Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>

ABSTRACT Protein folding is often considered the flux controlling process in protein synthesis and secretion. Here, two previously isolated Saccharomyces cerevisiae strains with increased α-amylase productivity were analyzed in chemostat cultures at different dilution rates using multi-omics data. B...

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Autores principales:	Qi Qi, Feiran Li, Rosemary Yu, Martin K. M. Engqvist, Verena Siewers, Johannes Fuchs, Jens Nielsen
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	protein secretory pathway protein folding precision multi-omics analysis protein production constraint-based modeling Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ef879989345f40879de143a94eb6b15d
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spelling	oai:doaj.org-article:ef879989345f40879de143a94eb6b15d2021-11-15T15:55:43ZDifferent Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>10.1128/mBio.02743-202150-7511https://doaj.org/article/ef879989345f40879de143a94eb6b15d2020-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02743-20https://doaj.org/toc/2150-7511ABSTRACT Protein folding is often considered the flux controlling process in protein synthesis and secretion. Here, two previously isolated Saccharomyces cerevisiae strains with increased α-amylase productivity were analyzed in chemostat cultures at different dilution rates using multi-omics data. Based on the analysis, we identified different routes of the protein folding pathway to improve protein production. In the first strain, the increased abundance of proteins working on the folding process, coordinated with upregulated glycogen metabolism and trehalose metabolism, helped increase α-amylase productivity 1.95-fold compared to the level in the original strain in chemostat culture at a dilution rate of 0.2/h. The second strain further strengthened the folding precision to improve protein production. More precise folding helps the cell improve protein production efficiency and reduce the expenditure of energy on the handling of misfolded proteins. As calculated using an enzyme-constrained genome-scale metabolic model, the second strain had an increased productivity of 2.36-fold with lower energy expenditure than that of the original under the same condition. Further study revealed that the regulation of N-glycans played an important role in the folding precision control and that overexpression of the glucosidase Cwh41p can significantly improve protein production, especially for the strains with improved folding capacity but lower folding precision. Our findings elucidated in detail the mechanisms in two strains having improved protein productivity and thereby provided novel insights for industrial recombinant protein production as well as demonstrating how multi-omics analysis can be used for identification of novel strain-engineering targets. IMPORTANCE Protein folding plays an important role in protein maturation and secretion. In recombinant protein production, many studies have focused on the folding pathway to improve productivity. Here, we identified two different routes for improving protein production by yeast. We found that improving folding precision is a better strategy. Dysfunction of this process is also associated with several aberrant protein-associated human diseases. Here, our findings about the role of glucosidase Cwh41p in the precision control system and the characterization of the strain with a more precise folding process could contribute to the development of novel therapeutic strategies.Qi QiFeiran LiRosemary YuMartin K. M. EngqvistVerena SiewersJohannes FuchsJens NielsenAmerican Society for Microbiologyarticleprotein secretory pathwayprotein folding precisionmulti-omics analysisprotein productionconstraint-based modelingMicrobiologyQR1-502ENmBio, Vol 11, Iss 6 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	protein secretory pathway protein folding precision multi-omics analysis protein production constraint-based modeling Microbiology QR1-502
spellingShingle	protein secretory pathway protein folding precision multi-omics analysis protein production constraint-based modeling Microbiology QR1-502 Qi Qi Feiran Li Rosemary Yu Martin K. M. Engqvist Verena Siewers Johannes Fuchs Jens Nielsen Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>
description	ABSTRACT Protein folding is often considered the flux controlling process in protein synthesis and secretion. Here, two previously isolated Saccharomyces cerevisiae strains with increased α-amylase productivity were analyzed in chemostat cultures at different dilution rates using multi-omics data. Based on the analysis, we identified different routes of the protein folding pathway to improve protein production. In the first strain, the increased abundance of proteins working on the folding process, coordinated with upregulated glycogen metabolism and trehalose metabolism, helped increase α-amylase productivity 1.95-fold compared to the level in the original strain in chemostat culture at a dilution rate of 0.2/h. The second strain further strengthened the folding precision to improve protein production. More precise folding helps the cell improve protein production efficiency and reduce the expenditure of energy on the handling of misfolded proteins. As calculated using an enzyme-constrained genome-scale metabolic model, the second strain had an increased productivity of 2.36-fold with lower energy expenditure than that of the original under the same condition. Further study revealed that the regulation of N-glycans played an important role in the folding precision control and that overexpression of the glucosidase Cwh41p can significantly improve protein production, especially for the strains with improved folding capacity but lower folding precision. Our findings elucidated in detail the mechanisms in two strains having improved protein productivity and thereby provided novel insights for industrial recombinant protein production as well as demonstrating how multi-omics analysis can be used for identification of novel strain-engineering targets. IMPORTANCE Protein folding plays an important role in protein maturation and secretion. In recombinant protein production, many studies have focused on the folding pathway to improve productivity. Here, we identified two different routes for improving protein production by yeast. We found that improving folding precision is a better strategy. Dysfunction of this process is also associated with several aberrant protein-associated human diseases. Here, our findings about the role of glucosidase Cwh41p in the precision control system and the characterization of the strain with a more precise folding process could contribute to the development of novel therapeutic strategies.
format	article
author	Qi Qi Feiran Li Rosemary Yu Martin K. M. Engqvist Verena Siewers Johannes Fuchs Jens Nielsen
author_facet	Qi Qi Feiran Li Rosemary Yu Martin K. M. Engqvist Verena Siewers Johannes Fuchs Jens Nielsen
author_sort	Qi Qi
title	Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>
title_short	Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>
title_full	Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>
title_fullStr	Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>
title_full_unstemmed	Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>
title_sort	different routes of protein folding contribute to improved protein production in <named-content content-type="genus-species">saccharomyces cerevisiae</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/ef879989345f40879de143a94eb6b15d
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Different Routes of Protein Folding Contribute to Improved Protein Production in <named-content content-type="genus-species">Saccharomyces cerevisiae</named-content>

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