Systems biology of protein synthesis and secretion in yeast
Doctoral thesis, 2021
Protein synthesis and secretion is a vital process to maintain cell function. As it demands numerous building blocks, cofactors and chaperones generated from metabolism and translation, the process is intertwined with metabolic and regulatory networks. To obtain an overall understanding of the protein synthesis and secretory system, multi-omics data are coupled with mathematical modeling to systematically quantify cellular resource reallocation in response to recombinant protein production and/or nutrient starvation.
In this thesis, we mainly use two recombinant proteins, α-amylase and insulin precursor, as model proteins to study the protein synthesis and secretion process in a model organism Saccharomyces cerevisiae. We find that the central metabolism is reprogrammed at a large scale to relieve the oxidative stress caused by recombinant protein production, and the activation of Gcn2p-mediated signaling pathway plays a crucial role in reshaping metabolism. As protein folding is often considered the flux controlling step in protein synthesis and secretion, we further identify two routes of the protein folding pathway to improve protein production, namely through improved folding capacity and increased folding precision, respectively. Additionally, protein translation is the initial step of protein synthesis. We find that cells maintain large and unequally distributed reserves in translational capacity by stepwise reducing nitrogen availability. Moreover, we also construct a proteome-constrained genome-scale protein secretory model for S. cerevisiae (pcSecYeast) to perform secretory simulations and provide genomic targets for cell engineering. Our findings elucidate the global responses to various perturbations on protein synthesis and secretion and provide valuable novel insights that can be leveraged for improving recombinant protein production.
In this thesis, we mainly use two recombinant proteins, α-amylase and insulin precursor, as model proteins to study the protein synthesis and secretion process in a model organism Saccharomyces cerevisiae. We find that the central metabolism is reprogrammed at a large scale to relieve the oxidative stress caused by recombinant protein production, and the activation of Gcn2p-mediated signaling pathway plays a crucial role in reshaping metabolism. As protein folding is often considered the flux controlling step in protein synthesis and secretion, we further identify two routes of the protein folding pathway to improve protein production, namely through improved folding capacity and increased folding precision, respectively. Additionally, protein translation is the initial step of protein synthesis. We find that cells maintain large and unequally distributed reserves in translational capacity by stepwise reducing nitrogen availability. Moreover, we also construct a proteome-constrained genome-scale protein secretory model for S. cerevisiae (pcSecYeast) to perform secretory simulations and provide genomic targets for cell engineering. Our findings elucidate the global responses to various perturbations on protein synthesis and secretion and provide valuable novel insights that can be leveraged for improving recombinant protein production.
recombinant protein production
protein synthesis
multi-omics analysis
protein secretion
genome-scale modeling
10:an, Kemigården 4, Göteborg
Opponent: Professor Paola Branduardi, University of Milano-Bicocca, Italy
Author
Qi Qi
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints
Nature Communications,;Vol. 13(2022)
Journal article
Different routes of protein folding contribute to improved protein production in saccharomyces cerevisiae
mBio,;Vol. 11(2020)p. 1-12
Journal article
Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast
Nature Communications,;Vol. 11(2020)
Journal article
Feiran Li, Yu Chen*, Qi Qi*, Yanyan Wang*, Le Yuan, Ibrahim EI-Semman, Amir Feizi, Eduard Kerkhoven, Jens Nielsen. Genome-scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast.
Protein, which takes ~18% of our body weight, is one of the most important macromolecules to maintain cellular structure and function. Cells have evolved a delicate protein synthesis and secretion system to ensure that proteins are correctly assembled and transported to various destinations. Disorder of the system can cause many severe diseases, including Alzheimer’s disease, Parkinson’s disease and Type II diabetes. Therefore, a comprehensive understanding of the protein synthesis and secretion system is necessary for human health and disease treatment. However, the system is intertwined with metabolic and regulatory networks, making it difficult to study. To unravel the underlying mechanisms in the system, multi-omics data can be coupled with mathematical modeling to map cellular processes at the genome scale and elucidate the impact of specific components on overall system features, that is, the methodology of systems biology.
In addition, the production of recombinant proteins, including industrial enzymes, biopharmaceuticals and antibodies, is an important component in the current biotech industry. A global understanding of the protein synthesis and secretion process would contribute to the identification of rate-limiting pathways in recombinant protein production, and then to improving the titer, rate and yield (TRY) in industrial settings.
In this thesis, I study the protein synthesis and secretion system of the budding yeast Saccharomyces cerevisiae, one of the most popular model organisms in biotechnology. I first investigate the cellular responses to recombinant protein production. I show that i) the central carbon metabolism is largely reshaped to relieve the oxidative stress caused by protein synthesis and secretion; ii) the activation of Gcn2p-mediated signaling pathway plays a crucial role in the metabolic reprogramming; iii) protein folding precision can be engineered to improve recombinant protein production; iv) Cwh41p plays a key role in the folding precision control. As translation is the initial step of protein synthesis, I next focus on the translation process and show that cells maintain large and unequally distributed reserves in translational capacity. Moreover, I introduce the construction of a proteome-constrained secretory model (pcSecYeast), and show its applications in evaluation of protein misfolding process and prediction of genomic targets for improving recombinant protein production.
The results presented in this thesis provide valuable novel insights into the protein synthesis and secretion system, and show that how integrative analysis of omics data can be coupled with mathematical modeling to investigate specific biological questions.
In addition, the production of recombinant proteins, including industrial enzymes, biopharmaceuticals and antibodies, is an important component in the current biotech industry. A global understanding of the protein synthesis and secretion process would contribute to the identification of rate-limiting pathways in recombinant protein production, and then to improving the titer, rate and yield (TRY) in industrial settings.
In this thesis, I study the protein synthesis and secretion system of the budding yeast Saccharomyces cerevisiae, one of the most popular model organisms in biotechnology. I first investigate the cellular responses to recombinant protein production. I show that i) the central carbon metabolism is largely reshaped to relieve the oxidative stress caused by protein synthesis and secretion; ii) the activation of Gcn2p-mediated signaling pathway plays a crucial role in the metabolic reprogramming; iii) protein folding precision can be engineered to improve recombinant protein production; iv) Cwh41p plays a key role in the folding precision control. As translation is the initial step of protein synthesis, I next focus on the translation process and show that cells maintain large and unequally distributed reserves in translational capacity. Moreover, I introduce the construction of a proteome-constrained secretory model (pcSecYeast), and show its applications in evaluation of protein misfolding process and prediction of genomic targets for improving recombinant protein production.
The results presented in this thesis provide valuable novel insights into the protein synthesis and secretion system, and show that how integrative analysis of omics data can be coupled with mathematical modeling to investigate specific biological questions.
Subject Categories
Biochemistry and Molecular Biology
Bioinformatics and Systems Biology
Biocatalysis and Enzyme Technology
Infrastructure
Chalmers Infrastructure for Mass spectrometry
C3SE (Chalmers Centre for Computational Science and Engineering)
ISBN
978-91-7905-556-1
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 5023
Publisher
Chalmers
10:an, Kemigården 4, Göteborg
Opponent: Professor Paola Branduardi, University of Milano-Bicocca, Italy