Systems biology of yeast metabolism - Understanding metabolism through proteomics and constraint-based modeling
Doctoral thesis, 2021
Metabolism is the set of all chemical reactions that occur inside of cells. By providing all the building blocks that are required for sustaining a cellular state and cell proliferation, metabolism is at the core of cellular function. Therefore, in order to understand cellular function it is important to understand cellular metabolism. The cellular metabolic network comprises thousands of reactions even in the simplest of organisms. Due to the high complexity, a holistic approach is required to study and understand the interactions between different parts of metabolism giving rise to cellular phenotypes.
In this thesis, a systems biology approach to study metabolism in yeast, mainly with a focus on Saccharomyces cerevisiae (baker’s yeast), was used. This approach consisted of combining proteomic analysis with constraint-based modeling to gain insights into different aspects of metabolism. First, the role of mitochondria in cellular metabolism throughout diauxic growth was evaluated, showing that mitochondria balance their role as a biosynthetic hub and center for energy generation depending on the mode of cellular metabolism. Next, the construction of a model of mitochondrial metabolism describing the essential mitochondrial processes of protein import and cofactor metabolism as well as proton motive force driving the generation of free energy (in the form of ATP) is described and evaluated. The model was used to investigate the dynamics in mitochondrial metabolism and the requirement of these processes.
Second, the constraints placed on cellular metabolism arising from finite protein resources is investigated in two studies. The first study evaluates the effect of amino acid supplementation of the physiology and allocation of protein resources. This study showed that as the burden of producing amino acids is relieved, the cells can allocate more protein to the translation, which allows the cells to grow faster. In the second study, a quantitative comparison of four yeast species was performed to evaluate the underlying causes of overflow metabolism, which is the seemingly wasteful strategy of aerobic fermentation instead of using the more efficient respiratory pathway for glucose utilization. We showed that overflow metabolism in yeast is linked to adaptations in metabolism and protein translation This phenomenon is seen in cells ranging from bacteria to yeast and cancer cells, and the insights provided in our study could therefore be valuable in understanding the metabolism not only in yeast but in more complex systems.
In this thesis, a systems biology approach to study metabolism in yeast, mainly with a focus on Saccharomyces cerevisiae (baker’s yeast), was used. This approach consisted of combining proteomic analysis with constraint-based modeling to gain insights into different aspects of metabolism. First, the role of mitochondria in cellular metabolism throughout diauxic growth was evaluated, showing that mitochondria balance their role as a biosynthetic hub and center for energy generation depending on the mode of cellular metabolism. Next, the construction of a model of mitochondrial metabolism describing the essential mitochondrial processes of protein import and cofactor metabolism as well as proton motive force driving the generation of free energy (in the form of ATP) is described and evaluated. The model was used to investigate the dynamics in mitochondrial metabolism and the requirement of these processes.
Second, the constraints placed on cellular metabolism arising from finite protein resources is investigated in two studies. The first study evaluates the effect of amino acid supplementation of the physiology and allocation of protein resources. This study showed that as the burden of producing amino acids is relieved, the cells can allocate more protein to the translation, which allows the cells to grow faster. In the second study, a quantitative comparison of four yeast species was performed to evaluate the underlying causes of overflow metabolism, which is the seemingly wasteful strategy of aerobic fermentation instead of using the more efficient respiratory pathway for glucose utilization. We showed that overflow metabolism in yeast is linked to adaptations in metabolism and protein translation This phenomenon is seen in cells ranging from bacteria to yeast and cancer cells, and the insights provided in our study could therefore be valuable in understanding the metabolism not only in yeast but in more complex systems.
proteomics
metabolism
Systems biology
constraint-based modeling
yeast
Author
Carl Malina
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift
Proceedings of the National Academy of Sciences of the United States of America,;Vol. 117(2020)p. 7524-7535
Journal article
Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media
Proceedings of the National Academy of Sciences of the United States of America,;Vol. 117(2020)p. 21804-21812
Journal article
Yeast mitochondria: An overview of mitochondrial biology and the potential of mitochondrial systems biology
FEMS Yeast Research,;Vol. 18(2018)
Other text in scientific journal
Every organism relies on the ability to take up and utilize nutrients from the environment to generate energy and building blocks required to proliferate. Metabolism represents the thousands of chemical reactions in the cell responsible for the interconversion of chemical compounds required to achieve this task. The large number of reactions makes metabolism a complex network that is difficult to study without a holistic approach. Systems biology is a scientific discipline that revolves around computational and mathematical models, and analysis of large datasets to study biological systems as a whole by quantitatively analyzing the cellular components and their interactions. In this thesis, I used a systems biology approach involving physiological characterization, quantification of protein levels, and computational models of metabolism to investigate metabolism using yeast as a model organism.
The metabolism of mitochondria, that are widely known as the powerhouses of the cell, was investigated. We studied the role of mitochondria in cellular metabolism by investigating changes in the structure and protein levels of mitochondria, and through construction and use of a computational model of mitochondrial metabolism. Then, the constraints placed on cellular metabolism arising from the finite protein resources of the cell were investigated. First, we cultivated yeast under supplementation of amino acids to lower the burden of protein synthesis and studied the effect on cellular physiology and allocation of resources. Lastly, we performed a comparative study of four yeast species to elucidate the underlying causes of overflow metabolism, which is a metabolic strategy of incomplete breakdown of sugar leading to secretion of by-products, used by cells ranging from bacteria to yeast and human cells under conditions of high sugar concentration.
The results presented in this thesis provide insight into the dual role of mitochondria in biosynthesis and energy generation, as well as the requirements of mitochondrial protein import and cofactor metabolism. Furthermore, it demonstrates the importance and implications of cellular resource allocation, and that overflow metabolism is coupled to adaptations in metabolism and protein synthesis. These findings are expected to be valuable for improving our understanding of metabolism, not only in yeast but in more complex organisms.
The metabolism of mitochondria, that are widely known as the powerhouses of the cell, was investigated. We studied the role of mitochondria in cellular metabolism by investigating changes in the structure and protein levels of mitochondria, and through construction and use of a computational model of mitochondrial metabolism. Then, the constraints placed on cellular metabolism arising from the finite protein resources of the cell were investigated. First, we cultivated yeast under supplementation of amino acids to lower the burden of protein synthesis and studied the effect on cellular physiology and allocation of resources. Lastly, we performed a comparative study of four yeast species to elucidate the underlying causes of overflow metabolism, which is a metabolic strategy of incomplete breakdown of sugar leading to secretion of by-products, used by cells ranging from bacteria to yeast and human cells under conditions of high sugar concentration.
The results presented in this thesis provide insight into the dual role of mitochondria in biosynthesis and energy generation, as well as the requirements of mitochondrial protein import and cofactor metabolism. Furthermore, it demonstrates the importance and implications of cellular resource allocation, and that overflow metabolism is coupled to adaptations in metabolism and protein synthesis. These findings are expected to be valuable for improving our understanding of metabolism, not only in yeast but in more complex organisms.
Subject Categories
Biological Sciences
ISBN
978-91-7905-520-2
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 4987
Publisher
Chalmers