide-bonded protein in yeast. Biotechnol Bioeng. 2004; 85(3):340-50. DOI: 10.1002/bit.10853. View

Liu F, Wu X, Li L, Liu Z, Wang Z . Use of baculovirus expression system for generation of virus-like particles: successes and challenges. Protein Expr Purif. 2013; 90(2):104-16. PMC: 7128112. DOI: 10.1016/j.pep.2013.05.009. View

Chen X, Li X, Ji B, Wang Y, Ishchuk O, Vorontsov E . Suppressors of amyloid-β toxicity improve recombinant protein production in yeast by reducing oxidative stress and tuning cellular metabolism. Metab Eng. 2022; 72:311-324. DOI: 10.1016/j.ymben.2022.04.005. View

Toikkanen J, Sundqvist L, Keranen S . Kluyveromyces lactis SSO1 and SEB1 genes are functional in Saccharomyces cerevisiae and enhance production of secreted proteins when overexpressed. Yeast. 2004; 21(12):1045-55. DOI: 10.1002/yea.1151. View

10.

Cripwell R, Rose S, van Zyl W . Expression and comparison of codon optimised Aspergillus tubingensis amylase variants in Saccharomyces cerevisiae. FEMS Yeast Res. 2017; 17(4). DOI: 10.1093/femsyr/fox040. View

11.

Solow S, Sengbusch J, Laird M . Heterologous protein production from the inducible MET25 promoter in Saccharomyces cerevisiae. Biotechnol Prog. 2005; 21(2):617-20. DOI: 10.1021/bp049916q. View

12.

Kim Y, Kang J, Gil J, Kim S, Shin K, Kang H . Abolishment of N-glycan mannosylphosphorylation in glyco-engineered Saccharomyces cerevisiae by double disruption of MNN4 and MNN14 genes. Appl Microbiol Biotechnol. 2017; 101(7):2979-2989. DOI: 10.1007/s00253-017-8101-3. View

13.

Aza P, Molpeceres G, de Salas F, Camarero S . Design of an improved universal signal peptide based on the α-factor mating secretion signal for enzyme production in yeast. Cell Mol Life Sci. 2021; 78(7):3691-3707. PMC: 8038962. DOI: 10.1007/s00018-021-03793-y. View

14.

Bussey H, Steinmetz O, Saville D . Protein secretion in yeast: Two chromosomal mutants that oversecrete killer toxin in Saccharomyces cerevisiae. Curr Genet. 2013; 7(6):449-56. DOI: 10.1007/BF00377610. View

15.

Tang H, Wu Y, Deng J, Chen N, Zheng Z, Wei Y . Promoter Architecture and Promoter Engineering in . Metabolites. 2020; 10(8). PMC: 7466126. DOI: 10.3390/metabo10080320. View

16.

Dudich E, Dudich I, Semenkova L, Benevolensky S, Morozkina E, Marchenko A . Engineering of the Saccharomyces cerevisiae yeast strain with multiple chromosome-integrated genes of human alpha-fetoprotein and its high-yield secretory production, purification, structural and functional characterization. Protein Expr Purif. 2012; 84(1):94-107. DOI: 10.1016/j.pep.2012.04.008. View

17.

Shah K, Cheng Y, Hahn B, Bridges R, Bradbury N, Mueller D . Synonymous codon usage affects the expression of wild type and F508del CFTR. J Mol Biol. 2015; 427(6 Pt B):1464-1479. PMC: 4355305. DOI: 10.1016/j.jmb.2015.02.003. View

18.

Aza P, de Salas F, Molpeceres G, Rodriguez-Escribano D, de la Fuente I, Camarero S . Protein Engineering Approaches to Enhance Fungal Laccase Production in . Int J Mol Sci. 2021; 22(3). PMC: 7866195. DOI: 10.3390/ijms22031157. View

19.

Gilbert S, Evans L, Ballance D . Disruption of the Saccharomyces cerevisiae YAP3 gene reduces the proteolytic degradation of secreted recombinant human albumin. Yeast. 1998; 14(2):161-9. DOI: 10.1002/(SICI)1097-0061(19980130)14:2<161::AID-YEA208>3.0.CO;2-Y. View

20.

Zhou S, Wu Y, Xie Z, Jia B, Yuan Y . Directed genome evolution driven by structural rearrangement techniques. Chem Soc Rev. 2021; 50(22):12788-12807. DOI: 10.1039/d1cs00722j. View