| 1. |
- Björkeroth, Johan, 1990, et al.
(author)
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Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media
- 2020
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:35, s. 21804-21812
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Journal article (peer-reviewed)abstract
- Several recent studies have shown that the concept of proteome constraint, i.e., the need for the cell to balance allocation of its proteome between different cellular processes, is essential for ensuring proper cell function. However, there have been no attempts to elucidate how cells' maximum capacity to grow depends on protein availability for different cellular processes. To experimentally address this, we cultivated Saccharomyces cerevisiae in bioreactors with or without amino acid supplementation and performed quantitative proteomics to analyze global changes in proteome allocation, during both anaerobic and aerobic growth on glucose. Analysis of the proteomic data implies that proteome mass is mainly reallocated from amino acid biosynthetic processes into translation, which enables an increased growth rate during supplementation. Similar findings were obtained from both aerobic and anaerobic cultivations. Our findings show that cells can increase their growth rate through increasing its proteome allocation toward the protein translational machinery.
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| 2. |
- Di Bartolomeo, Francesca, 1986, et al.
(author)
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Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift
- 2020
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:13, s. 7524-7535
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Journal article (peer-reviewed)abstract
- Saccharomyces cerevisiae constitutes a popular eukaryal model for research on mitochondrial physiology. Being Crabtree-positive, this yeast has evolved the ability to ferment glucose to ethanol and respire ethanol once glucose is consumed. Its transition phase from fermentative to respiratory metabolism, known as the diauxic shift, is reflected by dramatic rearrangements of mitochondrial function and structure. To date, the metabolic adaptations that occur during the diauxic shift have not been fully characterized at the organelle level. In this study, the absolute proteome of mitochondria was quantified alongside precise parametrization of biophysical properties associated with the mitochondrial network using state-of-the-art optical-imaging techniques. This allowed the determination of absolute protein abundances at a subcellular level. By tracking the transformation of mitochondrial mass and volume, alongside changes in the absolute mitochondrial proteome allocation, we could quantify how mitochondria balance their dual role as a biosynthetic hub as well as a center for cellular respiration. Furthermore, our findings suggest that in the transition from a fermentative to a respiratory metabolism, the diauxic shift represents the stage where major structural and functional reorganizations in mitochondrial metabolism occur. This metabolic transition, initiated at the mitochondria level, is then extended to the rest of the yeast cell.
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| 3. |
- Malina, Carl, 1992, et al.
(author)
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Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast
- 2021
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:51
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Journal article (peer-reviewed)abstract
- Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose availability. Not all yeasts exhibit the Crabtree effect, and it is not known why Crabtree-negative yeasts can grow at rates comparable to Crabtree-positive yeasts. Here, we quantitatively compared two Crabtree-positive yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and two Crabtree-negative yeasts, Kluyveromyces marxianus and Scheffersomyces stipitis, cultivated under glucose excess conditions. Combining physiological and proteome quantification with genome-scale metabolic modeling, we found that the two groups differ in energy metabolism and translation efficiency. In Crabtree-positive yeasts, the central carbon metabolism flux and proteome allocation favor a glucose utilization strategy minimizing proteome cost as proteins translation parameters, including ribosomal content and/or efficiency, are lower. Crabtree-negative yeasts, however, use a strategy of maximizing ATP yield, accompanied by higher protein translation parameters. Our analyses provide insight into the underlying reasons for the Crabtree effect, demonstrating a coupling to adaptations in both metabolism and protein translation.
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| 4. |
- Malina, Carl, 1992, et al.
(author)
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Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis
- 2021
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In: iScience. - : Elsevier BV. - 2589-0042. ; 24:11
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Journal article (peer-reviewed)abstract
- Mitochondria are a hallmark of eukaryal cells and play an important role in cellular metabolism. There is a vast amount of knowledge available on mitochondrial metabolism and essential mitochondrial functions, such as protein import and iron-sulfur cluster biosynthesis, including multiple studies on the mitochondrial proteome. Therefore, there is a need for in silico approaches to facilitate the analysis of these data. Here, we present a detailed model of mitochondrial metabolism Saccharomyces cerevisiae, including protein import, iron-sulfur cluster biosynthesis, and a description of the coupling between charge translocation processes and ATP synthesis. Model analysis implied a dual dependence of absolute levels of proteins in protein import, iron-sulfur cluster biogenesis and cluster abundance on growth rate and respiratory activity. The model is instrumental in studying dynamics and perturbations in these processes and given the high conservation of mitochondrial metabolism in humans, it can provide insight into their role in human disease.
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| 5. |
- Malina, Carl, 1992
(author)
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Systems biology of yeast metabolism - Understanding metabolism through proteomics and constraint-based modeling
- 2021
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Doctoral thesis (other academic/artistic)abstract
- 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.
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| 6. |
- Malina, Carl, 1992, et al.
(author)
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Yeast mitochondria: An overview of mitochondrial biology and the potential of mitochondrial systems biology
- 2018
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In: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 18:5
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Journal article (other academic/artistic)abstract
- Mitochondria are dynamic organelles of endosymbiotic origin that are essential components of eukaryal cells. They contain their own genetic machinery, have multicopy genomes and like their bacterial ancestors they consist of two membranes. However, the majority of the ancestral genome has been lost or transferred to the nuclear genome of the host, preserving only a core set of genes involved in oxidative phosphorylation. Mitochondria perform numerous biological tasks ranging from bioenergetics to production of protein co-factors, including heme and iron-sulfur clusters. Due to the importance of mitochondria in many cellular processes, mitochondrial dysfunction is implicated in a wide variety of human disorders. Much of our current knowledge on mitochondrial function and dysfunction comes from studies using Saccharomyces cerevisiae. This yeast has good fermenting capacity, rendering tolerance to mutations that inactivate oxidative phosphorylation and complete loss of mitochondrial DNA. Here, we review yeast mitochondrial metabolism and function with focus on S. cerevisiae and its contribution in understanding mitochondrial biology. We further review how systems biology studies, including mathematical modeling, has allowed gaining new insight into mitochondrial function, and argue that this approach may enable us to gain a holistic view on how mitochondrial function interacts with different cellular processes.
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| 7. |
- Pereira, Rui, 1986, et al.
(author)
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Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae
- 2019
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In: Metabolic Engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 56, s. 130-141
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Journal article (peer-reviewed)abstract
- Improving the growth phenotypes of microbes in high product concentrations is an essential design objective in the development of robust cell factories. However, the limited knowledge regarding tolerance mechanisms makes rational design of such traits complicated. Here, adaptive laboratory evolution was used to explore the tolerance mechanisms that Saccharomyces cerevisiae can evolve in the presence of inhibiting concentrations of three dicarboxylic acids: glutaric acid, adipic acid and pimelic acid. Whole-genome sequencing of tolerant mutants enabled the discovery of the genetic changes behind tolerance and most mutations could be linked to the up-regulation of multidrug resistance transporters. The amplification of QDR3, in particular, was shown to confer tolerance not only to the three dicarboxylic acids investigated, but also towards muconic acid and glutaconic acid. In addition to increased acid tolerance, QDR3 overexpression also improved the production of muconic acid in the context of a strain engineered for producing this compound.
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